Daily Papers

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

Spatio-temporal localization is vital for precise interactions across diverse domains, from biological research to autonomous navigation and interactive interfaces. Current video-based approaches, while proficient in tracking, lack the sophisticated reasoning capabilities of large language models, limiting their contextual understanding and generalization. We introduce VideoMolmo, a large multimodal model tailored for fine-grained spatio-temporal pointing conditioned on textual descriptions. Building upon the Molmo architecture, VideoMolmo incorporates a temporal module utilizing an attention mechanism to condition each frame on preceding frames, ensuring temporal consistency. Additionally, our novel temporal mask fusion pipeline employs SAM2 for bidirectional point propagation, significantly enhancing coherence across video sequences. This two-step decomposition, i.e., first using the LLM to generate precise pointing coordinates, then relying on a sequential mask-fusion module to produce coherent segmentation, not only simplifies the task for the language model but also enhances interpretability. Due to the lack of suitable datasets, we curate a comprehensive dataset comprising 72k video-caption pairs annotated with 100k object points. To evaluate the generalization of VideoMolmo, we introduce VPoS-Bench, a challenging out-of-distribution benchmark spanning five real-world scenarios: Cell Tracking, Egocentric Vision, Autonomous Driving, Video-GUI Interaction, and Robotics. We also evaluate our model on Referring Video Object Segmentation (Refer-VOS) and Reasoning VOS tasks. In comparison to existing models, VideoMolmo substantially improves spatio-temporal pointing accuracy and reasoning capability. Our code and models are publicly available at https://github.com/mbzuai-oryx/VideoMolmo.

This paper introduces two significant contributions to address the issue of grounding claims in a given context. Grounding means that given a context (document) and a claim, there's at least one supportive evidence for the claim in the document. We will introduce Paladin-mini, a compact (3.8B parameters) open-source classifier model (used for labeling data as grounded or ungrounded) engineered for robust performance in real-world scenarios, and the grounding-benchmark, a new evaluation dataset designed to assess performance on critical reasoning tasks. We'll also demonstrate the results of Paladin-mini with benchmarks against the current State-of-the-art and share clear and reproducible results.

In October 2007, a Research Proposal for the University of Sydney, Australia, the author suggested that biovie-physical phenomenon as `electrodynamic dependant biological vision', is governed by relativistic quantum laws and biovision. The phenomenon on the basis of `biovielectroluminescence', satisfies man/microbio/megabio/computer vision (MMMCV), as a robust candidate for physical and visual sciences. The general aim of this addendum is to present a refined text of Sections 1-3 of that proposal and highlighting the contents of its Appendix in form of a `Mechanisms' Section. We then briefly remind in an article aimed for December 2007, by appending two more equations into Section 3, a theoretical II-time scenario as a time model well-proposed for the phenomenon. The time model within the core of the proposal, plays a significant role in emphasizing the principle points on Objectives no. 1-8, Sub-hypothesis 3.1.2, mentioned in Article [arXiv:0710.0410]. It also expresses the time concept in terms of causing quantized energy f(|E|) of time |t|, emit in regard to shortening the probability of particle loci as predictable patterns of particle's un-occurred motion, a solution to Heisenberg's uncertainty principle (HUP) into a simplistic manner. We conclude that, practical frames via a time algorithm to this model, fixates such predictable patterns of motion of scenery bodies onto recordable observation points of a MMMCV system. It even suppresses/predicts superposition phenomena coming from a human subject and/or other bio-subjects for any decision making event, e.g., brainwave quantum patterns based on vision. Maintaining the existential probability of Riemann surfaces of II-time scenarios in the context of biovielectroluminescence, makes motion-prediction a possibility.

Medical image grounding aims to align natural language phrases with specific regions in medical images, serving as a foundational task for intelligent diagnosis, visual question answering (VQA), and automated report generation (MRG). However, existing research is constrained by limited modality coverage, coarse-grained annotations, and the absence of a unified, generalizable grounding framework. To address these challenges, we construct a large-scale medical grounding dataset Med-GLIP-5M comprising over 5.3 million region-level annotations across seven imaging modalities, covering diverse anatomical structures and pathological findings. The dataset supports both segmentation and grounding tasks with hierarchical region labels, ranging from organ-level boundaries to fine-grained lesions. Based on this foundation, we propose Med-GLIP, a modality-aware grounding framework trained on Med-GLIP-5M. Rather than relying on explicitly designed expert modules, Med-GLIP implicitly acquires hierarchical semantic understanding from diverse training data -- enabling it to recognize multi-granularity structures, such as distinguishing lungs from pneumonia lesions. Extensive experiments demonstrate that Med-GLIP consistently outperforms state-of-the-art baselines across multiple grounding benchmarks. Furthermore, integrating its spatial outputs into downstream tasks, including medical VQA and report generation, leads to substantial performance gains. Our dataset will be released soon.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

Grounding natural language in physical 3D environments is essential for the advancement of embodied artificial intelligence. Current datasets and models for 3D visual grounding predominantly focus on identifying and localizing objects from static, object-centric descriptions. These approaches do not adequately address the dynamic and sequential nature of task-oriented grounding necessary for practical applications. In this work, we propose a new task: Task-oriented Sequential Grounding in 3D scenes, wherein an agent must follow detailed step-by-step instructions to complete daily activities by locating a sequence of target objects in indoor scenes. To facilitate this task, we introduce SG3D, a large-scale dataset containing 22,346 tasks with 112,236 steps across 4,895 real-world 3D scenes. The dataset is constructed using a combination of RGB-D scans from various 3D scene datasets and an automated task generation pipeline, followed by human verification for quality assurance. We adapted three state-of-the-art 3D visual grounding models to the sequential grounding task and evaluated their performance on SG3D. Our results reveal that while these models perform well on traditional benchmarks, they face significant challenges with task-oriented sequential grounding, underscoring the need for further research in this area.

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Biological nervous systems are created in a fundamentally different way than current artificial neural networks. Despite its impressive results in a variety of different domains, deep learning often requires considerable engineering effort to design high-performing neural architectures. By contrast, biological nervous systems are grown through a dynamic self-organizing process. In this paper, we take initial steps toward neural networks that grow through a developmental process that mirrors key properties of embryonic development in biological organisms. The growth process is guided by another neural network, which we call a Neural Developmental Program (NDP) and which operates through local communication alone. We investigate the role of neural growth on different machine learning benchmarks and different optimization methods (evolutionary training, online RL, offline RL, and supervised learning). Additionally, we highlight future research directions and opportunities enabled by having self-organization driving the growth of neural networks.

We present ScienceWorld, a benchmark to test agents' scientific reasoning abilities in a new interactive text environment at the level of a standard elementary school science curriculum. Despite the transformer-based progress seen in question-answering and scientific text processing, we find that current models cannot reason about or explain learned science concepts in novel contexts. For instance, models can easily answer what the conductivity of a known material is but struggle when asked how they would conduct an experiment in a grounded environment to find the conductivity of an unknown material. This begs the question of whether current models are simply retrieving answers by way of seeing a large number of similar examples or if they have learned to reason about concepts in a reusable manner. We hypothesize that agents need to be grounded in interactive environments to achieve such reasoning capabilities. Our experiments provide empirical evidence supporting this hypothesis -- showing that a 1.5 million parameter agent trained interactively for 100k steps outperforms a 11 billion parameter model statically trained for scientific question-answering and reasoning from millions of expert demonstrations.

This technical monograph provides a comprehensive overview of the field of quantum biology. It approaches quantum biology from a physical perspective with core quantum mechanical concepts presented foremost to provide a theoretical foundation for the field. An extensive body of research is covered to clarify the significance of quantum biology as a scientific field, outlining the field's long-standing importance in the historical development of quantum theory. This lays the essential groundwork to enable further advances in nanomedicine and biotechnology. Written for academics, biological science researchers, physicists, biochemists, medical technologists, and students of quantum mechanics, this text brings clarity to fundamental advances being made in the emerging science of quantum biology.

Language models excel at following instructions but often struggle with the collaborative aspects of conversation that humans naturally employ. This limitation in grounding -- the process by which conversation participants establish mutual understanding -- can lead to outcomes ranging from frustrated users to serious consequences in high-stakes scenarios. To systematically study grounding challenges in human-LLM interactions, we analyze logs from three human-assistant datasets: WildChat, MultiWOZ, and Bing Chat. We develop a taxonomy of grounding acts and build models to annotate and forecast grounding behavior. Our findings reveal significant differences in human-human and human-LLM grounding: LLMs were three times less likely to initiate clarification and sixteen times less likely to provide follow-up requests than humans. Additionally, early grounding failures predicted later interaction breakdowns. Building on these insights, we introduce RIFTS: a benchmark derived from publicly available LLM interaction data containing situations where LLMs fail to initiate grounding. We note that current frontier models perform poorly on RIFTS, highlighting the need to reconsider how we train and prompt LLMs for human interaction. To this end, we develop a preliminary intervention that mitigates grounding failures.

Humans can ground natural language commands to tasks at both abstract and fine-grained levels of specificity. For instance, a human forklift operator can be instructed to perform a high-level action, like "grab a pallet" or a low-level action like "tilt back a little bit." While robots are also capable of grounding language commands to tasks, previous methods implicitly assume that all commands and tasks reside at a single, fixed level of abstraction. Additionally, methods that do not use multiple levels of abstraction encounter inefficient planning and execution times as they solve tasks at a single level of abstraction with large, intractable state-action spaces closely resembling real world complexity. In this work, by grounding commands to all the tasks or subtasks available in a hierarchical planning framework, we arrive at a model capable of interpreting language at multiple levels of specificity ranging from coarse to more granular. We show that the accuracy of the grounding procedure is improved when simultaneously inferring the degree of abstraction in language used to communicate the task. Leveraging hierarchy also improves efficiency: our proposed approach enables a robot to respond to a command within one second on 90% of our tasks, while baselines take over twenty seconds on half the tasks. Finally, we demonstrate that a real, physical robot can ground commands at multiple levels of abstraction allowing it to efficiently plan different subtasks within the same planning hierarchy.

Unlocking deep, interpretable biological reasoning from complex genomic data is a major AI challenge hindering scientific discovery. Current DNA foundation models, despite strong sequence representation, struggle with multi-step reasoning and lack inherent transparent, biologically intuitive explanations. We introduce BioReason, a pioneering architecture that, for the first time, deeply integrates a DNA foundation model with a Large Language Model (LLM). This novel connection enables the LLM to directly process and reason with genomic information as a fundamental input, fostering a new form of multimodal biological understanding. BioReason's sophisticated multi-step reasoning is developed through supervised fine-tuning and targeted reinforcement learning, guiding the system to generate logical, biologically coherent deductions. On biological reasoning benchmarks including KEGG-based disease pathway prediction - where accuracy improves from 88% to 97% - and variant effect prediction, BioReason demonstrates an average 15% performance gain over strong single-modality baselines. BioReason reasons over unseen biological entities and articulates decision-making through interpretable, step-by-step biological traces, offering a transformative approach for AI in biology that enables deeper mechanistic insights and accelerates testable hypothesis generation from genomic data. Data, code, and checkpoints are publicly available at https://github.com/bowang-lab/BioReason

Multi-modal AI systems will likely become a ubiquitous presence in our everyday lives. A promising approach to making these systems more interactive is to embody them as agents within physical and virtual environments. At present, systems leverage existing foundation models as the basic building blocks for the creation of embodied agents. Embedding agents within such environments facilitates the ability of models to process and interpret visual and contextual data, which is critical for the creation of more sophisticated and context-aware AI systems. For example, a system that can perceive user actions, human behavior, environmental objects, audio expressions, and the collective sentiment of a scene can be used to inform and direct agent responses within the given environment. To accelerate research on agent-based multimodal intelligence, we define "Agent AI" as a class of interactive systems that can perceive visual stimuli, language inputs, and other environmentally-grounded data, and can produce meaningful embodied action with infinite agent. In particular, we explore systems that aim to improve agents based on next-embodied action prediction by incorporating external knowledge, multi-sensory inputs, and human feedback. We argue that by developing agentic AI systems in grounded environments, one can also mitigate the hallucinations of large foundation models and their tendency to generate environmentally incorrect outputs. The emerging field of Agent AI subsumes the broader embodied and agentic aspects of multimodal interactions. Beyond agents acting and interacting in the physical world, we envision a future where people can easily create any virtual reality or simulated scene and interact with agents embodied within the virtual environment.

Effective dialogue involves grounding, the process of establishing mutual knowledge that is essential for communication between people. Modern dialogue systems are not explicitly trained to build common ground, and therefore overlook this important aspect of communication. Improvisational theater (improv) intrinsically contains a high proportion of dialogue focused on building common ground, and makes use of the yes-and principle, a strong grounding speech act, to establish coherence and an actionable objective reality. We collect a corpus of more than 26,000 yes-and turns, transcribing them from improv dialogues and extracting them from larger, but more sparsely populated movie script dialogue corpora, via a bootstrapped classifier. We fine-tune chit-chat dialogue systems with our corpus to encourage more grounded, relevant conversation and confirm these findings with human evaluations.

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space.

Generative artificial intelligence (AI) systems based on large-scale pretrained foundation models (PFMs) such as vision-language models, large language models (LLMs), diffusion models and vision-language-action (VLA) models have demonstrated the ability to solve complex and truly non-trivial AI problems in a wide variety of domains and contexts. Multimodal large language models (MLLMs), in particular, learn from vast and diverse data sources, allowing rich and nuanced representations of the world and, thereby, providing extensive capabilities, including the ability to reason, engage in meaningful dialog; collaborate with humans and other agents to jointly solve complex problems; and understand social and emotional aspects of humans. Despite this impressive feat, the cognitive abilities of state-of-the-art LLMs trained on large-scale datasets are still superficial and brittle. Consequently, generic LLMs are severely limited in their generalist capabilities. A number of foundational problems -- embodiment, symbol grounding, causality and memory -- are required to be addressed for LLMs to attain human-level general intelligence. These concepts are more aligned with human cognition and provide LLMs with inherent human-like cognitive properties that support the realization of physically-plausible, semantically meaningful, flexible and more generalizable knowledge and intelligence. In this work, we discuss the aforementioned foundational issues and survey state-of-the art approaches for implementing these concepts in LLMs. Specifically, we discuss how the principles of embodiment, symbol grounding, causality and memory can be leveraged toward the attainment of artificial general intelligence (AGI) in an organic manner.

Visual grounding refers to the ability of a model to identify a region within some visual input that matches a textual description. Consequently, a model equipped with visual grounding capabilities can target a wide range of applications in various domains, including referring expression comprehension, answering questions pertinent to fine-grained details in images or videos, caption visual context by explicitly referring to entities, as well as low and high-level control in simulated and real environments. In this survey paper, we review representative works across the key areas of research on modern general-purpose vision language models (VLMs). We first outline the importance of grounding in VLMs, then delineate the core components of the contemporary paradigm for developing grounded models, and examine their practical applications, including benchmarks and evaluation metrics for grounded multimodal generation. We also discuss the multifaceted interrelations among visual grounding, multimodal chain-of-thought, and reasoning in VLMs. Finally, we analyse the challenges inherent to visual grounding and suggest promising directions for future research.

Visual Grounding is also known as Referring Expression Comprehension and Phrase Grounding. It involves localizing a natural number of specific regions within an image based on a given textual description. The objective of this task is to emulate the prevalent referential relationships in social conversations, equipping machines with human-like multimodal comprehension capabilities. Consequently, it has extensive applications in various domains. However, since 2021, visual grounding has witnessed significant advancements, with emerging new concepts such as grounded pre-training, grounding multimodal LLMs, generalized visual grounding, and giga-pixel grounding, which have brought numerous new challenges. In this survey, we initially examine the developmental history of visual grounding and provide an overview of essential background knowledge. We systematically track and summarize the advancements and meticulously organize the various settings in visual grounding, thereby establishing precise definitions of these settings to standardize future research and ensure a fair comparison. Additionally, we delve into several advanced topics and highlight numerous applications of visual grounding. Finally, we outline the challenges confronting visual grounding and propose valuable directions for future research, which may serve as inspiration for subsequent researchers. By extracting common technical details, this survey encompasses the representative works in each subtopic over the past decade. To the best, this paper presents the most comprehensive overview currently available in the field of grounding. This survey is designed to be suitable for both beginners and experienced researchers, serving as an invaluable resource for understanding key concepts and tracking the latest research developments. We keep tracing related works at https://github.com/linhuixiao/Awesome-Visual-Grounding.

Spatial grounding, the process of associating natural language expressions with corresponding image regions, has rapidly advanced due to the introduction of transformer-based models, significantly enhancing multimodal representation and cross-modal alignment. Despite this progress, the field lacks a comprehensive synthesis of current methodologies, dataset usage, evaluation metrics, and industrial applicability. This paper presents a systematic literature review of transformer-based spatial grounding approaches from 2018 to 2025. Our analysis identifies dominant model architectures, prevalent datasets, and widely adopted evaluation metrics, alongside highlighting key methodological trends and best practices. This study provides essential insights and structured guidance for researchers and practitioners, facilitating the development of robust, reliable, and industry-ready transformer-based spatial grounding models.

The current work addresses a virtual environment with self-replicating agents whose decisions are based on a form of "somatic computation" (soma - body) in which basic emotional responses, taken in parallelism to actual living organisms, are introduced as a way to provide the agents with greater reflexive abilities. The work provides a contribution to the field of Artificial Intelligence (AI) and Artificial Life (ALife) in connection to a neurobiology-based cognitive framework for artificial systems and virtual environments' simulations. The performance of the agents capable of emotional responses is compared with that of self-replicating automata, and the implications of research on emotions and AI, in connection to both virtual agents as well as robots, is addressed regarding possible future directions and applications.

Graphical user interface (GUI) grounding, the ability to map natural language instructions to specific actions on graphical user interfaces, remains a critical bottleneck in computer use agent development. Current benchmarks oversimplify grounding tasks as short referring expressions, failing to capture the complexity of real-world interactions that require software commonsense, layout understanding, and fine-grained manipulation capabilities. To address these limitations, we introduce OSWorld-G, a comprehensive benchmark comprising 564 finely annotated samples across diverse task types including text matching, element recognition, layout understanding, and precise manipulation. Additionally, we synthesize and release the largest computer use grounding dataset Jedi, which contains 4 million examples through multi-perspective decoupling of tasks. Our multi-scale models trained on Jedi demonstrate its effectiveness by outperforming existing approaches on ScreenSpot-v2, ScreenSpot-Pro, and our OSWorld-G. Furthermore, we demonstrate that improved grounding with Jedi directly enhances agentic capabilities of general foundation models on complex computer tasks, improving from 5% to 27% on OSWorld. Through detailed ablation studies, we identify key factors contributing to grounding performance and verify that combining specialized data for different interface elements enables compositional generalization to novel interfaces. All benchmark, data, checkpoints, and code are open-sourced and available at https://osworld-grounding.github.io.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

Large language models can encode a wealth of semantic knowledge about the world. Such knowledge could be extremely useful to robots aiming to act upon high-level, temporally extended instructions expressed in natural language. However, a significant weakness of language models is that they lack real-world experience, which makes it difficult to leverage them for decision making within a given embodiment. For example, asking a language model to describe how to clean a spill might result in a reasonable narrative, but it may not be applicable to a particular agent, such as a robot, that needs to perform this task in a particular environment. We propose to provide real-world grounding by means of pretrained skills, which are used to constrain the model to propose natural language actions that are both feasible and contextually appropriate. The robot can act as the language model's "hands and eyes," while the language model supplies high-level semantic knowledge about the task. We show how low-level skills can be combined with large language models so that the language model provides high-level knowledge about the procedures for performing complex and temporally-extended instructions, while value functions associated with these skills provide the grounding necessary to connect this knowledge to a particular physical environment. We evaluate our method on a number of real-world robotic tasks, where we show the need for real-world grounding and that this approach is capable of completing long-horizon, abstract, natural language instructions on a mobile manipulator. The project's website and the video can be found at https://say-can.github.io/.

Artificial neural networks achieve strong performance on benchmark tasks but remain fundamentally brittle under perturbations, limiting their deployment in real-world settings. In contrast, biological nervous systems sustain reliable function across decades through homeostatic regulation coordinated across multiple temporal scales. Inspired by this principle, this presents Multi-Scale Temporal Homeostasis (MSTH), a biologically grounded framework that integrates ultra-fast (5-ms), fast (2-s), medium (5-min) and slow (1-hrs) regulation into artificial networks. MSTH implements the cross-scale coordination system for artificial neural networks, providing a unified temporal hierarchy that moves beyond superficial biomimicry. The cross-scale coordination enhances computational efficiency through evolutionary-refined optimization mechanisms. Experiments across molecular, graph and image classification benchmarks show that MSTH consistently improves accuracy, eliminates catastrophic failures and enhances recovery from perturbations. Moreover, MSTH outperforms both single-scale bio-inspired models and established state-of-the-art methods, demonstrating generality across diverse domains. These findings establish cross-scale temporal coordination as a core principle for stabilizing artificial neural systems, positioning MSTH as a foundation for building robust, resilient and biologically faithful intelligence.

Effective conversation requires common ground: a shared understanding between the participants. Common ground, however, does not emerge spontaneously in conversation. Speakers and listeners work together to both identify and construct a shared basis while avoiding misunderstanding. To accomplish grounding, humans rely on a range of dialogue acts, like clarification (What do you mean?) and acknowledgment (I understand.). However, it is unclear whether large language models (LLMs) generate text that reflects human grounding. To this end, we curate a set of grounding acts and propose corresponding metrics that quantify attempted grounding. We study whether LLM generations contain grounding acts, simulating turn-taking from several dialogue datasets and comparing results to humans. We find that -- compared to humans -- LLMs generate language with less conversational grounding, instead generating text that appears to simply presume common ground. To understand the roots of the identified grounding gap, we examine the role of instruction tuning and preference optimization, finding that training on contemporary preference data leads to a reduction in generated grounding acts. Altogether, we highlight the need for more research investigating conversational grounding in human-AI interaction.

Visual grounding is essential for precise perception and reasoning in multimodal large language models (MLLMs), especially in medical imaging domains. While existing medical visual grounding benchmarks primarily focus on single-image scenarios, real-world clinical applications often involve sequential images, where accurate lesion localization across different modalities and temporal tracking of disease progression (e.g., pre- vs. post-treatment comparison) require fine-grained cross-image semantic alignment and context-aware reasoning. To remedy the underrepresentation of image sequences in existing medical visual grounding benchmarks, we propose MedSG-Bench, the first benchmark tailored for Medical Image Sequences Grounding. It comprises eight VQA-style tasks, formulated into two paradigms of the grounding tasks, including 1) Image Difference Grounding, which focuses on detecting change regions across images, and 2) Image Consistency Grounding, which emphasizes detection of consistent or shared semantics across sequential images. MedSG-Bench covers 76 public datasets, 10 medical imaging modalities, and a wide spectrum of anatomical structures and diseases, totaling 9,630 question-answer pairs. We benchmark both general-purpose MLLMs (e.g., Qwen2.5-VL) and medical-domain specialized MLLMs (e.g., HuatuoGPT-vision), observing that even the advanced models exhibit substantial limitations in medical sequential grounding tasks. To advance this field, we construct MedSG-188K, a large-scale instruction-tuning dataset tailored for sequential visual grounding, and further develop MedSeq-Grounder, an MLLM designed to facilitate future research on fine-grained understanding across medical sequential images. The benchmark, dataset, and model are available at https://huggingface.co/MedSG-Bench

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

Large language models (LLMs) still produce plausible-sounding but ungrounded factual claims, a problem that worsens in multi-turn dialogue as context grows and early errors cascade. We introduce HalluHard, a challenging multi-turn hallucination benchmark with 950 seed questions spanning four high-stakes domains: legal cases, research questions, medical guidelines, and coding. We operationalize groundedness by requiring inline citations for factual assertions. To support reliable evaluation in open-ended settings, we propose a judging pipeline that iteratively retrieves evidence via web search. It can fetch, filter, and parse full-text sources (including PDFs) to assess whether cited material actually supports the generated content. Across a diverse set of frontier proprietary and open-weight models, hallucinations remain substantial even with web search (approx 30% for the strongest configuration, Opus-4.5 with web search), with content-grounding errors persisting at high rates. Finally, we show that hallucination behavior is shaped by model capacity, turn position, effective reasoning, and the type of knowledge required.

Despite the ecological significance of invertebrates, global trait databases remain heavily biased toward vertebrates and plants, limiting comprehensive ecological analyses of high-diversity groups like ground beetles. Ground beetles (Coleoptera: Carabidae) serve as critical bioindicators of ecosystem health, providing valuable insights into biodiversity shifts driven by environmental changes. While the National Ecological Observatory Network (NEON) maintains an extensive collection of carabid specimens from across the United States, these primarily exist as physical collections, restricting widespread research access and large-scale analysis. To address these gaps, we present a multimodal dataset digitizing over 13,200 NEON carabids from 30 sites spanning the continental US and Hawaii through high-resolution imaging, enabling broader access and computational analysis. The dataset includes digitally measured elytra length and width of each specimen, establishing a foundation for automated trait extraction using AI. Validated against manual measurements, our digital trait extraction achieves sub-millimeter precision, ensuring reliability for ecological and computational studies. By addressing invertebrate under-representation in trait databases, this work supports AI-driven tools for automated species identification and trait-based research, fostering advancements in biodiversity monitoring and conservation.

The web provides a rich, open-domain environment with textual, structural, and spatial properties. We propose a new task for grounding language in this environment: given a natural language command (e.g., "click on the second article"), choose the correct element on the web page (e.g., a hyperlink or text box). We collected a dataset of over 50,000 commands that capture various phenomena such as functional references (e.g. "find who made this site"), relational reasoning (e.g. "article by john"), and visual reasoning (e.g. "top-most article"). We also implemented and analyzed three baseline models that capture different phenomena present in the dataset.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Large language models (LLMs) are often supplemented with external knowledge to provide information not encoded in their parameters or to reduce hallucination. In such cases, we expect the model to generate responses by grounding its response in the provided external context. However, prior work has shown that simply appending context at inference time does not ensure grounded generation. To address this, we propose Context-INformed Grounding Supervision (CINGS), a post-training supervision in which the model is trained with relevant context prepended to the response, while computing the loss only over the response tokens and masking out the context. Our experiments demonstrate that models trained with CINGS exhibit stronger grounding in both textual and visual domains compared to standard instruction-tuned models. In the text domain, CINGS outperforms other training methods across 11 information-seeking datasets and is complementary to inference-time grounding techniques. In the vision-language domain, replacing a vision-language model's LLM backbone with a CINGS-trained model reduces hallucinations across four benchmarks and maintains factual consistency throughout the generated response. This improved grounding comes without degradation in general downstream performance. Finally, we analyze the mechanism underlying the enhanced grounding in CINGS and find that it induces a shift in the model's prior knowledge and behavior, implicitly encouraging greater reliance on the external context.

Answer grounding is the task of locating relevant visual evidence for the Visual Question Answering task. While a wide variety of attention methods have been introduced for this task, they suffer from the following three problems: designs that do not allow the usage of pre-trained networks and do not benefit from large data pre-training, custom designs that are not based on well-grounded previous designs, therefore limiting the learning power of the network, or complicated designs that make it challenging to re-implement or improve them. In this paper, we propose a novel architectural block, which we term Sentence Attention Block, to solve these problems. The proposed block re-calibrates channel-wise image feature-maps by explicitly modeling inter-dependencies between the image feature-maps and sentence embedding. We visually demonstrate how this block filters out irrelevant feature-maps channels based on sentence embedding. We start our design with a well-known attention method, and by making minor modifications, we improve the results to achieve state-of-the-art accuracy. The flexibility of our method makes it easy to use different pre-trained backbone networks, and its simplicity makes it easy to understand and be re-implemented. We demonstrate the effectiveness of our method on the TextVQA-X, VQS, VQA-X, and VizWiz-VQA-Grounding datasets. We perform multiple ablation studies to show the effectiveness of our design choices.

While recent multimodal large language models (MLLMs) have advanced automated ECG interpretation, they still face two key limitations: (1) insufficient multimodal synergy between time series signals and visual ECG representations, and (2) limited explainability in linking diagnoses to granular waveform evidence. We introduce GEM, the first MLLM unifying ECG time series, 12-lead ECG images and text for grounded and clinician-aligned ECG interpretation. GEM enables feature-grounded analysis, evidence-driven reasoning, and a clinician-like diagnostic process through three core innovations: a dual-encoder framework extracting complementary time series and image features, cross-modal alignment for effective multimodal understanding, and knowledge-guided instruction generation for generating high-granularity grounding data (ECG-Grounding) linking diagnoses to measurable parameters (e.g., QRS/PR Intervals). Additionally, we propose the Grounded ECG Understanding task, a clinically motivated benchmark designed to comprehensively assess the MLLM's capability in grounded ECG understanding. Experimental results on both existing and our proposed benchmarks show GEM significantly improves predictive performance (CSN 7.4% uparrow), explainability (22.7% uparrow), and grounding (24.8% uparrow), making it more suitable for real-world clinical applications. GitHub repository: https://github.com/lanxiang1017/GEM.git

Language grounding to vision is an active field of research aiming to enrich text-based representations of word meanings by leveraging perceptual knowledge from vision. Despite many attempts at language grounding, it is still unclear how to effectively inject visual knowledge into the word embeddings of a language in such a way that a proper balance of textual and visual knowledge is maintained. Some common concerns are the following. Is visual grounding beneficial for abstract words or is its contribution only limited to concrete words? What is the optimal way of bridging the gap between text and vision? How much do we gain by visually grounding textual embeddings? The present study addresses these questions by proposing a simple yet very effective grounding approach for pre-trained word embeddings. Our model aligns textual embeddings with vision while largely preserving the distributional statistics that characterize word use in text corpora. By applying a learned alignment, we are able to generate visually grounded embeddings for unseen words, including abstract words. A series of evaluations on word similarity benchmarks shows that visual grounding is beneficial not only for concrete words, but also for abstract words. We also show that our method for visual grounding offers advantages for contextualized embeddings, but only when these are trained on corpora of relatively modest size. Code and grounded embeddings for English are available at https://github.com/Hazel1994/Visually_Grounded_Word_Embeddings_2.

Affordance grounding refers to the task of finding the area of an object with which one can interact. It is a fundamental but challenging task, as a successful solution requires the comprehensive understanding of a scene in multiple aspects including detection, localization, and recognition of objects with their parts, of geo-spatial configuration/layout of the scene, of 3D shapes and physics, as well as of the functionality and potential interaction of the objects and humans. Much of the knowledge is hidden and beyond the image content with the supervised labels from a limited training set. In this paper, we make an attempt to improve the generalization capability of the current affordance grounding by taking the advantage of the rich world, abstract, and human-object-interaction knowledge from pretrained large-scale vision language models. Under the AGD20K benchmark, our proposed model demonstrates a significant performance gain over the competing methods for in-the-wild object affordance grounding. We further demonstrate it can ground affordance for objects from random Internet images, even if both objects and actions are unseen during training. Project site: https://jasonqsy.github.io/AffordanceLLM/

Grounding the common-sense reasoning of Large Language Models in physical domains remains a pivotal yet unsolved problem for embodied AI. Whereas prior works have focused on leveraging LLMs directly for planning in symbolic spaces, this work uses LLMs to guide the search of task structures and constraints implicit in multi-step demonstrations. Specifically, we borrow from manipulation planning literature the concept of mode families, which group robot configurations by specific motion constraints, to serve as an abstraction layer between the high-level language representations of an LLM and the low-level physical trajectories of a robot. By replaying a few human demonstrations with synthetic perturbations, we generate coverage over the demonstrations' state space with additional successful executions as well as counterfactuals that fail the task. Our explanation-based learning framework trains an end-to-end differentiable neural network to predict successful trajectories from failures and as a by-product learns classifiers that ground low-level states and images in mode families without dense labeling. The learned grounding classifiers can further be used to translate language plans into reactive policies in the physical domain in an interpretable manner. We show our approach improves the interpretability and reactivity of imitation learning through 2D navigation and simulated and real robot manipulation tasks. Website: https://sites.google.com/view/grounding-plans

Generative Artificial Intelligence (AI) has rapidly advanced the field of computer vision by enabling machines to create and interpret visual data with unprecedented sophistication. This transformation builds upon a foundation of generative models to produce realistic images, videos, and 3D/4D content. Conventional generative models primarily focus on visual fidelity while often neglecting the physical plausibility of the generated content. This gap limits their effectiveness in applications that require adherence to real-world physical laws, such as robotics, autonomous systems, and scientific simulations. As generative models evolve to increasingly integrate physical realism and dynamic simulation, their potential to function as "world simulators" expands. Therefore, the field of physics-aware generation in computer vision is rapidly growing, calling for a comprehensive survey to provide a structured analysis of current efforts. To serve this purpose, the survey presents a systematic review, categorizing methods based on how they incorporate physical knowledge, either through explicit simulation or implicit learning. It also analyzes key paradigms, discusses evaluation protocols, and identifies future research directions. By offering a comprehensive overview, this survey aims to help future developments in physically grounded generation for computer vision. The reviewed papers are summarized at https://tinyurl.com/Physics-Aware-Generation.

In this paper, we introduce a unified and generalist Biomedical Generative Pre-trained Transformer (BiomedGPT) model, which leverages self-supervision on large and diverse datasets to accept multi-modal inputs and perform a range of downstream tasks. Our experiments demonstrate that BiomedGPT delivers expansive and inclusive representations of biomedical data, outperforming the majority of preceding state-of-the-art models across five distinct tasks with 20 public datasets spanning over 15 unique biomedical modalities. Through the ablation study, we also showcase the efficacy of our multi-modal and multi-task pretraining approach in transferring knowledge to previously unseen data. Overall, our work presents a significant step forward in developing unified and generalist models for biomedicine, with far-reaching implications for improving healthcare outcomes.

In living organisms, homeostasis is the natural regulation of internal states aimed at maintaining conditions compatible with life. Typical artificial systems are not equipped with comparable regulatory features. Here, we introduce an artificial neural network that incorporates homeostatic features. Its own computing substrate is placed in a needful and vulnerable relation to the very objects over which it computes. For example, artificial neurons performing classification of MNIST digits or Fashion-MNIST articles of clothing may receive excitatory or inhibitory effects, which alter their own learning rate as a direct result of perceiving and classifying the digits. In this scenario, accurate recognition is desirable to the agent itself because it guides decisions to regulate its vulnerable internal states and functionality. Counterintuitively, the addition of vulnerability to a learner does not necessarily impair its performance. On the contrary, self-regulation in response to vulnerability confers benefits under certain conditions. We show that homeostatic design confers increased adaptability under concept shift, in which the relationships between labels and data change over time, and that the greatest advantages are obtained under the highest rates of shift. This necessitates the rapid un-learning of past associations and the re-learning of new ones. We also demonstrate the superior abilities of homeostatic learners in environments with dynamically changing rates of concept shift. Our homeostatic design exposes the artificial neural network's thinking machinery to the consequences of its own "thoughts", illustrating the advantage of putting one's own "skin in the game" to improve fluid intelligence.

Grounding-DINO is a state-of-the-art open-set detection model that tackles multiple vision tasks including Open-Vocabulary Detection (OVD), Phrase Grounding (PG), and Referring Expression Comprehension (REC). Its effectiveness has led to its widespread adoption as a mainstream architecture for various downstream applications. However, despite its significance, the original Grounding-DINO model lacks comprehensive public technical details due to the unavailability of its training code. To bridge this gap, we present MM-Grounding-DINO, an open-source, comprehensive, and user-friendly baseline, which is built with the MMDetection toolbox. It adopts abundant vision datasets for pre-training and various detection and grounding datasets for fine-tuning. We give a comprehensive analysis of each reported result and detailed settings for reproduction. The extensive experiments on the benchmarks mentioned demonstrate that our MM-Grounding-DINO-Tiny outperforms the Grounding-DINO-Tiny baseline. We release all our models to the research community. Codes and trained models are released at https://github.com/open-mmlab/mmdetection/tree/main/configs/mm_grounding_dino.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems, particularly during the origins of life. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. These forces can be quantified using the Price equation, which is a standard tool used in evolutionary biology to quantify evolutionary change. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. We demonstrate this using the Graded Autocatalysis Replication Domain computer model, describing simple protocell composed out of molecules and its replication, which respectively analogue to the group and the individuals. In contrast to previous treatments of this model, we treat the lipid molecules themselves as replicating individuals and the protocells they form as groups of individuals. Our goal is to demonstrate how evolutionary biology tools and concepts can be applied in chemistry and we suggest that molecular cooperation may arise as a result of group selection. Further, the biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology.

This work investigates descriptive captions as an additional source of supervision for biological multimodal foundation models. Images and captions can be viewed as complementary samples from the latent morphospace of a species, each capturing certain biological traits. Incorporating captions during training encourages alignment with this shared latent structure, emphasizing potentially diagnostic characters while suppressing spurious correlations. The main challenge, however, lies in obtaining faithful, instance-specific captions at scale. This requirement has limited the utilization of natural language supervision in organismal biology compared with many other scientific domains. We complement this gap by generating synthetic captions with multimodal large language models (MLLMs), guided by Wikipedia-derived visual information and taxon-tailored format examples. These domain-specific contexts help reduce hallucination and yield accurate, instance-based descriptive captions. Using these captions, we train BIOCAP (i.e., BIOCLIP with Captions), a biological foundation model that captures rich semantics and achieves strong performance in species classification and text-image retrieval. These results demonstrate the value of descriptive captions beyond labels in bridging biological images with multimodal foundation models.

Existing work in language grounding typically study single environments. How do we build unified models that apply across multiple environments? We propose the multi-environment Symbolic Interactive Language Grounding benchmark (SILG), which unifies a collection of diverse grounded language learning environments under a common interface. SILG consists of grid-world environments that require generalization to new dynamics, entities, and partially observed worlds (RTFM, Messenger, NetHack), as well as symbolic counterparts of visual worlds that require interpreting rich natural language with respect to complex scenes (ALFWorld, Touchdown). Together, these environments provide diverse grounding challenges in richness of observation space, action space, language specification, and plan complexity. In addition, we propose the first shared model architecture for RL on these environments, and evaluate recent advances such as egocentric local convolution, recurrent state-tracking, entity-centric attention, and pretrained LM using SILG. Our shared architecture achieves comparable performance to environment-specific architectures. Moreover, we find that many recent modelling advances do not result in significant gains on environments other than the one they were designed for. This highlights the need for a multi-environment benchmark. Finally, the best models significantly underperform humans on SILG, which suggests ample room for future work. We hope SILG enables the community to quickly identify new methodologies for language grounding that generalize to a diverse set of environments and their associated challenges.

Natural language serves as the primary mode of communication when an intelligent agent with a physical presence engages with human beings. While a plethora of research focuses on natural language understanding (NLU), encompassing endeavors such as sentiment analysis, intent prediction, question answering, and summarization, the scope of NLU directed at situations necessitating tangible actions by an embodied agent remains limited. The inherent ambiguity and incompleteness inherent in natural language present challenges for intelligent agents striving to decipher human intention. To tackle this predicament head-on, we introduce a novel system known as task and argument grounding for Embodied agents (tagE). At its core, our system employs an inventive neural network model designed to extract a series of tasks from complex task instructions expressed in natural language. Our proposed model adopts an encoder-decoder framework enriched with nested decoding to effectively extract tasks and their corresponding arguments from these intricate instructions. These extracted tasks are then mapped (or grounded) to the robot's established collection of skills, while the arguments find grounding in objects present within the environment. To facilitate the training and evaluation of our system, we have curated a dataset featuring complex instructions. The results of our experiments underscore the prowess of our approach, as it outperforms robust baseline models.

Recent works successfully leveraged Large Language Models' (LLM) abilities to capture abstract knowledge about world's physics to solve decision-making problems. Yet, the alignment between LLMs' knowledge and the environment can be wrong and limit functional competence due to lack of grounding. In this paper, we study an approach (named GLAM) to achieve this alignment through functional grounding: we consider an agent using an LLM as a policy that is progressively updated as the agent interacts with the environment, leveraging online Reinforcement Learning to improve its performance to solve goals. Using an interactive textual environment designed to study higher-level forms of functional grounding, and a set of spatial and navigation tasks, we study several scientific questions: 1) Can LLMs boost sample efficiency for online learning of various RL tasks? 2) How can it boost different forms of generalization? 3) What is the impact of online learning? We study these questions by functionally grounding several variants (size, architecture) of FLAN-T5.

Visual grounding, which aims to ground a visual region via natural language, is a task that heavily relies on cross-modal alignment. Existing works utilized uni-modal pre-trained models to transfer visual/linguistic knowledge separately while ignoring the multimodal corresponding information. Motivated by recent advancements in contrastive language-image pre-training and low-rank adaptation (LoRA) methods, we aim to solve the grounding task based on multimodal pre-training. However, there exists significant task gaps between pre-training and grounding. Therefore, to address these gaps, we propose a concise and efficient hierarchical multimodal fine-grained modulation framework, namely HiVG. Specifically, HiVG consists of a multi-layer adaptive cross-modal bridge and a hierarchical multimodal low-rank adaptation (Hi LoRA) paradigm. The cross-modal bridge can address the inconsistency between visual features and those required for grounding, and establish a connection between multi-level visual and text features. Hi LoRA prevents the accumulation of perceptual errors by adapting the cross-modal features from shallow to deep layers in a hierarchical manner. Experimental results on five datasets demonstrate the effectiveness of our approach and showcase the significant grounding capabilities as well as promising energy efficiency advantages. The project page: https://github.com/linhuixiao/HiVG.

With the development of multimodal reasoning models, Computer Use Agents (CUAs), akin to Jarvis from "Iron Man", are becoming a reality. GUI grounding is a core component for CUAs to execute actual actions, similar to mechanical control in robotics, and it directly leads to the success or failure of the system. It determines actions such as clicking and typing, as well as related parameters like the coordinates for clicks. Current end-to-end grounding models still achieve less than 65\% accuracy on challenging benchmarks like ScreenSpot-pro and UI-Vision, indicating they are far from being ready for deployment. % , as a single misclick can result in unacceptable consequences. In this work, we conduct an empirical study on the training of grounding models, examining details from data collection to model training. Ultimately, we developed the Phi-Ground model family, which achieves state-of-the-art performance across all five grounding benchmarks for models under 10B parameters in agent settings. In the end-to-end model setting, our model still achieves SOTA results with scores of \textbf{43.2} on ScreenSpot-pro and \textbf{27.2} on UI-Vision. We believe that the various details discussed in this paper, along with our successes and failures, not only clarify the construction of grounding models but also benefit other perception tasks. Project homepage: https://zhangmiaosen2000.github.io/Phi-Ground/{https://zhangmiaosen2000.github.io/Phi-Ground/}

The emergence of complex life on Earth is often attributed to the arms race that ensued from a huge number of organisms all competing for finite resources. We present an artificial intelligence research environment, inspired by the human game genre of MMORPGs (Massively Multiplayer Online Role-Playing Games, a.k.a. MMOs), that aims to simulate this setting in microcosm. As with MMORPGs and the real world alike, our environment is persistent and supports a large and variable number of agents. Our environment is well suited to the study of large-scale multiagent interaction: it requires that agents learn robust combat and navigation policies in the presence of large populations attempting to do the same. Baseline experiments reveal that population size magnifies and incentivizes the development of skillful behaviors and results in agents that outcompete agents trained in smaller populations. We further show that the policies of agents with unshared weights naturally diverge to fill different niches in order to avoid competition.

We introduce the task of 3D visual grounding in large-scale dynamic scenes based on natural linguistic descriptions and online captured multi-modal visual data, including 2D images and 3D LiDAR point clouds. We present a novel method, dubbed WildRefer, for this task by fully utilizing the rich appearance information in images, the position and geometric clues in point cloud as well as the semantic knowledge of language descriptions. Besides, we propose two novel datasets, i.e., STRefer and LifeRefer, which focus on large-scale human-centric daily-life scenarios accompanied with abundant 3D object and natural language annotations. Our datasets are significant for the research of 3D visual grounding in the wild and has huge potential to boost the development of autonomous driving and service robots. Extensive experiments and ablation studies demonstrate that our method achieves state-of-the-art performance on the proposed benchmarks. The code is provided in https://github.com/4DVLab/WildRefer.

GUI grounding is a critical component in building capable GUI agents. However, existing grounding benchmarks suffer from significant limitations: they either provide insufficient data volume and narrow domain coverage, or focus excessively on a single platform and require highly specialized domain knowledge. In this work, we present VenusBench-GD, a comprehensive, bilingual benchmark for GUI grounding that spans multiple platforms, enabling hierarchical evaluation for real-word applications. VenusBench-GD contributes as follows: (i) we introduce a large-scale, cross-platform benchmark with extensive coverage of applications, diverse UI elements, and rich annotated data, (ii) we establish a high-quality data construction pipeline for grounding tasks, achieving higher annotation accuracy than existing benchmarks, and (iii) we extend the scope of element grounding by proposing a hierarchical task taxonomy that divides grounding into basic and advanced categories, encompassing six distinct subtasks designed to evaluate models from complementary perspectives. Our experimental findings reveal critical insights: general-purpose multimodal models now match or even surpass specialized GUI models on basic grounding tasks. In contrast, advanced tasks, still favor GUI-specialized models, though they exhibit significant overfitting and poor robustness. These results underscore the necessity of comprehensive, multi-tiered evaluation frameworks.

Spatial cognition enables adaptive goal-directed behavior by constructing internal models of space. Robust biological systems consolidate spatial knowledge into three interconnected forms: landmarks for salient cues, route knowledge for movement trajectories, and survey knowledge for map-like representations. While recent advances in multi-modal large language models (MLLMs) have enabled visual-language reasoning in embodied agents, these efforts lack structured spatial memory and instead operate reactively, limiting their generalization and adaptability in complex real-world environments. Here we present Brain-inspired Spatial Cognition for Navigation (BSC-Nav), a unified framework for constructing and leveraging structured spatial memory in embodied agents. BSC-Nav builds allocentric cognitive maps from egocentric trajectories and contextual cues, and dynamically retrieves spatial knowledge aligned with semantic goals. Integrated with powerful MLLMs, BSC-Nav achieves state-of-the-art efficacy and efficiency across diverse navigation tasks, demonstrates strong zero-shot generalization, and supports versatile embodied behaviors in the real physical world, offering a scalable and biologically grounded path toward general-purpose spatial intelligence.

Biodiversity research requires complete and detailed information to study ecosystem dynamics at different scales. Employing data-driven methods like Machine Learning is getting traction in ecology and more specific biodiversity, offering alternative modelling pathways. For these methods to deliver accurate results there is the need for large, curated and multimodal datasets that offer granular spatial and temporal resolutions. In this work, we introduce BioCube, a multimodal, fine-grained global dataset for ecology and biodiversity research. BioCube incorporates species observations through images, audio recordings and descriptions, environmental DNA, vegetation indices, agricultural, forest, land indicators, and high-resolution climate variables. All observations are geospatially aligned under the WGS84 geodetic system, spanning from 2000 to 2020. The dataset will become available at https://huggingface.co/datasets/BioDT/BioCube while the acquisition and processing code base at https://github.com/BioDT/bfm-data.

When an image generation process is guided by both a text prompt and spatial cues, such as a set of bounding boxes, do these elements work in harmony, or does one dominate the other? Our analysis of a pretrained image diffusion model that integrates gated self-attention into the U-Net reveals that spatial grounding often outweighs textual grounding due to the sequential flow from gated self-attention to cross-attention. We demonstrate that such bias can be significantly mitigated without sacrificing accuracy in either grounding by simply rewiring the network architecture, changing from sequential to parallel for gated self-attention and cross-attention. This surprisingly simple yet effective solution does not require any fine-tuning of the network but significantly reduces the trade-off between the two groundings. Our experiments demonstrate significant improvements from the original GLIGEN to the rewired version in the trade-off between textual grounding and spatial grounding.

Backpropagation (BP) is the most successful and widely used algorithm in deep learning. However, the computations required by BP are challenging to reconcile with known neurobiology. This difficulty has stimulated interest in more biologically plausible alternatives to BP. One such algorithm is the inference learning algorithm (IL). IL has close connections to neurobiological models of cortical function and has achieved equal performance to BP on supervised learning and auto-associative tasks. In contrast to BP, however, the mathematical foundations of IL are not well-understood. Here, we develop a novel theoretical framework for IL. Our main result is that IL closely approximates an optimization method known as implicit stochastic gradient descent (implicit SGD), which is distinct from the explicit SGD implemented by BP. Our results further show how the standard implementation of IL can be altered to better approximate implicit SGD. Our novel implementation considerably improves the stability of IL across learning rates, which is consistent with our theory, as a key property of implicit SGD is its stability. We provide extensive simulation results that further support our theoretical interpretations and also demonstrate IL achieves quicker convergence when trained with small mini-batches while matching the performance of BP for large mini-batches.

While reinforcement learning (RL) over chains of thought has significantly advanced language models in tasks such as mathematics and coding, visual reasoning introduces added complexity by requiring models to direct visual attention, interpret perceptual inputs, and ground abstract reasoning in spatial evidence. We introduce ViGoRL (Visually Grounded Reinforcement Learning), a vision-language model trained with RL to explicitly anchor each reasoning step to specific visual coordinates. Inspired by human visual decision-making, ViGoRL learns to produce spatially grounded reasoning traces, guiding visual attention to task-relevant regions at each step. When fine-grained exploration is required, our novel multi-turn RL framework enables the model to dynamically zoom into predicted coordinates as reasoning unfolds. Across a diverse set of visual reasoning benchmarks--including SAT-2 and BLINK for spatial reasoning, V*bench for visual search, and ScreenSpot and VisualWebArena for web-based grounding--ViGoRL consistently outperforms both supervised fine-tuning and conventional RL baselines that lack explicit grounding mechanisms. Incorporating multi-turn RL with zoomed-in visual feedback significantly improves ViGoRL's performance on localizing small GUI elements and visual search, achieving 86.4% on V*Bench. Additionally, we find that grounding amplifies other visual behaviors such as region exploration, grounded subgoal setting, and visual verification. Finally, human evaluations show that the model's visual references are not only spatially accurate but also helpful for understanding model reasoning steps. Our results show that visually grounded RL is a strong paradigm for imbuing models with general-purpose visual reasoning.

The brain has computational capabilities that surpass those of modern systems, being able to solve complex problems efficiently in a simple way. Neuromorphic engineering aims to mimic biology in order to develop new systems capable of incorporating such capabilities. Bio-inspired learning systems continue to be a challenge that must be solved, and much work needs to be done in this regard. Among all brain regions, the hippocampus stands out as an autoassociative short-term memory with the capacity to learn and recall memories from any fragment of them. These characteristics make the hippocampus an ideal candidate for developing bio-inspired learning systems that, in addition, resemble content-addressable memories. Therefore, in this work we propose a bio-inspired spiking content-addressable memory model based on the CA3 region of the hippocampus with the ability to learn, forget and recall memories, both orthogonal and non-orthogonal, from any fragment of them. The model was implemented on the SpiNNaker hardware platform using Spiking Neural Networks. A set of experiments based on functional, stress and applicability tests were performed to demonstrate its correct functioning. This work presents the first hardware implementation of a fully-functional bio-inspired spiking hippocampal content-addressable memory model, paving the way for the development of future more complex neuromorphic systems.

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

The fields of Origin of Life and Artificial Life both question what life is and how it emerges from a distinct set of "pre-life" dynamics. One common feature of most substrates where life emerges is a marked shift in dynamics when self-replication appears. While there are some hypotheses regarding how self-replicators arose in nature, we know very little about the general dynamics, computational principles, and necessary conditions for self-replicators to emerge. This is especially true on "computational substrates" where interactions involve logical, mathematical, or programming rules. In this paper we take a step towards understanding how self-replicators arise by studying several computational substrates based on various simple programming languages and machine instruction sets. We show that when random, non self-replicating programs are placed in an environment lacking any explicit fitness landscape, self-replicators tend to arise. We demonstrate how this occurs due to random interactions and self-modification, and can happen with and without background random mutations. We also show how increasingly complex dynamics continue to emerge following the rise of self-replicators. Finally, we show a counterexample of a minimalistic programming language where self-replicators are possible, but so far have not been observed to arise.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited adaptability to dynamic lab conditions, inadequate error handling, and high operational complexity. Here we introduce BioMARS (Biological Multi-Agent Robotic System), an intelligent platform that integrates LLMs, VLMs, and modular robotics to autonomously design, plan, and execute biological experiments. BioMARS uses a hierarchical architecture: the Biologist Agent synthesizes protocols via retrieval-augmented generation; the Technician Agent translates them into executable robotic pseudo-code; and the Inspector Agent ensures procedural integrity through multimodal perception and anomaly detection. The system autonomously conducts cell passaging and culture tasks, matching or exceeding manual performance in viability, consistency, and morphological integrity. It also supports context-aware optimization, outperforming conventional strategies in differentiating retinal pigment epithelial cells. A web interface enables real-time human-AI collaboration, while a modular backend allows scalable integration with laboratory hardware. These results highlight the feasibility of generalizable, AI-driven laboratory automation and the transformative role of language-based reasoning in biological research.

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

Natural language inference (NLI) is critical for complex decision-making in biomedical domain. One key question, for example, is whether a given biomedical mechanism is supported by experimental evidence. This can be seen as an NLI problem but there are no directly usable datasets to address this. The main challenge is that manually creating informative negative examples for this task is difficult and expensive. We introduce a novel semi-supervised procedure that bootstraps an NLI dataset from existing biomedical dataset that pairs mechanisms with experimental evidence in abstracts. We generate a range of negative examples using nine strategies that manipulate the structure of the underlying mechanisms both with rules, e.g., flip the roles of the entities in the interaction, and, more importantly, as perturbations via logical constraints in a neuro-logical decoding system. We use this procedure to create a novel dataset for NLI in the biomedical domain, called BioNLI and benchmark two state-of-the-art biomedical classifiers. The best result we obtain is around mid 70s in F1, suggesting the difficulty of the task. Critically, the performance on the different classes of negative examples varies widely, from 97% F1 on the simple role change negative examples, to barely better than chance on the negative examples generated using neuro-logic decoding.

Recent progress in large language models (LLMs) has demonstrated the ability to learn and leverage Internet-scale knowledge through pre-training with autoregressive models. Unfortunately, applying such models to settings with embodied agents, such as robots, is challenging due to their lack of experience with the physical world, inability to parse non-language observations, and ignorance of rewards or safety constraints that robots may require. On the other hand, language-conditioned robotic policies that learn from interaction data can provide the necessary grounding that allows the agent to be correctly situated in the real world, but such policies are limited by the lack of high-level semantic understanding due to the limited breadth of the interaction data available for training them. Thus, if we want to make use of the semantic knowledge in a language model while still situating it in an embodied setting, we must construct an action sequence that is both likely according to the language model and also realizable according to grounded models of the environment. We frame this as a problem similar to probabilistic filtering: decode a sequence that both has high probability under the language model and high probability under a set of grounded model objectives. We demonstrate this guided decoding strategy is able to solve complex, long-horizon embodiment tasks in a robotic setting by leveraging the knowledge of both models. The project's website can be found at grounded-decoding.github.io.

Communication via natural language is a crucial aspect of intelligence, and it requires computational models to learn and reason about world concepts, with varying levels of supervision. While there has been significant progress made on fully-supervised non-interactive tasks, such as question-answering and procedural text understanding, much of the community has turned to various sequential interactive tasks, as in semi-Markov text-based games, which have revealed limitations of existing approaches in terms of coherence, contextual awareness, and their ability to learn effectively from the environment. In this paper, we propose a framework for enabling improved functional grounding of agents in text-based games. Specifically, we consider two forms of domain knowledge that we inject into learning-based agents: memory of previous correct actions and affordances of relevant objects in the environment. Our framework supports three representative model classes: `pure' reinforcement learning (RL) agents, RL agents enhanced with knowledge graphs, and agents equipped with language models. Furthermore, we devise multiple injection strategies for the above domain knowledge types and agent architectures, including injection via knowledge graphs and augmentation of the existing input encoding strategies. We perform all experiments on the ScienceWorld text-based game environment, to illustrate the performance of various model configurations in challenging science-related instruction-following tasks. Our findings provide crucial insights on the development of effective natural language processing systems for interactive contexts.

Solving complex real-world tasks requires cycles of actions and observations. This is particularly true in science, where tasks require many cycles of analysis, tool use, and experimentation. Language agents are promising for automating intellectual tasks in science because they can interact with tools via natural language or code. Yet their flexibility creates conceptual and practical challenges for software implementations, since agents may comprise non-standard components such as internal reasoning, planning, tool usage, as well as the inherent stochasticity of temperature-sampled language models. Here, we introduce Aviary, an extensible gymnasium for language agents. We formalize agents as policies solving language-grounded partially observable Markov decision processes, which we term language decision processes. We then implement five environments, including three challenging scientific environments: (1) manipulating DNA constructs for molecular cloning, (2) answering research questions by accessing scientific literature, and (3) engineering protein stability. These environments were selected for their focus on multi-step reasoning and their relevance to contemporary biology research. Finally, with online training and scaling inference-time compute, we show that language agents backed by open-source, non-frontier LLMs can match and exceed both frontier LLM agents and human experts on multiple tasks at up to 100x lower inference cost.

Biological tissues exhibit complex behaviors with their dynamics often resembling inert soft matter such as liquids, polymers, colloids, and liquid crystals. These analogies enable physics-based approaches for investigations of emergent behaviors in biological processes. A well-studied case is the spreading of cellular aggregates on solid surfaces, where they display dynamics similar to viscous droplets. In vivo, however, cells and tissues are in a confined environment with varying geometries and mechanical properties to which they need to adapt. In this work, we compressed cellular aggregates between two solid surfaces and studied their dynamics using microscopy, and computer simulations. The confined cellular aggregates transitioned from compressed spheres into dynamic living capillary bridges exhibiting bridge thinning and a convex-to-concave meniscus curvature transition. We found that the stability of the bridge is determined by the interplay between cell growth and cell spreading on the confining surfaces. This interaction leads to bridge rupture at a critical length scale determined by the distance between the plates. The force distributions, formation and stability regimes of the living capillary bridges were characterized with full 3D computer simulations that included cell division, migration and growth dynamics, directly showing how mechanical principles govern the behavior of the living bridges; cellular aggregates display jamming and stiffening analogously to granular matter, and cell division along the long axis enhances thinning. Based on our results, we propose a new class of active soft matter behavior, where cellular aggregates exhibit liquid-like adaptation to confinement, but with self-organized rupturing driven by biological activity.

We introduce a pipeline that enhances a general-purpose Vision Language Model, GPT-4V(ision), by integrating observations of human actions to facilitate robotic manipulation. This system analyzes videos of humans performing tasks and creates executable robot programs that incorporate affordance insights. The computation starts by analyzing the videos with GPT-4V to convert environmental and action details into text, followed by a GPT-4-empowered task planner. In the following analyses, vision systems reanalyze the video with the task plan. Object names are grounded using an open-vocabulary object detector, while focus on the hand-object relation helps to detect the moment of grasping and releasing. This spatiotemporal grounding allows the vision systems to further gather affordance data (e.g., grasp type, way points, and body postures). Experiments across various scenarios demonstrate this method's efficacy in achieving real robots' operations from human demonstrations in a zero-shot manner. The prompts of GPT-4V/GPT-4 are available at this project page: https://microsoft.github.io/GPT4Vision-Robot-Manipulation-Prompts/

The ability to connect language units to their referents in the physical world, referred to as grounding, is crucial to learning and understanding grounded meanings of words. While humans demonstrate fast mapping in new word learning, it remains unclear whether modern vision-language models can truly represent language with their grounded meanings and how grounding may further bootstrap new word learning. To this end, we introduce Grounded Open Vocabulary Acquisition (GOVA) to examine grounding and bootstrapping in open-world language learning. As an initial attempt, we propose object-oriented BERT (OctoBERT), a novel visually-grounded language model by pre-training on image-text pairs highlighting grounding as an objective. Through extensive experiments and analysis, we demonstrate that OctoBERT is a more coherent and fast grounded word learner, and that the grounding ability acquired during pre-training helps the model to learn unseen words more rapidly and robustly. Our code is available at https://github.com/sled-group/world-to-words

Large Multimodal Models (LMMs) extend Large Language Models to the vision domain. Initial efforts towards LMMs used holistic images and text prompts to generate ungrounded textual responses. Very recently, region-level LMMs have been used to generate visually grounded responses. However, they are limited to only referring a single object category at a time, require users to specify the regions in inputs, or cannot offer dense pixel-wise object grounding. In this work, we present Grounding LMM (GLaMM), the first model that can generate natural language responses seamlessly intertwined with corresponding object segmentation masks. GLaMM not only grounds objects appearing in the conversations but is flexible enough to accept both textual and optional visual prompts (region of interest) as input. This empowers users to interact with the model at various levels of granularity, both in textual and visual domains. Due to the lack of standard benchmarks for the novel setting of generating visually grounded detailed conversations, we introduce a comprehensive evaluation protocol with our curated grounded conversations. Our proposed Grounded Conversation Generation (GCG) task requires densely grounded concepts in natural scenes at a large-scale. To this end, we propose a densely annotated Grounding-anything Dataset (GranD) using our proposed automated annotation pipeline that encompasses 7.5M unique concepts grounded in a total of 810M regions available with segmentation masks. Besides GCG, GLaMM also performs effectively on several downstream tasks e.g., referring expression segmentation, image and region-level captioning and vision-language conversations. Project Page: https://mbzuai-oryx.github.io/groundingLMM.

Visual grounding, a crucial vision-language task involving the understanding of the visual context based on the query expression, necessitates the model to capture the interactions between objects, as well as various spatial and attribute information. However, the annotation data of visual grounding task is limited due to its time-consuming and labor-intensive annotation process, resulting in the trained models being constrained from generalizing its capability to a broader domain. To address this challenge, we propose GroundVLP, a simple yet effective zero-shot method that harnesses visual grounding ability from the existing models trained from image-text pairs and pure object detection data, both of which are more conveniently obtainable and offer a broader domain compared to visual grounding annotation data. GroundVLP proposes a fusion mechanism that combines the heatmap from GradCAM and the object proposals of open-vocabulary detectors. We demonstrate that the proposed method significantly outperforms other zero-shot methods on RefCOCO/+/g datasets, surpassing prior zero-shot state-of-the-art by approximately 28\% on the test split of RefCOCO and RefCOCO+. Furthermore, GroundVLP performs comparably to or even better than some non-VLP-based supervised models on the Flickr30k entities dataset. Our code is available at https://github.com/om-ai-lab/GroundVLP.

Visual Grounding (VG) methods in Visual Question Answering (VQA) attempt to improve VQA performance by strengthening a model's reliance on question-relevant visual information. The presence of such relevant information in the visual input is typically assumed in training and testing. This assumption, however, is inherently flawed when dealing with imperfect image representations common in large-scale VQA, where the information carried by visual features frequently deviates from expected ground-truth contents. As a result, training and testing of VG-methods is performed with largely inaccurate data, which obstructs proper assessment of their potential benefits. In this study, we demonstrate that current evaluation schemes for VG-methods are problematic due to the flawed assumption of availability of relevant visual information. Our experiments show that these methods can be much more effective when evaluation conditions are corrected. Code is provided on GitHub.

In this work, we address the problem of grounding abnormalities in medical images, where the goal is to localize clinical findings based on textual descriptions. While generalist Vision-Language Models (VLMs) excel in natural grounding tasks, they often struggle in the medical domain due to rare, compositional, and domain-specific terms that are poorly aligned with visual patterns. Specialized medical VLMs address this challenge via large-scale domain pretraining, but at the cost of substantial annotation and computational resources. To overcome these limitations, we propose Knowledge to Sight (K2Sight), a framework that introduces structured semantic supervision by decomposing clinical concepts into interpretable visual attributes, such as shape, density, and anatomical location. These attributes are distilled from domain ontologies and encoded into concise instruction-style prompts, which guide region-text alignment during training. Unlike conventional report-level supervision, our approach explicitly bridges domain knowledge and spatial structure, enabling data-efficient training of compact models. We train compact models with 0.23B and 2B parameters using only 1.5\% of the data required by state-of-the-art medical VLMs. Despite their small size and limited training data, these models achieve performance on par with or better than 7B+ medical VLMs, with up to 9.82\% improvement in mAP_{50}. Code and models: https://lijunrio.github.io/K2Sight/{SOTAPink{https://lijunrio.github.io/K2Sight/}}.

We estimate the relative likelihood of success in the searches for primitive versus intelligent life on other planets. Taking into account the larger search volume for detectable artificial electromagnetic signals, we conclude that both searches should be performed concurrently, albeit with significantly more funding dedicated to primitive life. Based on the current federal funding allocated to the search for biosignatures, our analysis suggests that the search for extraterrestrial intelligence (SETI) may merit a federal funding level of at least 10$ million per year, assuming that the average lifetime of technological species exceeds a millennium.

Visual grounding in 3D is the key for embodied agents to localize language-referred objects in open-world environments. However, existing benchmarks are limited to indoor focus, single-platform constraints, and small scale. We introduce 3EED, a multi-platform, multi-modal 3D grounding benchmark featuring RGB and LiDAR data from vehicle, drone, and quadruped platforms. We provide over 128,000 objects and 22,000 validated referring expressions across diverse outdoor scenes -- 10x larger than existing datasets. We develop a scalable annotation pipeline combining vision-language model prompting with human verification to ensure high-quality spatial grounding. To support cross-platform learning, we propose platform-aware normalization and cross-modal alignment techniques, and establish benchmark protocols for in-domain and cross-platform evaluations. Our findings reveal significant performance gaps, highlighting the challenges and opportunities of generalizable 3D grounding. The 3EED dataset and benchmark toolkit are released to advance future research in language-driven 3D embodied perception.

3D vision-language grounding, which focuses on aligning language with the 3D physical environment, stands as a cornerstone in the development of embodied agents. In comparison to recent advancements in the 2D domain, grounding language in 3D scenes faces several significant challenges: (i) the inherent complexity of 3D scenes due to the diverse object configurations, their rich attributes, and intricate relationships; (ii) the scarcity of paired 3D vision-language data to support grounded learning; and (iii) the absence of a unified learning framework to distill knowledge from grounded 3D data. In this work, we aim to address these three major challenges in 3D vision-language by examining the potential of systematically upscaling 3D vision-language learning in indoor environments. We introduce the first million-scale 3D vision-language dataset, SceneVerse, encompassing about 68K 3D indoor scenes and comprising 2.5M vision-language pairs derived from both human annotations and our scalable scene-graph-based generation approach. We demonstrate that this scaling allows for a unified pre-training framework, Grounded Pre-training for Scenes (GPS), for 3D vision-language learning. Through extensive experiments, we showcase the effectiveness of GPS by achieving state-of-the-art performance on all existing 3D visual grounding benchmarks. The vast potential of SceneVerse and GPS is unveiled through zero-shot transfer experiments in the challenging 3D vision-language tasks. Project website: https://scene-verse.github.io .

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Visual grounding aims to ground an image region through natural language, which heavily relies on cross-modal alignment. Most existing methods transfer visual/linguistic knowledge separately by fully fine-tuning uni-modal pre-trained models, followed by a simple stack of visual-language transformers for multimodal fusion. However, these approaches not only limit adequate interaction between visual and linguistic contexts, but also incur significant computational costs. Therefore, to address these issues, we explore a step-wise multimodal fusion and adaption framework, namely SwimVG. Specifically, SwimVG proposes step-wise multimodal prompts (Swip) and cross-modal interactive adapters (CIA) for visual grounding, replacing the cumbersome transformer stacks for multimodal fusion. Swip can improve {the} alignment between the vision and language representations step by step, in a token-level fusion manner. In addition, weight-level CIA further promotes multimodal fusion by cross-modal interaction. Swip and CIA are both parameter-efficient paradigms, and they fuse the cross-modal features from shallow to deep layers gradually. Experimental results on four widely-used benchmarks demonstrate that SwimVG achieves remarkable abilities and considerable benefits in terms of efficiency. Our code is available at https://github.com/liuting20/SwimVG.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

Human intelligence, the most evident and accessible form of source of reasoning, hosted by biological hardware, has evolved and been refined over thousands of years, positioning itself today to create new artificial forms and preparing to self--design their evolutionary path forward. Beginning with the advent of foundation models, the rate at which human and artificial intelligence interact with each other has surpassed any anticipated quantitative figures. The close engagement led to both bits of intelligence to be impacted in various ways, which naturally resulted in complex confluences that warrant close scrutiny. In the sequel, we shall explore the interplay between human and machine intelligence, focusing on the crucial role humans play in developing ethical, responsible, and robust intelligent systems. We slightly delve into interesting aspects of implementation inspired by the mechanisms underlying neuroscience and human cognition. Additionally, we propose future perspectives, capitalizing on the advantages of symbiotic designs to suggest a human-centered direction for next-generation AI development. We finalize this evolving document with a few thoughts and open questions yet to be addressed by the broader community.

Large Vision-Language Models (LVLMs) have demonstrated impressive general capabilities across a wide range of multi-modal tasks. However, the reasoning processes of LVLMs often suffer from unreliable outputs and limited interpretability. To address this, grounded visual reasoning has emerged as a promising paradigm that enforces responses anchored on salient visual evidence regions. However, existing approaches typically rely on costly supervision such as bounding box annotations, chain-of-thought rationale or external tool calls, limiting their scalability. In this work, we propose Ground-R1, a reinforcement learning framework that enables grounded visual reasoning without requiring explicit evidence or rationale annotations. Ground-R1 consists of a grounding phase that generates evidence region rollouts based on format constraints, and an answering phase that produces responses guided by both answer correctness and format adherence rewards. Extensive experiments across multiple visual reasoning benchmarks manifest that Ground-R1 achieves superior performance and exhibits emergent cognitive behaviors such as uncertainty awareness, spatial perception, and iterative refinement, offering a scalable and interpretable alternative to existing approaches.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

Generative AI systems across modalities, ranging from text (including code), image, audio, and video, have broad social impacts, but there is no official standard for means of evaluating those impacts or for which impacts should be evaluated. In this paper, we present a guide that moves toward a standard approach in evaluating a base generative AI system for any modality in two overarching categories: what can be evaluated in a base system independent of context and what can be evaluated in a societal context. Importantly, this refers to base systems that have no predetermined application or deployment context, including a model itself, as well as system components, such as training data. Our framework for a base system defines seven categories of social impact: bias, stereotypes, and representational harms; cultural values and sensitive content; disparate performance; privacy and data protection; financial costs; environmental costs; and data and content moderation labor costs. Suggested methods for evaluation apply to listed generative modalities and analyses of the limitations of existing evaluations serve as a starting point for necessary investment in future evaluations. We offer five overarching categories for what can be evaluated in a broader societal context, each with its own subcategories: trustworthiness and autonomy; inequality, marginalization, and violence; concentration of authority; labor and creativity; and ecosystem and environment. Each subcategory includes recommendations for mitigating harm.

Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-correcting codes and by organizing in a modular fashion that physically separates functionally distinct subsystems. These elaborate structures represent a vanishing volume in the massive genetic configuration space. How is it possible that the primitive process of evolution, by which all biological systems evolved, achieved such unusual results? In this work, through experiments in Boolean networks, we show that the simultaneous presence of error correction and modularity in biological systems is no coincidence. Rather, it is a typical co-occurrence in noisy dynamic systems undergoing evolution. From this, we deduce the principle of error correction enhanced evolvability: systems possessing error-correcting codes are more effectively improved by evolution than those without.

3D visual grounding is the ability to localize objects in 3D scenes conditioned by utterances. Most existing methods devote the referring head to localize the referred object directly, causing failure in complex scenarios. In addition, it does not illustrate how and why the network reaches the final decision. In this paper, we address this question Can we design an interpretable 3D visual grounding framework that has the potential to mimic the human perception system?. To this end, we formulate the 3D visual grounding problem as a sequence-to-sequence task by first predicting a chain of anchors and then the final target. Interpretability not only improves the overall performance but also helps us identify failure cases. Following the chain of thoughts approach enables us to decompose the referring task into interpretable intermediate steps, boosting the performance and making our framework extremely data-efficient. Moreover, our proposed framework can be easily integrated into any existing architecture. We validate our approach through comprehensive experiments on the Nr3D, Sr3D, and Scanrefer benchmarks and show consistent performance gains compared to existing methods without requiring manually annotated data. Furthermore, our proposed framework, dubbed CoT3DRef, is significantly data-efficient, whereas on the Sr3D dataset, when trained only on 10% of the data, we match the SOTA performance that trained on the entire data.

Graphical user interface (GUI) grounding is a key function of computer-use agents, which maps natural-language instructions to actionable screen regions. Existing approaches based on Multimodal Large Language Models (MLLMs) typically formulate it as a text-based coordinate generation task, yet directly generating precise coordinates from visual inputs remains challenging and computationally intensive. An intuitive way to implement GUI grounding is to first select visual patches relevant to the instructions and then determine the precise click location within those patches. Based on the observations that general MLLMs have some native grounding capability, nested within their attentions, we propose GUI-AIMA, an attention-based and coordinate-free supervised fine-tuning framework for efficient GUI grounding. GUI-AIMA aligns the intrinsic multimodal attention of MLLMs with patch-wise grounding signals. These signals are calculated adaptively for diverse user instructions by multi-head aggregation on simplified query-visual attention matrices. Besides, its coordinate-free manner can easily integrate a plug-and-play zoom-in stage. GUI-AIMA-3B was trained with only 85k screenshots, demonstrating exceptional data efficiency and verifying that light training can trigger the native grounding capability of MLLMs. It achieves state-of-the-art performance among 3B models, attaining an average accuracy of 58.6% on ScreenSpot-Pro and 62.2% on OSWorld-G. Project page: https://github.com/sjz5202/GUI-AIMA

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Visual Grounding (VG) tasks, such as referring expression detection and segmentation tasks are important for linking visual entities to context, especially in complex reasoning tasks that require detailed query interpretation. This paper explores VG beyond basic perception, highlighting challenges for methods that require reasoning like human cognition. Recent advances in large language methods (LLMs) and Vision-Language methods (VLMs) have improved abilities for visual comprehension, contextual understanding, and reasoning. These methods are mainly split into end-to-end and compositional methods, with the latter offering more flexibility. Compositional approaches that integrate LLMs and foundation models show promising performance but still struggle with complex reasoning with language-based logical representations. To address these limitations, we propose NAVER, a compositional visual grounding method that integrates explicit probabilistic logic reasoning within a finite-state automaton, equipped with a self-correcting mechanism. This design improves robustness and interpretability in inference through explicit logic reasoning. Our results show that NAVER achieves SoTA performance comparing to recent end-to-end and compositional baselines. The code is available at https://github.com/ControlNet/NAVER .

Habitat assessment at local scales -- critical for enhancing biodiversity and guiding conservation priorities -- often relies on expert field survey that can be costly, motivating the exploration of AI-driven tools to automate and refine this process. While most AI-driven habitat mapping depends on remote sensing, it is often constrained by sensor availability, weather, and coarse resolution. In contrast, ground-level imagery captures essential structural and compositional cues invisible from above and remains underexplored for robust, fine-grained habitat classification. This study addresses this gap by applying state-of-the-art deep neural network architectures to ground-level habitat imagery. Leveraging data from the UK Countryside Survey covering 18 broad habitat types, we evaluate two families of models -- convolutional neural networks (CNNs) and vision transformers (ViTs) -- under both supervised and supervised contrastive learning paradigms. Our results demonstrate that ViTs consistently outperform state-of-the-art CNN baselines on key classification metrics (Top-3 accuracy = 91\%, MCC = 0.66) and offer more interpretable scene understanding tailored to ground-level images. Moreover, supervised contrastive learning significantly reduces misclassification rates among visually similar habitats (e.g., Improved vs. Neutral Grassland), driven by a more discriminative embedding space. Finally, our best model performs on par with experienced ecological experts in habitat classification from images, underscoring the promise of expert-level automated assessment. By integrating advanced AI with ecological expertise, this research establishes a scalable, cost-effective framework for ground-level habitat monitoring to accelerate biodiversity conservation and inform land-use decisions at the national scale.

In natural language processing, most models try to learn semantic representations merely from texts. The learned representations encode the distributional semantics but fail to connect to any knowledge about the physical world. In contrast, humans learn language by grounding concepts in perception and action and the brain encodes grounded semantics for cognition. Inspired by this notion and recent work in vision-language learning, we design a two-stream model for grounding language learning in vision. The model includes a VGG-based visual stream and a Bert-based language stream. The two streams merge into a joint representational space. Through cross-modal contrastive learning, the model first learns to align visual and language representations with the MS COCO dataset. The model further learns to retrieve visual objects with language queries through a cross-modal attention module and to infer the visual relations between the retrieved objects through a bilinear operator with the Visual Genome dataset. After training, the language stream of this model is a stand-alone language model capable of embedding concepts in a visually grounded semantic space. This semantic space manifests principal dimensions explainable with human intuition and neurobiological knowledge. Word embeddings in this semantic space are predictive of human-defined norms of semantic features and are segregated into perceptually distinctive clusters. Furthermore, the visually grounded language model also enables compositional language understanding based on visual knowledge and multimodal image search with queries based on images, texts, or their combinations.

Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection. In this paper I show that for those processes to be possible without the design of biological adaptations being encoded in the laws of physics, those laws must have certain other properties. The theory of what these properties are is not part of evolution theory proper, and has not been developed, yet without it the neo-Darwinian theory does not fully achieve its purpose of explaining the appearance of design. To this end I apply Constructor Theory's new mode of explanation to provide an exact formulation of the appearance of design, of no-design laws, and of the logic of self-reproduction and natural selection, within fundamental physics. I conclude that self-reproduction, replication and natural selection are possible under no-design laws, the only non-trivial condition being that they allow digital information to be physically instantiated. This has an exact characterisation in the constructor theory of information. I also show that under no-design laws an accurate replicator requires the existence of a "vehicle" constituting, together with the replicator, a self-reproducer.

Despite its widespread use in neural networks, error backpropagation has faced criticism for its lack of biological plausibility, suffering from issues such as the backward locking problem and the weight transport problem. These limitations have motivated researchers to explore more biologically plausible learning algorithms that could potentially shed light on how biological neural systems adapt and learn. Inspired by the counter-current exchange mechanisms observed in biological systems, we propose counter-current learning (CCL), a biologically plausible framework for credit assignment in neural networks. This framework employs a feedforward network to process input data and a feedback network to process targets, with each network enhancing the other through anti-parallel signal propagation. By leveraging the more informative signals from the bottom layer of the feedback network to guide the updates of the top layer of the feedforward network and vice versa, CCL enables the simultaneous transformation of source inputs to target outputs and the dynamic mutual influence of these transformations. Experimental results on MNIST, FashionMNIST, CIFAR10, and CIFAR100 datasets using multi-layer perceptrons and convolutional neural networks demonstrate that CCL achieves comparable performance to other biologically plausible algorithms while offering a more biologically realistic learning mechanism. Furthermore, we showcase the applicability of our approach to an autoencoder task, underscoring its potential for unsupervised representation learning. Our work presents a direction for biologically inspired and plausible learning algorithms, offering an alternative mechanism of learning and adaptation in neural networks.

3D visual grounding allows an embodied agent to understand visual information in real-world 3D environments based on human instructions, which is crucial for embodied intelligence. Existing 3D visual grounding methods typically rely on separate encoders for different modalities (e.g., RGB images, text, and 3D point clouds), resulting in large and complex models that are inefficient to train. While some approaches use pre-trained 2D multi-modal models like CLIP for 3D tasks, they still struggle with aligning point cloud data to 2D encoders. As a result, these methods continue to depend on 3D encoders for feature extraction, further increasing model complexity and training inefficiency. In this paper, we propose a unified 2D pre-trained multi-modal network to process all three modalities (RGB images, text, and point clouds), significantly simplifying the architecture. By leveraging a 2D CLIP bi-modal model with adapter-based fine-tuning, this framework effectively adapts to the tri-modal setting, improving both adaptability and performance across modalities. Our Geometric-Aware 2D-3D Feature Recovery and Fusion (GARF) module is designed to fuse geometric multi-scale features from point clouds and images. We then integrate textual features for final modality fusion and introduce a multi-modal decoder to facilitate deep cross-modal understanding. Together, our method achieves unified feature extraction and fusion across the three modalities, enabling an end-to-end 3D visual grounding model. Compared to the baseline, our method reduces the number of trainable parameters by approximately 58\%, while achieving a 6.52\% improvement in the 3D detection task and a 6.25\% improvement in the 3D visual grounding task.

Living systems face both environmental complexity and limited access to free-energy resources. Survival under these conditions requires a control system that can activate, or deploy, available perception and action resources in a context specific way. We show here that when systems are described as executing active inference driven by the free-energy principle (and hence can be considered Bayesian prediction-error minimizers), their control flow systems can always be represented as tensor networks (TNs). We show how TNs as control systems can be implmented within the general framework of quantum topological neural networks, and discuss the implications of these results for modeling biological systems at multiple scales.

The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an investigation of intelligent monitoring systems as a means of tackling the issue of the reproducibility crisis. Specifically, we first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. This dataset comprises fine-grained hierarchical annotations intended for the purpose of studying activity understanding in BioLab. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings. Finally, we provide a thorough experimental evaluation of contemporary video understanding models and highlight their limitations in this specialized domain to identify potential avenues for future research. We hope ProBio with associated benchmarks may garner increased focus on modern AI techniques in the realm of molecular biology.

Modern neural networks rely on generic activation functions (ReLU, GELU, SiLU) that ignore the mathematical structure inherent in scientific data. We propose Neuro-Symbolic Activation Discovery, a framework that uses Genetic Programming to extract interpretable mathematical formulas from data and inject them as custom activation functions. Our key contribution is the discovery of a Geometric Transfer phenomenon: activation functions learned from particle physics data successfully generalize to ecological classification, outperforming standard activations (ReLU, GELU, SiLU) in both accuracy and parameter efficiency. On the Forest Cover dataset, our Hybrid Transfer model achieves 82.4% accuracy with only 5,825 parameters, compared to 83.4% accuracy requiring 31,801 parameters for a conventional heavy network -- a 5.5x parameter reduction with only 1% accuracy loss. We introduce a Parameter Efficiency Score (E_{param} = AUC / log_{10}(Params)) and demonstrate that lightweight hybrid architectures consistently achieve 18-21% higher efficiency than over-parameterized baselines. Crucially, we establish boundary conditions: while Physics to Ecology transfer succeeds (both involve continuous Euclidean measurements), Physics to Text transfer fails (discrete word frequencies require different mathematical structures). Our work opens pathways toward domain-specific activation libraries for efficient scientific machine learning.

3D visual grounding is an emerging research area dedicated to making connections between the 3D physical world and natural language, which is crucial for achieving embodied intelligence. In this paper, we propose DASANet, a Dual Attribute-Spatial relation Alignment Network that separately models and aligns object attributes and spatial relation features between language and 3D vision modalities. We decompose both the language and 3D point cloud input into two separate parts and design a dual-branch attention module to separately model the decomposed inputs while preserving global context in attribute-spatial feature fusion by cross attentions. Our DASANet achieves the highest grounding accuracy 65.1% on the Nr3D dataset, 1.3% higher than the best competitor. Besides, the visualization of the two branches proves that our method is efficient and highly interpretable.

Cells that collide with each other repolarize away from contact, in a process called contact inhibition of locomotion (CIL), which is necessary for correct development of the embryo. CIL can occur even when cells make a micron-scale contact with a neighbor - much smaller than their size. How precisely can a cell sense cell-cell contact and repolarize in the correct direction? What factors control whether a cell recognizes it has contacted a neighbor? We propose a theoretical model for the limits of CIL where cells recognize the presence of another cell by binding the protein ephrin with the Eph receptor. This recognition is made difficult by the presence of interfering ligands that bind nonspecifically. Both theoretical predictions and simulation results show that it becomes more difficult to sense cell-cell contact when it is difficult to distinguish ephrin from the interfering ligands, or when there are more interfering ligands, or when the contact width decreases. However, the error of estimating contact position remains almost constant when the contact width changes. This happens because the cell gains spatial information largely from the boundaries of cell-cell contact. We study using statistical decision theory the likelihood of a false positive CIL event in the absence of cell-cell contact, and the likelihood of a false negative where CIL does not occur when another cell is present. Our results suggest that the cell is more likely to make incorrect decisions when the contact width is very small or so large that it nears the cell's perimeter. However, in general, we find that cells have the ability to make reasonably reliable CIL decisions even for very narrow (micron-scale) contacts, even if the concentration of interfering ligands is ten times that of the correct ligands.

Visual grounding is the task of locating objects specified by natural language expressions. Existing methods extend generic object detection frameworks to tackle this task. They typically extract visual and textual features separately using independent visual and textual encoders, then fuse these features in a multi-modal decoder for final prediction. However, visual grounding presents unique challenges. It often involves locating objects with different text descriptions within the same image. Existing methods struggle with this task because the independent visual encoder produces identical visual features for the same image, limiting detection performance. Some recently approaches propose various language-guided visual encoders to address this issue, but they mostly rely solely on textual information and require sophisticated designs. In this paper, we introduce Multi-modal Conditional Adaptation (MMCA), which enables the visual encoder to adaptively update weights, directing its focus towards text-relevant regions. Specifically, we first integrate information from different modalities to obtain multi-modal embeddings. Then we utilize a set of weighting coefficients, which generated from the multimodal embeddings, to reorganize the weight update matrices and apply them to the visual encoder of the visual grounding model. Extensive experiments on four widely used datasets demonstrate that MMCA achieves significant improvements and state-of-the-art results. Ablation experiments further demonstrate the lightweight and efficiency of our method. Our source code is available at: https://github.com/Mr-Bigworth/MMCA.

The rapid advancement of vision-language models has catalyzed the emergence of GUI agents, which hold immense potential for automating complex tasks, from online shopping to flight booking, thereby alleviating the burden of repetitive digital workflows. As a foundational capability, GUI grounding is typically established as a prerequisite for end-to-end task execution. It enables models to precisely locate interface elements, such as text and icons, to perform accurate operations like clicking and typing. Unlike prior works that fine-tune models already possessing strong spatial awareness (e.g., Qwen3-VL), we aim to master the full technical pipeline by starting from a base model with minimal grounding ability, such as POINTS-1.5. We introduce POINTS-GUI-G-8B, which achieves state-of-the-art performance with scores of 59.9 on ScreenSpot-Pro, 66.0 on OSWorld-G, 95.7 on ScreenSpot-v2, and 49.9 on UI-Vision. Our model's success is driven by three key factors: (1) Refined Data Engineering, involving the unification of diverse open-source datasets format alongside sophisticated strategies for augmentation, filtering, and difficulty grading; (2) Improved Training Strategies, including continuous fine-tuning of the vision encoder to enhance perceptual accuracy and maintaining resolution consistency between training and inference; and (3) Reinforcement Learning (RL) with Verifiable Rewards. While RL is traditionally used to bolster reasoning, we demonstrate that it significantly improves precision in the perception-intensive GUI grounding task. Furthermore, GUI grounding provides a natural advantage for RL, as rewards are easily verifiable and highly accurate.

Consider a robot tasked with tidying a desk with a meticulously constructed Lego sports car. A human may recognize that it is not socially appropriate to disassemble the sports car and put it away as part of the "tidying". How can a robot reach that conclusion? Although large language models (LLMs) have recently been used to enable social reasoning, grounding this reasoning in the real world has been challenging. To reason in the real world, robots must go beyond passively querying LLMs and *actively gather information from the environment* that is required to make the right decision. For instance, after detecting that there is an occluded car, the robot may need to actively perceive the car to know whether it is an advanced model car made out of Legos or a toy car built by a toddler. We propose an approach that leverages an LLM and vision language model (VLM) to help a robot actively perceive its environment to perform grounded social reasoning. To evaluate our framework at scale, we release the MessySurfaces dataset which contains images of 70 real-world surfaces that need to be cleaned. We additionally illustrate our approach with a robot on 2 carefully designed surfaces. We find an average 12.9% improvement on the MessySurfaces benchmark and an average 15% improvement on the robot experiments over baselines that do not use active perception. The dataset, code, and videos of our approach can be found at https://minaek.github.io/groundedsocialreasoning.

We introduce Look and Tell, a multimodal dataset for studying referential communication across egocentric and exocentric perspectives. Using Meta Project Aria smart glasses and stationary cameras, we recorded synchronized gaze, speech, and video as 25 participants instructed a partner to identify ingredients in a kitchen. Combined with 3D scene reconstructions, this setup provides a benchmark for evaluating how different spatial representations (2D vs. 3D; ego vs. exo) affect multimodal grounding. The dataset contains 3.67 hours of recordings, including 2,707 richly annotated referential expressions, and is designed to advance the development of embodied agents that can understand and engage in situated dialogue.

Passive acoustic monitoring has become a key strategy in biodiversity assessment, conservation, and behavioral ecology, especially as Internet-of-Things (IoT) devices enable continuous in situ audio collection at scale. While recent self-supervised learning (SSL)-based audio encoders, such as BEATs and AVES, have shown strong performance in bioacoustic tasks, their computational cost and limited robustness to unseen environments hinder deployment on resource-constrained platforms. In this work, we introduce BioME, a resource-efficient audio encoder designed for bioacoustic applications. BioME is trained via layer-to-layer distillation from a high-capacity teacher model, enabling strong representational transfer while reducing the parameter count by 75%. To further improve ecological generalization, the model is pretrained on multi-domain data spanning speech, environmental sounds, and animal vocalizations. A key contribution is the integration of modulation-aware acoustic features via FiLM conditioning, injecting a DSP-inspired inductive bias that enhances feature disentanglement in low-capacity regimes. Across multiple bioacoustic tasks, BioME matches or surpasses the performance of larger models, including its teacher, while being suitable for resource-constrained IoT deployments. For reproducibility, code and pretrained checkpoints are publicly available.

Artificial neural networks for motor control usually adopt generic architectures like fully connected MLPs. While general, these tabula rasa architectures rely on large amounts of experience to learn, are not easily transferable to new bodies, and have internal dynamics that are difficult to interpret. In nature, animals are born with highly structured connectivity in their nervous systems shaped by evolution; this innate circuitry acts synergistically with learning mechanisms to provide inductive biases that enable most animals to function well soon after birth and learn efficiently. Convolutional networks inspired by visual circuitry have encoded useful biases for vision. However, it is unknown the extent to which ANN architectures inspired by neural circuitry can yield useful biases for other AI domains. In this work, we ask what advantages biologically inspired ANN architecture can provide in the domain of motor control. Specifically, we translate C. elegans locomotion circuits into an ANN model controlling a simulated Swimmer agent. On a locomotion task, our architecture achieves good initial performance and asymptotic performance comparable with MLPs, while dramatically improving data efficiency and requiring orders of magnitude fewer parameters. Our architecture is interpretable and transfers to new body designs. An ablation analysis shows that constrained excitation/inhibition is crucial for learning, while weight initialization contributes to good initial performance. Our work demonstrates several advantages of biologically inspired ANN architecture and encourages future work in more complex embodied control.

We introduce MIRAGE, a new benchmark for multimodal expert-level reasoning and decision-making in consultative interaction settings. Designed for the agriculture domain, MIRAGE captures the full complexity of expert consultations by combining natural user queries, expert-authored responses, and image-based context, offering a high-fidelity benchmark for evaluating models on grounded reasoning, clarification strategies, and long-form generation in a real-world, knowledge-intensive domain. Grounded in over 35,000 real user-expert interactions and curated through a carefully designed multi-step pipeline, MIRAGE spans diverse crop health, pest diagnosis, and crop management scenarios. The benchmark includes more than 7,000 unique biological entities, covering plant species, pests, and diseases, making it one of the most taxonomically diverse benchmarks available for vision-language models, grounded in the real world. Unlike existing benchmarks that rely on well-specified user inputs and closed-set taxonomies, MIRAGE features underspecified, context-rich scenarios with open-world settings, requiring models to infer latent knowledge gaps, handle rare entities, and either proactively guide the interaction or respond. Project Page: https://mirage-benchmark.github.io

Building reliable computer-use agents requires grounding: accurately connecting natural language instructions to the correct on-screen elements. While large datasets exist for web and mobile interactions, high-quality resources for desktop environments are limited. To address this gap, we introduce GroundCUA, a large-scale desktop grounding dataset built from expert human demonstrations. It covers 87 applications across 12 categories and includes 56K screenshots, with every on-screen element carefully annotated for a total of over 3.56M human-verified annotations. From these demonstrations, we generate diverse instructions that capture a wide range of real-world tasks, providing high-quality data for model training. Using GroundCUA, we develop the GroundNext family of models that map instructions to their target UI elements. At both 3B and 7B scales, GroundNext achieves state-of-the-art results across five benchmarks using supervised fine-tuning, while requiring less than one-tenth the training data of prior work. Reinforcement learning post-training further improves performance, and when evaluated in an agentic setting on the OSWorld benchmark using o3 as planner, GroundNext attains comparable or superior results to models trained with substantially more data,. These results demonstrate the critical role of high-quality, expert-driven datasets in advancing general-purpose computer-use agents.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

Recent advances in generative modeling have spurred a resurgence in the field of Embodied Artificial Intelligence (EAI). EAI systems typically deploy large language models to physical systems capable of interacting with their environment. In our exploration of EAI for industrial domains, we successfully demonstrate the feasibility of co-located, human-robot teaming. Specifically, we construct an experiment where an Augmented Reality (AR) headset mediates information exchange between an EAI agent and human operator for a variety of inspection tasks. To our knowledge the use of an AR headset for multimodal grounding and the application of EAI to industrial tasks are novel contributions within Embodied AI research. In addition, we highlight potential pitfalls in EAI's construction by providing quantitative and qualitative analysis on prompt robustness.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Grounding natural language in images, such as localizing "the black dog on the left of the tree", is one of the core problems in artificial intelligence, as it needs to comprehend the fine-grained and compositional language space. However, existing solutions rely on the association between the holistic language features and visual features, while neglect the nature of compositional reasoning implied in the language. In this paper, we propose a natural language grounding model that can automatically compose a binary tree structure for parsing the language and then perform visual reasoning along the tree in a bottom-up fashion. We call our model RVG-TREE: Recursive Grounding Tree, which is inspired by the intuition that any language expression can be recursively decomposed into two constituent parts, and the grounding confidence score can be recursively accumulated by calculating their grounding scores returned by sub-trees. RVG-TREE can be trained end-to-end by using the Straight-Through Gumbel-Softmax estimator that allows the gradients from the continuous score functions passing through the discrete tree construction. Experiments on several benchmarks show that our model achieves the state-of-the-art performance with more explainable reasoning.

Games have been vital test beds for the rapid development of Agent-based research. Remarkable progress has been achieved in the past, but it is unclear if the findings equip for real-world problems. While pressure grows, some of the most critical ecological challenges can find mitigation and prevention solutions through technology and its applications. Most real-world domains include multi-agent scenarios and require machine-machine and human-machine collaboration. Open-source environments have not advanced and are often toy scenarios, too abstract or not suitable for multi-agent research. By mimicking real-world problems and increasing the complexity of environments, we hope to advance state-of-the-art multi-agent research and inspire researchers to work on immediate real-world problems. Here, we present HIVEX, an environment suite to benchmark multi-agent research focusing on ecological challenges. HIVEX includes the following environments: Wind Farm Control, Wildfire Resource Management, Drone-Based Reforestation, Ocean Plastic Collection, and Aerial Wildfire Suppression. We provide environments, training examples, and baselines for the main and sub-tasks. All trained models resulting from the experiments of this work are hosted on Hugging Face. We also provide a leaderboard on Hugging Face and encourage the community to submit models trained on our environment suite.