Daily Papers

Business intelligence (BI) transforms large volumes of data within modern organizations into actionable insights for informed decision-making. Recently, large language model (LLM)-based agents have streamlined the BI workflow by automatically performing task planning, reasoning, and actions in executable environments based on natural language (NL) queries. However, existing approaches primarily focus on individual BI tasks such as NL2SQL and NL2VIS. The fragmentation of tasks across different data roles and tools lead to inefficiencies and potential errors due to the iterative and collaborative nature of BI. In this paper, we introduce DataLab, a unified BI platform that integrates a one-stop LLM-based agent framework with an augmented computational notebook interface. DataLab supports a wide range of BI tasks for different data roles by seamlessly combining LLM assistance with user customization within a single environment. To achieve this unification, we design a domain knowledge incorporation module tailored for enterprise-specific BI tasks, an inter-agent communication mechanism to facilitate information sharing across the BI workflow, and a cell-based context management strategy to enhance context utilization efficiency in BI notebooks. Extensive experiments demonstrate that DataLab achieves state-of-the-art performance on various BI tasks across popular research benchmarks. Moreover, DataLab maintains high effectiveness and efficiency on real-world datasets from Tencent, achieving up to a 58.58% increase in accuracy and a 61.65% reduction in token cost on enterprise-specific BI tasks.

Large language models (LLMs) have revolutionized AI, but are constrained by limited context windows, hindering their utility in tasks like extended conversations and document analysis. To enable using context beyond limited context windows, we propose virtual context management, a technique drawing inspiration from hierarchical memory systems in traditional operating systems that provide the appearance of large memory resources through data movement between fast and slow memory. Using this technique, we introduce MemGPT (Memory-GPT), a system that intelligently manages different memory tiers in order to effectively provide extended context within the LLM's limited context window, and utilizes interrupts to manage control flow between itself and the user. We evaluate our OS-inspired design in two domains where the limited context windows of modern LLMs severely handicaps their performance: document analysis, where MemGPT is able to analyze large documents that far exceed the underlying LLM's context window, and multi-session chat, where MemGPT can create conversational agents that remember, reflect, and evolve dynamically through long-term interactions with their users. We release MemGPT code and data for our experiments at https://memgpt.ai.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks-such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction-using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.

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.

The performance of Large Language Models (LLMs) is fundamentally determined by the contextual information provided during inference. This survey introduces Context Engineering, a formal discipline that transcends simple prompt design to encompass the systematic optimization of information payloads for LLMs. We present a comprehensive taxonomy decomposing Context Engineering into its foundational components and the sophisticated implementations that integrate them into intelligent systems. We first examine the foundational components: context retrieval and generation, context processing and context management. We then explore how these components are architecturally integrated to create sophisticated system implementations: retrieval-augmented generation (RAG), memory systems and tool-integrated reasoning, and multi-agent systems. Through this systematic analysis of over 1300 research papers, our survey not only establishes a technical roadmap for the field but also reveals a critical research gap: a fundamental asymmetry exists between model capabilities. While current models, augmented by advanced context engineering, demonstrate remarkable proficiency in understanding complex contexts, they exhibit pronounced limitations in generating equally sophisticated, long-form outputs. Addressing this gap is a defining priority for future research. Ultimately, this survey provides a unified framework for both researchers and engineers advancing context-aware AI.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

Successfully handling context is essential for any dialog understanding task. This context maybe be conversational (relying on previous user queries or system responses), visual (relying on what the user sees, for example, on their screen), or background (based on signals such as a ringing alarm or playing music). In this work, we present an overview of MARRS, or Multimodal Reference Resolution System, an on-device framework within a Natural Language Understanding system, responsible for handling conversational, visual and background context. In particular, we present different machine learning models to enable handing contextual queries; specifically, one to enable reference resolution, and one to handle context via query rewriting. We also describe how these models complement each other to form a unified, coherent, lightweight system that can understand context while preserving user privacy.

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.

Multi-agent systems represent a significant advancement in artificial intelligence, enabling complex problem-solving through coordinated specialized agents. However, these systems face fundamental challenges in context management, coordination efficiency, and scalable operation. This paper introduces a comprehensive framework for advancing multi-agent systems through Model Context Protocol (MCP), addressing these challenges through standardized context sharing and coordination mechanisms. We extend previous work on AI agent architectures by developing a unified theoretical foundation, advanced context management techniques, and scalable coordination patterns. Through detailed implementation case studies across enterprise knowledge management, collaborative research, and distributed problem-solving domains, we demonstrate significant performance improvements compared to traditional approaches. Our evaluation methodology provides a systematic assessment framework with benchmark tasks and datasets specifically designed for multi-agent systems. We identify current limitations, emerging research opportunities, and potential transformative applications across industries. This work contributes to the evolution of more capable, collaborative, and context-aware artificial intelligence systems that can effectively address complex real-world challenges.

We introduce Latent Meaning Cells, a deep latent variable model which learns contextualized representations of words by combining local lexical context and metadata. Metadata can refer to granular context, such as section type, or to more global context, such as unique document ids. Reliance on metadata for contextualized representation learning is apropos in the clinical domain where text is semi-structured and expresses high variation in topics. We evaluate the LMC model on the task of zero-shot clinical acronym expansion across three datasets. The LMC significantly outperforms a diverse set of baselines at a fraction of the pre-training cost and learns clinically coherent representations. We demonstrate that not only is metadata itself very helpful for the task, but that the LMC inference algorithm provides an additional large benefit.

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry and biology. However, the field of single-cell biology, which forms the foundational building blocks of living organisms, still faces several challenges. High knowledge barriers and limited scalability in current methods restrict the full exploitation of LLMs in mastering single-cell data, impeding direct accessibility and rapid iteration. To this end, we introduce ChatCell, which signifies a paradigm shift by facilitating single-cell analysis with natural language. Leveraging vocabulary adaptation and unified sequence generation, ChatCell has acquired profound expertise in single-cell biology and the capability to accommodate a diverse range of analysis tasks. Extensive experiments further demonstrate ChatCell's robust performance and potential to deepen single-cell insights, paving the way for more accessible and intuitive exploration in this pivotal field. Our project homepage is available at https://zjunlp.github.io/project/ChatCell.

Recent advancements in Large Language Model (LLM)-based frameworks have extended their capabilities to complex real-world applications, such as interactive web navigation. These systems, driven by user commands, navigate web browsers to complete tasks through multi-turn dialogues, offering both innovative opportunities and significant challenges. Despite the introduction of benchmarks for conversational web navigation, a detailed understanding of the key contextual components that influence the performance of these agents remains elusive. This study aims to fill this gap by analyzing the various contextual elements crucial to the functioning of web navigation agents. We investigate the optimization of context management, focusing on the influence of interaction history and web page representation. Our work highlights improved agent performance across out-of-distribution scenarios, including unseen websites, categories, and geographic locations through effective context management. These findings provide insights into the design and optimization of LLM-based agents, enabling more accurate and effective web navigation in real-world applications.

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 advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. To address this, we introduce CellAgent (http://cell.agent4science.cn/), an LLM-driven multi-agent framework, specifically designed for the automatic processing and execution of scRNA-seq data analysis tasks, providing high-quality results with no human intervention. Firstly, to adapt general LLMs to the biological field, CellAgent constructs LLM-driven biological expert roles - planner, executor, and evaluator - each with specific responsibilities. Then, CellAgent introduces a hierarchical decision-making mechanism to coordinate these biological experts, effectively driving the planning and step-by-step execution of complex data analysis tasks. Furthermore, we propose a self-iterative optimization mechanism, enabling CellAgent to autonomously evaluate and optimize solutions, thereby guaranteeing output quality. We evaluate CellAgent on a comprehensive benchmark dataset encompassing dozens of tissues and hundreds of distinct cell types. Evaluation results consistently show that CellAgent effectively identifies the most suitable tools and hyperparameters for single-cell analysis tasks, achieving optimal performance. This automated framework dramatically reduces the workload for science data analyses, bringing us into the "Agent for Science" era.

Pre-trained language models (PLMs) have revolutionized scientific research, yet their application to single-cell analysis remains limited. Text PLMs cannot process single-cell RNA sequencing data, while cell PLMs lack the ability to handle free text, restricting their use in multimodal tasks. Existing efforts to bridge these modalities often suffer from information loss or inadequate single-modal pre-training, leading to suboptimal performances. To address these challenges, we propose Single-Cell MultiModal Generative Pre-trained Transformer (scMMGPT), a unified PLM for joint cell and text modeling. scMMGPT effectively integrates the state-of-the-art cell and text PLMs, facilitating cross-modal knowledge sharing for improved performance. To bridge the text-cell modality gap, scMMGPT leverages dedicated cross-modal projectors, and undergoes extensive pre-training on 27 million cells -- the largest dataset for multimodal cell-text PLMs to date. This large-scale pre-training enables scMMGPT to excel in joint cell-text tasks, achieving an 84\% relative improvement of textual discrepancy for cell description generation, 20.5\% higher accuracy for cell type annotation, and 4\% improvement in k-NN accuracy for text-conditioned pseudo-cell generation, outperforming baselines.

Contextual memory integration remains a high challenge in the development of language models, particularly in tasks that require maintaining coherence over extended sequences. Traditional approaches, such as self-attention mechanisms and memory-augmented architectures, often prioritize short-term dependencies, leading to fragmentation and inconsistency in long-range contextual understanding. Inspired by principles of synaptic plasticity observed in biological neural systems, a novel mechanism, Synaptic Resonance, is introduced to dynamically reinforce relevant memory pathways during training and inference. Unlike static memory representations, this mechanism continuously adjusts synaptic weight matrices based on contextual relevance, allowing for improved information retention without excessive computational overhead. Evaluations conducted on an open-source language model demonstrate reductions in perplexity, enhancements in contextual coherence, and increased robustness against input noise, highlighting the effectiveness of reinforcement-driven memory modulation. Comparative analysis against baseline models further reveals that the proposed approach achieves higher memory retention efficiency while maintaining computational feasibility. The architectural modifications integrate seamlessly into existing transformer-based frameworks, ensuring stable convergence and efficient inference without sacrificing scalability. Applications benefiting from improved long-term contextual consistency, such as dialogue systems and document summarization, stand to gain from this approach. Empirical findings suggest that dynamically reinforced memory pathways offer a promising alternative to conventional memory mechanisms, addressing longstanding limitations in extended sequence modeling.

We study reinforcement learning (RL) fine-tuning of large language model (LLM) agents for long-horizon multi-turn tool use, where context length quickly becomes a fundamental bottleneck. Existing RL pipelines can suffer from degraded instruction following, excessive rollout costs, and most importantly, strict context limits. To address these challenges, we introduce summarization-based context management to training. In specific, it periodically compresses the tool using history by LLM-generated summaries that retain task-relevant information to keep a compact context while enabling the agent to scale beyond the fixed context window. Building on this formulation, we derive a policy gradient representation that seamlessly enables standard LLM RL infrastructures to optimize both tool-use behaviors as well as summarization strategies in an end-to-end fashion. We instantiate this framework with SUmmarization augmented Policy Optimization (SUPO), an LLM RL algorithm that enables long-horizon training beyond a fixed context limit. Experiments on interactive function calling and searching tasks demonstrate that SUPO significantly improves the success rate while maintaining the same or even lower working context length compared to baselines. We also demonstrate that for complex searching tasks, SUPO can further improve the evaluation performance when scaling test-time maximum round of summarization beyond that of training time. Our results establish summarization-based context management as a principled and scalable approach for training RL agents beyond a fixed context length limit.

It is widely acknowledged that large language models (LLMs) encode a vast reservoir of knowledge after being trained on mass data. Recent studies disclose knowledge conflicts in LLM generation, wherein outdated or incorrect parametric knowledge (i.e., encoded knowledge) contradicts new knowledge provided in the context. To mitigate such knowledge conflicts, we propose a novel framework, IRCAN (Identifying and Reweighting Context-Aware Neurons) to capitalize on neurons that are crucial in processing contextual cues. Specifically, IRCAN first identifies neurons that significantly contribute to context processing, utilizing a context-aware attribution score derived from integrated gradients. Subsequently, the identified context-aware neurons are strengthened via reweighting. In doing so, we steer LLMs to generate context-sensitive outputs with respect to the new knowledge provided in the context. Extensive experiments conducted across a variety of models and tasks demonstrate that IRCAN not only achieves remarkable improvements in handling knowledge conflicts but also offers a scalable, plug-andplay solution that can be integrated seamlessly with existing models.

Large Language Models (LLMs) suffer from significant performance degradation when processing long contexts due to proactive interference, where irrelevant information in earlier parts of the context disrupts reasoning and memory recall. While most research focuses on external memory systems to augment LLMs' capabilities, we propose a complementary approach: empowering LLMs with Active Context Management (ACM) tools to actively sculpt their internal working memory. We introduce Sculptor, a framework that equips LLMs with three categories of tools: (1) context fragmentation, (2) summary, hide, and restore, and (3) intelligent search. Our approach enables LLMs to proactively manage their attention and working memory, analogous to how humans selectively focus on relevant information while filtering out distractions. Experimental evaluation on information-sparse benchmarks-PI-LLM (proactive interference) and NeedleBench Multi-Needle Reasoning-demonstrates that Sculptor significantly improves performance even without specific training, leveraging LLMs' inherent tool calling generalization capabilities. By enabling Active Context Management, Sculptor not only mitigates proactive interference but also provides a cognitive foundation for more reliable reasoning across diverse long-context tasks-highlighting that explicit context-control strategies, rather than merely larger token windows, are key to robustness at scale.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Large language model (LLM) agents are fundamentally constrained by context length on long-horizon tasks. We introduce Context-Folding, a framework that empowers agents to actively manage their working context. An agent can procedurally branch into a sub-trajectory to handle a subtask and then fold it upon completion, collapsing the intermediate steps while retaining a concise summary of the outcome. To make this behavior learnable, we develop an end-to-end reinforcement learning framework FoldGRPO with specific process rewards to encourage effective task decomposition and context management. On complex long-horizon tasks (Deep Research and SWE), our folding agent matches or outperforms the ReAct baselines while using an active context 10times smaller and significantly outperforms models that rely on summarization-based context management.

We introduce a dynamic benchmarking system for conversational agents that evaluates their performance through a single, simulated, and lengthy userleftrightarrowagent interaction. The interaction is a conversation between the user and agent, where multiple tasks are introduced and then undertaken concurrently. We context switch regularly to interleave the tasks, which constructs a realistic testing scenario in which we assess the Long-Term Memory, Continual Learning, and Information Integration capabilities of the agents. Results from both proprietary and open-source Large-Language Models show that LLMs in general perform well on single-task interactions, but they struggle on the same tasks when they are interleaved. Notably, short-context LLMs supplemented with an LTM system perform as well as or better than those with larger contexts. Our benchmark suggests that there are other challenges for LLMs responding to more natural interactions that contemporary benchmarks have heretofore not been able to capture.

Large language model (LLM) applications such as agents and domain-specific reasoning increasingly rely on context adaptation -- modifying inputs with instructions, strategies, or evidence, rather than weight updates. Prior approaches improve usability but often suffer from brevity bias, which drops domain insights for concise summaries, and from context collapse, where iterative rewriting erodes details over time. Building on the adaptive memory introduced by Dynamic Cheatsheet, we introduce ACE (Agentic Context Engineering), a framework that treats contexts as evolving playbooks that accumulate, refine, and organize strategies through a modular process of generation, reflection, and curation. ACE prevents collapse with structured, incremental updates that preserve detailed knowledge and scale with long-context models. Across agent and domain-specific benchmarks, ACE optimizes contexts both offline (e.g., system prompts) and online (e.g., agent memory), consistently outperforming strong baselines: +10.6% on agents and +8.6% on finance, while significantly reducing adaptation latency and rollout cost. Notably, ACE could adapt effectively without labeled supervision and instead by leveraging natural execution feedback. On the AppWorld leaderboard, ACE matches the top-ranked production-level agent on the overall average and surpasses it on the harder test-challenge split, despite using a smaller open-source model. These results show that comprehensive, evolving contexts enable scalable, efficient, and self-improving LLM systems with low overhead.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

The visual examination of tissue biopsy sections is fundamental for cancer diagnosis, with pathologists analyzing sections at multiple magnifications to discern tumor cells and their subtypes. However, existing attention-based multiple instance learning (MIL) models, used for analyzing Whole Slide Images (WSIs) in cancer diagnostics, often overlook the contextual information of tumor and neighboring tiles, leading to misclassifications. To address this, we propose the Context-Aware Multiple Instance Learning (CAMIL) architecture. CAMIL incorporates neighbor-constrained attention to consider dependencies among tiles within a WSI and integrates contextual constraints as prior knowledge into the MIL model. We evaluated CAMIL on subtyping non-small cell lung cancer (TCGA-NSCLC) and detecting lymph node (CAMELYON16) metastasis, achieving test AUCs of 0.959\% and 0.975\%, respectively, outperforming other state-of-the-art methods. Additionally, CAMIL enhances model interpretability by identifying regions of high diagnostic value.

The rapid advancement of Large Language Models (LLMs) has inaugurated a transformative epoch in natural language processing, fostering unprecedented proficiency in text generation, comprehension, and contextual scrutiny. Nevertheless, effectively handling extensive contexts, crucial for myriad applications, poses a formidable obstacle owing to the intrinsic constraints of the models' context window sizes and the computational burdens entailed by their operations. This investigation presents an innovative framework that strategically tailors LLMs for streamlined context processing by harnessing the synergies among natural language summarization, soft prompt compression, and augmented utility preservation mechanisms. Our methodology, dubbed SoftPromptComp, amalgamates natural language prompts extracted from summarization methodologies with dynamically generated soft prompts to forge a concise yet semantically robust depiction of protracted contexts. This depiction undergoes further refinement via a weighting mechanism optimizing information retention and utility for subsequent tasks. We substantiate that our framework markedly diminishes computational overhead and enhances LLMs' efficacy across various benchmarks, while upholding or even augmenting the caliber of the produced content. By amalgamating soft prompt compression with sophisticated summarization, SoftPromptComp confronts the dual challenges of managing lengthy contexts and ensuring model scalability. Our findings point towards a propitious trajectory for augmenting LLMs' applicability and efficiency, rendering them more versatile and pragmatic for real-world applications. This research enriches the ongoing discourse on optimizing language models, providing insights into the potency of soft prompts and summarization techniques as pivotal instruments for the forthcoming generation of NLP solutions.

The automation of scientific discovery represents a critical milestone in Artificial Intelligence (AI) research. However, existing agentic systems for science suffer from two fundamental limitations: rigid, pre-programmed workflows that cannot adapt to intermediate findings, and inadequate context management that hinders long-horizon research. We present freephdlabor, an open-source multiagent framework featuring fully dynamic workflows determined by real-time agent reasoning and a \textit{modular architecture} enabling seamless customization -- users can modify, add, or remove agents to address domain-specific requirements. The framework provides comprehensive infrastructure including automatic context compaction, workspace-based communication to prevent information degradation, memory persistence across sessions, and non-blocking human intervention mechanisms. These features collectively transform automated research from isolated, single-run attempts into continual research programs that build systematically on prior explorations and incorporate human feedback. By providing both the architectural principles and practical implementation for building customizable co-scientist systems, this work aims to facilitate broader adoption of automated research across scientific domains, enabling practitioners to deploy interactive multiagent systems that autonomously conduct end-to-end research -- from ideation through experimentation to publication-ready manuscripts.

Recent advancements in large language models (LLMs) have revolutionized their ability to handle single-turn tasks, yet real-world applications demand sophisticated multi-turn interactions. This survey provides a comprehensive review of recent advancements in evaluating and enhancing multi-turn interactions in LLMs. Focusing on task-specific scenarios, from instruction following in diverse domains such as math and coding to complex conversational engagements in roleplay, healthcare, education, and even adversarial jailbreak settings, we systematically examine the challenges of maintaining context, coherence, fairness, and responsiveness over prolonged dialogues. The paper organizes current benchmarks and datasets into coherent categories that reflect the evolving landscape of multi-turn dialogue evaluation. In addition, we review a range of enhancement methodologies under multi-turn settings, including model-centric strategies (contextual learning, supervised fine-tuning, reinforcement learning, and new architectures), external integration approaches (memory-augmented, retrieval-based methods, and knowledge graph), and agent-based techniques for collaborative interactions. Finally, we discuss open challenges and propose future directions for research to further advance the robustness and effectiveness of multi-turn interactions in LLMs. Related resources and papers are available at https://github.com/yubol-cmu/Awesome-Multi-Turn-LLMs.

The process of quantifying and analyzing animal behavior involves translating the naturally occurring descriptive language of their actions into machine-readable code. Yet, codifying behavior analysis is often challenging without deep understanding of animal behavior and technical machine learning knowledge. To limit this gap, we introduce AmadeusGPT: a natural language interface that turns natural language descriptions of behaviors into machine-executable code. Large-language models (LLMs) such as GPT3.5 and GPT4 allow for interactive language-based queries that are potentially well suited for making interactive behavior analysis. However, the comprehension capability of these LLMs is limited by the context window size, which prevents it from remembering distant conversations. To overcome the context window limitation, we implement a novel dual-memory mechanism to allow communication between short-term and long-term memory using symbols as context pointers for retrieval and saving. Concretely, users directly use language-based definitions of behavior and our augmented GPT develops code based on the core AmadeusGPT API, which contains machine learning, computer vision, spatio-temporal reasoning, and visualization modules. Users then can interactively refine results, and seamlessly add new behavioral modules as needed. We benchmark AmadeusGPT and show we can produce state-of-the-art performance on the MABE 2022 behavior challenge tasks. Note, an end-user would not need to write any code to achieve this. Thus, collectively AmadeusGPT presents a novel way to merge deep biological knowledge, large-language models, and core computer vision modules into a more naturally intelligent system. Code and demos can be found at: https://github.com/AdaptiveMotorControlLab/AmadeusGPT.

Recent advances in interactive video generation have shown promising results, yet existing approaches struggle with scene-consistent memory capabilities in long video generation due to limited use of historical context. In this work, we propose Context-as-Memory, which utilizes historical context as memory for video generation. It includes two simple yet effective designs: (1) storing context in frame format without additional post-processing; (2) conditioning by concatenating context and frames to be predicted along the frame dimension at the input, requiring no external control modules. Furthermore, considering the enormous computational overhead of incorporating all historical context, we propose the Memory Retrieval module to select truly relevant context frames by determining FOV (Field of View) overlap between camera poses, which significantly reduces the number of candidate frames without substantial information loss. Experiments demonstrate that Context-as-Memory achieves superior memory capabilities in interactive long video generation compared to SOTAs, even generalizing effectively to open-domain scenarios not seen during training. The link of our project page is https://context-as-memory.github.io/.

Reference resolution is an important problem, one that is essential to understand and successfully handle context of different kinds. This context includes both previous turns and context that pertains to non-conversational entities, such as entities on the user's screen or those running in the background. While LLMs have been shown to be extremely powerful for a variety of tasks, their use in reference resolution, particularly for non-conversational entities, remains underutilized. This paper demonstrates how LLMs can be used to create an extremely effective system to resolve references of various types, by showing how reference resolution can be converted into a language modeling problem, despite involving forms of entities like those on screen that are not traditionally conducive to being reduced to a text-only modality. We demonstrate large improvements over an existing system with similar functionality across different types of references, with our smallest model obtaining absolute gains of over 5% for on-screen references. We also benchmark against GPT-3.5 and GPT-4, with our smallest model achieving performance comparable to that of GPT-4, and our larger models substantially outperforming it.

Zero-shot, training-free, image-based text-to-video generation is an emerging area that aims to generate videos using existing image-based diffusion models. Current methods in this space require specific architectural changes to image generation models, which limit their adaptability and scalability. In contrast to such methods, we provide a model-agnostic approach. We use intersections in diffusion trajectories, working only with the latent values. We could not obtain localized frame-wise coherence and diversity using only the intersection of trajectories. Thus, we instead use a grid-based approach. An in-context trained LLM is used to generate coherent frame-wise prompts; another is used to identify differences between frames. Based on these, we obtain a CLIP-based attention mask that controls the timing of switching the prompts for each grid cell. Earlier switching results in higher variance, while later switching results in more coherence. Therefore, our approach can ensure appropriate control between coherence and variance for the frames. Our approach results in state-of-the-art performance while being more flexible when working with diverse image-generation models. The empirical analysis using quantitative metrics and user studies confirms our model's superior temporal consistency, visual fidelity and user satisfaction, thus providing a novel way to obtain training-free, image-based text-to-video generation.

Large language models have shown remarkable performance across a wide range of language tasks, owing to their exceptional capabilities in context modeling. The most commonly used method of context modeling is full self-attention, as seen in standard decoder-only Transformers. Although powerful, this method can be inefficient for long sequences and may overlook inherent input structures. To address these problems, an alternative approach is parallel context encoding, which splits the context into sub-pieces and encodes them parallelly. Because parallel patterns are not encountered during training, naively applying parallel encoding leads to performance degradation. However, the underlying reasons and potential mitigations are unclear. In this work, we provide a detailed analysis of this issue and identify that unusually high attention entropy can be a key factor. Furthermore, we adopt two straightforward methods to reduce attention entropy by incorporating attention sinks and selective mechanisms. Experiments on various tasks reveal that these methods effectively lower irregular attention entropy and narrow performance gaps. We hope this study can illuminate ways to enhance context modeling mechanisms.

Large Language Model (LLM) agents have shown significant autonomous capabilities in dynamically searching and incorporating relevant tools or Model Context Protocol (MCP) servers for individual queries. However, fixed context windows limit effectiveness in multi-turn interactions requiring repeated, independent tool usage. We introduce MemTool, a short-term memory framework enabling LLM agents to dynamically manage tools or MCP server contexts across multi-turn conversations. MemTool offers three agentic architectures: 1) Autonomous Agent Mode, granting full tool management autonomy, 2) Workflow Mode, providing deterministic control without autonomy, and 3) Hybrid Mode, combining autonomous and deterministic control. Evaluating each MemTool mode across 13+ LLMs on the ScaleMCP benchmark, we conducted experiments over 100 consecutive user interactions, measuring tool removal ratios (short-term memory efficiency) and task completion accuracy. In Autonomous Agent Mode, reasoning LLMs achieve high tool-removal efficiency (90-94% over a 3-window average), while medium-sized models exhibit significantly lower efficiency (0-60%). Workflow and Hybrid modes consistently manage tool removal effectively, whereas Autonomous and Hybrid modes excel at task completion. We present trade-offs and recommendations for each MemTool mode based on task accuracy, agency, and model capabilities.

The recent advancement of autonomous agents powered by Large Language Models (LLMs) has demonstrated significant potential for automating tasks on mobile devices through graphical user interfaces (GUIs). Despite initial progress, these agents still face challenges when handling complex real-world tasks. These challenges arise from a lack of knowledge about real-life mobile applications in LLM-based agents, which may lead to ineffective task planning and even cause hallucinations. To address these challenges, we propose a novel LLM-based agent framework called MapAgent that leverages memory constructed from historical trajectories to augment current task planning. Specifically, we first propose a trajectory-based memory mechanism that transforms task execution trajectories into a reusable and structured page-memory database. Each page within a trajectory is extracted as a compact yet comprehensive snapshot, capturing both its UI layout and functional context. Secondly, we introduce a coarse-to-fine task planning approach that retrieves relevant pages from the memory database based on similarity and injects them into the LLM planner to compensate for potential deficiencies in understanding real-world app scenarios, thereby achieving more informed and context-aware task planning. Finally, planned tasks are transformed into executable actions through a task executor supported by a dual-LLM architecture, ensuring effective tracking of task progress. Experimental results in real-world scenarios demonstrate that MapAgent achieves superior performance to existing methods. The code will be open-sourced to support further research.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Incorporating external context can significantly enhance the response quality of Large Language Models (LLMs). However, real-world contexts often mix relevant information with disproportionate inappropriate content, posing reliability risks. How do LLMs process and prioritize mixed context? To study this, we introduce the Poisoned Context Testbed, pairing queries with real-world contexts containing relevant and inappropriate content. Inspired by associative learning in animals, we adapt the Rescorla-Wagner (RW) model from neuroscience to quantify how competing contextual signals influence LLM outputs. Our adapted model reveals a consistent behavioral pattern: LLMs exhibit a strong tendency to incorporate information that is less prevalent in the context. This susceptibility is harmful in real-world settings, where small amounts of inappropriate content can substantially degrade response quality. Empirical evaluations on our testbed further confirm this vulnerability. To tackle this, we introduce RW-Steering, a two-stage finetuning-based approach that enables the model to internally identify and ignore inappropriate signals. Unlike prior methods that rely on extensive supervision across diverse context mixtures, RW-Steering generalizes robustly across varying proportions of inappropriate content. Experiments show that our best fine-tuned model improves response quality by 39.8% and reverses the undesirable behavior curve, establishing RW-Steering as a robust, generalizable context engineering solution for improving LLM safety in real-world use.

Context-augmented generation (CAG) techniques, including RAG and ICL, require the efficient combination of multiple contexts to generate responses to user queries. Directly inputting these contexts as a sequence introduces a considerable computational burden by re-encoding the combined selection of contexts for every request. To address this, we explore the promising potential of parallel encoding to independently pre-compute and cache each context's KV states. This approach enables the direct loading of cached states during inference while accommodating more contexts through position reuse across contexts. However, due to misalignments in attention distribution, directly applying parallel encoding results in a significant performance drop. To enable effective and efficient CAG, we propose Adaptive Parallel Encoding (APE), which brings shared prefix, attention temperature, and scaling factor to align the distribution of parallel encoding with sequential encoding. Results on RAG and ICL tasks demonstrate that APE can preserve 98% and 93% sequential encoding performance using the same inputs while outperforming parallel encoding by 3.6% and 7.9%, respectively. It also scales to many-shot CAG, effectively encoding hundreds of contexts in parallel. Efficiency evaluation shows that APE can achieve an end-to-end 4.5times speedup by reducing 28times prefilling time for a 128K-length context.

Long-context large language models (LLMs) are prone to be distracted by irrelevant contexts. The reason for distraction remains poorly understood. In this paper, we first identify the contextual heads, a special group of attention heads that control the overall attention of the LLM. Then, we demonstrate that distraction arises when contextual heads fail to allocate sufficient attention to relevant contexts and can be mitigated by increasing attention to these contexts. We further identify focus directions, located at the key and query activations of these heads, which enable them to allocate more attention to relevant contexts without explicitly specifying which context is relevant. We comprehensively evaluate the effect of focus direction on various long-context tasks and find out focus directions could help to mitigate the poor task alignment of the long-context LLMs. We believe our findings could promote further research on long-context LLM alignment.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

The rapid advancement of large language models (LLMs) has accelerated the emergence of in-context learning (ICL) as a cutting-edge approach in the natural language processing domain. Recently, ICL has been employed in visual understanding tasks, such as semantic segmentation and image captioning, yielding promising results. However, existing visual ICL framework can not enable producing content across multiple modalities, which limits their potential usage scenarios. To address this issue, we present a new ICL framework for visual understanding with multi-modal output enabled. First, we quantize and embed both text and visual prompt into a unified representational space, structured as interleaved in-context sequences. Then a decoder-only sparse transformer architecture is employed to perform generative modeling on them, facilitating in-context learning. Thanks to this design, the model is capable of handling in-context vision understanding tasks with multimodal output in a unified pipeline. Experimental results demonstrate that our model achieves competitive performance compared with specialized models and previous ICL baselines. Overall, our research takes a further step toward unified multimodal in-context learning.

Large language models (LLMs) are increasingly deployed as agents in dynamic, real-world environments, where success requires both reasoning and effective tool use. A central challenge for agentic tasks is the growing context length, as agents must accumulate long histories of actions and observations. This expansion raises costs and reduces efficiency in long-horizon tasks, yet prior work on context compression has mostly focused on single-step tasks or narrow applications. We introduce Agent Context Optimization (ACON), a unified framework that optimally compresses both environment observations and interaction histories into concise yet informative condensations. ACON leverages compression guideline optimization in natural language space: given paired trajectories where full context succeeds but compressed context fails, capable LLMs analyze the causes of failure, and the compression guideline is updated accordingly. Furthermore, we propose distilling the optimized LLM compressor into smaller models to reduce the overhead of the additional module. Experiments on AppWorld, OfficeBench, and Multi-objective QA show that ACON reduces memory usage by 26-54% (peak tokens) while largely preserving task performance, preserves over 95% of accuracy when distilled into smaller compressors, and enhances smaller LMs as long-horizon agents with up to 46% performance improvement.

Human interaction with the external world fundamentally involves the exchange of personal memory, whether with other individuals, websites, applications, or, in the future, AI agents. A significant portion of this interaction is redundant, requiring users to repeatedly provide the same information across different contexts. Existing solutions, such as browser-stored credentials, autofill mechanisms, and unified authentication systems, have aimed to mitigate this redundancy by serving as intermediaries that store and retrieve commonly used user data. The advent of large language models (LLMs) presents an opportunity to redefine memory management through an AI-native paradigm: SECOND ME. SECOND ME acts as an intelligent, persistent memory offload system that retains, organizes, and dynamically utilizes user-specific knowledge. By serving as an intermediary in user interactions, it can autonomously generate context-aware responses, prefill required information, and facilitate seamless communication with external systems, significantly reducing cognitive load and interaction friction. Unlike traditional memory storage solutions, SECOND ME extends beyond static data retention by leveraging LLM-based memory parameterization. This enables structured organization, contextual reasoning, and adaptive knowledge retrieval, facilitating a more systematic and intelligent approach to memory management. As AI-driven personal agents like SECOND ME become increasingly integrated into digital ecosystems, SECOND ME further represents a critical step toward augmenting human-world interaction with persistent, contextually aware, and self-optimizing memory systems. We have open-sourced the fully localizable deployment system at GitHub: https://github.com/Mindverse/Second-Me.

In multi-agent systems utilizing Large Language Models (LLMs), communication between agents traditionally relies on natural language. This communication often includes the full context of the query so far, which can introduce significant prefill-phase latency, especially with long contexts. We introduce DroidSpeak, a novel framework to target this cross-LLM communication by leveraging the reuse of intermediate data, such as input embeddings (E-cache) and key-value caches (KV-cache). We efficiently bypass the need to reprocess entire contexts for fine-tuned versions of the same foundational model. This approach allows faster context integration while maintaining the quality of task performance. Experimental evaluations demonstrate DroidSpeak's ability to significantly accelerate inter-agent communication, achieving up to a 2.78x speedup in prefill latency with negligible loss in accuracy. Our findings underscore the potential to create more efficient and scalable multi-agent systems.

Large language models are prominently used in real-world applications, often tasked with reasoning over large volumes of documents. An exciting development in this space is models boasting extended context capabilities, with some accommodating over 2 million tokens. Such long context model capabilities remain uncertain in production systems, motivating the need to benchmark their performance on real world use cases. We address this challenge by proposing SWiM, an evaluation framework that addresses the limitations of standard tests. Testing the framework on eight long context models, we find that even strong models such as GPT-4 and Claude 3 Opus degrade in performance when information is present in the middle of the context window (lost-in-the-middle effect). Next, in addition to our benchmark, we propose medoid voting, a simple, but effective training-free approach that helps alleviate this effect, by generating responses a few times, each time randomly permuting documents in the context, and selecting the medoid answer. We evaluate medoid voting on single document QA tasks, achieving up to a 24% lift in accuracy.

The recent advances in Large Language Models (LLMs) have stimulated interest among researchers and industry professionals, particularly in their application to tasks concerning mobile user interfaces (UIs). This position paper investigates the use of LLMs for UI layout generation. Central to our exploration is the introduction of UI grammar -- a novel approach we proposed to represent the hierarchical structure inherent in UI screens. The aim of this approach is to guide the generative capacities of LLMs more effectively and improve the explainability and controllability of the process. Initial experiments conducted with GPT-4 showed the promising capability of LLMs to produce high-quality user interfaces via in-context learning. Furthermore, our preliminary comparative study suggested the potential of the grammar-based approach in improving the quality of generative results in specific aspects.

Large Language Models (LLMs) have shown promise in automating code generation and software engineering tasks, yet they often struggle with complex, multi-file projects due to context limitations and knowledge gaps. We propose a novel context engineering workflow that combines multiple AI components: an Intent Translator (GPT-5) for clarifying user requirements, an Elicit-powered semantic literature retrieval for injecting domain knowledge, NotebookLM-based document synthesis for contextual understanding, and a Claude Code multi-agent system for code generation and validation. Our integrated approach leverages intent clarification, retrieval-augmented generation, and specialized sub-agents orchestrated via Claude's agent framework. We demonstrate that this method significantly improves the accuracy and reliability of code assistants in real-world repositories, yielding higher single-shot success rates and better adherence to project context than baseline single-agent approaches. Qualitative results on a large Next.js codebase show the multi-agent system effectively plans, edits, and tests complex features with minimal human intervention. We compare our system with recent frameworks like CodePlan, MASAI, and HyperAgent, highlighting how targeted context injection and agent role decomposition lead to state-of-the-art performance. Finally, we discuss the implications for deploying LLM-based coding assistants in production, along with lessons learned on context management and future research directions.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Large Language Models face challenges in long-horizon agentic tasks as their constrained memory is easily overwhelmed by distracting or irrelevant context. Existing working memory methods typically rely on external, heuristic mechanisms that are decoupled from the agent's core policy. In this work, we reframe working memory management as a learnable, intrinsic capability. We propose a novel framework, Memory-as-Action, where an agent actively manages its working memory by executing explicit editing operations as part of a unified policy. This formulation allows an agent, trained via reinforcement learning, to balance memory curation against long-term task objectives under given resource constraints. However, such memory editing actions break the standard assumption of a continuously growing prefix in LLM interactions, leading to what we call trajectory fractures. These non-prefix changes disrupt the causal continuity required by standard policy gradient methods, making those methods inapplicable. To address this, we propose a new algorithm, Dynamic Context Policy Optimization, which enables stable end-to-end reinforcement learning by segmenting trajectories at memory action points and applying trajectory-level advantages to the resulting action segments. Our results demonstrate that jointly optimizing for task reasoning and memory management in an end-to-end fashion not only reduces overall computational consumption but also improves task performance, driven by adaptive context curation strategies tailored to the model's intrinsic capabilities.

Recent advances in Large Language Models (LLMs) have propelled intelligent agents from reactive responses to proactive support. While promising, existing proactive agents either rely exclusively on observations from enclosed environments (e.g., desktop UIs) with direct LLM inference or employ rule-based proactive notifications, leading to suboptimal user intent understanding and limited functionality for proactive service. In this paper, we introduce ContextAgent, the first context-aware proactive agent that incorporates extensive sensory contexts to enhance the proactive capabilities of LLM agents. ContextAgent first extracts multi-dimensional contexts from massive sensory perceptions on wearables (e.g., video and audio) to understand user intentions. ContextAgent then leverages the sensory contexts and the persona contexts from historical data to predict the necessity for proactive services. When proactive assistance is needed, ContextAgent further automatically calls the necessary tools to assist users unobtrusively. To evaluate this new task, we curate ContextAgentBench, the first benchmark for evaluating context-aware proactive LLM agents, covering 1,000 samples across nine daily scenarios and twenty tools. Experiments on ContextAgentBench show that ContextAgent outperforms baselines by achieving up to 8.5% and 6.0% higher accuracy in proactive predictions and tool calling, respectively. We hope our research can inspire the development of more advanced, human-centric, proactive AI assistants.

With the advancement of language models (LMs), their exposure to private data is increasingly inevitable, and their deployment (especially for smaller ones) on personal devices, such as PCs and smartphones, has become a prevailing trend. In contexts laden with user information, enabling models to both safeguard user privacy and execute commands efficiently emerges as an essential research imperative. In this paper, we propose CoGenesis, a collaborative generation framework integrating large (hosted on cloud infrastructure) and small models (deployed on local devices) to address privacy concerns logically. Initially, we design a pipeline to create personalized writing instruction datasets enriched with extensive context details as the testbed of this research issue. Subsequently, we introduce two variants of CoGenesis based on sketch and logits respectively. Our experimental findings, based on our synthesized dataset and two additional open-source datasets, indicate that: 1) Large-scale models perform well when provided with user context but struggle in the absence of such context. 2) While specialized smaller models fine-tuned on the synthetic dataset show promise, they still lag behind their larger counterparts. 3) Our CoGenesis framework, utilizing mixed-scale models, showcases competitive performance, providing a feasible solution to privacy issues.

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale Spatial Transcriptomics Foundation Model. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

Large language models (LLMs) have enabled powerful advances in natural language understanding and generation. Yet their application to complex, real-world scientific workflows remain limited by challenges in memory, planning, and tool integration. Here, we introduce SciBORG (Scientific Bespoke Artificial Intelligence Agents Optimized for Research Goals), a modular agentic framework that allows LLM-based agents to autonomously plan, reason, and achieve robust and reliable domain-specific task execution. Agents are constructed dynamically from source code documentation and augmented with finite-state automata (FSA) memory, enabling persistent state tracking and context-aware decision-making. This approach eliminates the need for manual prompt engineering and allows for robust, scalable deployment across diverse applications via maintaining context across extended workflows and to recover from tool or execution failures. We validate SciBORG through integration with both physical and virtual hardware, such as microwave synthesizers for executing user-specified reactions, with context-aware decision making and demonstrate its use in autonomous multi-step bioassay retrieval from the PubChem database utilizing multi-step planning, reasoning, agent-to-agent communication and coordination for execution of exploratory tasks. Systematic benchmarking shows that SciBORG agents achieve reliable execution, adaptive planning, and interpretable state transitions. Our results show that memory and state awareness are critical enablers of agentic planning and reliability, offering a generalizable foundation for deploying AI agents in complex environments.

The rapid expansion of interconnected devices, autonomous systems, and AI applications has created severe fragmentation in adaptive transport systems, where diverse protocols and context sources remain isolated. This survey provides the first systematic investigation of the Model Context Protocol (MCP) as a unifying paradigm, highlighting its ability to bridge protocol-level adaptation with context-aware decision making. Analyzing established literature, we show that existing efforts have implicitly converged toward MCP-like architectures, signaling a natural evolution from fragmented solutions to standardized integration frameworks. We propose a five-category taxonomy covering adaptive mechanisms, context-aware frameworks, unification models, integration strategies, and MCP-enabled architectures. Our findings reveal three key insights: traditional transport protocols have reached the limits of isolated adaptation, MCP's client-server and JSON-RPC structure enables semantic interoperability, and AI-driven transport demands integration paradigms uniquely suited to MCP. Finally, we present a research roadmap positioning MCP as a foundation for next-generation adaptive, context-aware, and intelligent transport infrastructures.

Existing frameworks for evaluating long-context language models (LCLM) can be broadly categorized into real-world and synthetic tasks. Despite their utility, both approaches are accompanied by certain intrinsic limitations. Real-world tasks are too complex to interpret or characterize and are susceptible to data contamination. In contrast, synthetic tasks often adopt the needle-in-the-haystack (NIAH) format, wherein a lack of coherence between the "needle" and the "haystack" compromises their validity as proxies for realistic applications. In response to these challenges, we posit that an ideal long-context evaluation framework should be characterized by three essential features: seamless context, controllable setting, and sound evaluation. This study introduces LongBioBench, a novel benchmark that utilizes artificially generated biographies as a controlled environment for assessing LCLMs across dimensions of understanding, reasoning, and trustworthiness. Our experimental evaluation, which includes 18 LCLMs in total, demonstrates that most models still exhibit deficiencies in semantic understanding and elementary reasoning over retrieved results and are less trustworthy as context length increases. Our further analysis indicates some design choices employed by existing synthetic benchmarks, such as contextual non-coherence, numerical needles, and the absence of distractors, rendering them vulnerable to test the model long-context capabilities. Moreover, we also reveal that long-context continual pretraining primarily adjusts RoPE embedding to accommodate extended context lengths. To sum up, compared to previous synthetic benchmarks, LongBioBench achieves a better trade-off between mirroring authentic language tasks and maintaining controllability, and is highly interpretable and configurable.

Text detoxification aims to minimize the risk of language models producing toxic content. Existing detoxification methods of directly constraining the model output or further training the model on the non-toxic corpus fail to achieve a decent balance between detoxification effectiveness and generation quality. This issue stems from the neglect of constrain imposed by the context since language models are designed to generate output that closely matches the context while detoxification methods endeavor to ensure the safety of the output even if it semantically deviates from the context. In view of this, we introduce a Context-aware Model self-Detoxification~(CMD) framework that pays attention to both the context and the detoxification process, i.e., first detoxifying the context and then making the language model generate along the safe context. Specifically, CMD framework involves two phases: utilizing language models to synthesize data and applying these data for training. We also introduce a toxic contrastive loss that encourages the model generation away from the negative toxic samples. Experiments on various LLMs have verified the effectiveness of our MSD framework, which can yield the best performance compared to baselines.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Large Language Models (LLMs) have revolutionized various aspects of engineering and science. Their utility is often bottlenecked by the lack of interaction with the external digital environment. To overcome this limitation and achieve integration of LLMs and Artificial Intelligence (AI) into real-world applications, customized AI agents are being constructed. Based on the technological trends and techniques, we extract a high-level approach for constructing these AI agents, focusing on their underlying architecture. This thesis serves as a comprehensive guide that elucidates a multi-faceted approach for empowering LLMs with the capability to leverage Application Programming Interfaces (APIs). We present a 7-step methodology that begins with the selection of suitable LLMs and the task decomposition that is necessary for complex problem-solving. This methodology includes techniques for generating training data for API interactions and heuristics for selecting the appropriate API among a plethora of options. These steps eventually lead to the generation of API calls that are both syntactically and semantically aligned with the LLM's understanding of a given task. Moreover, we review existing frameworks and tools that facilitate these processes and highlight the gaps in current attempts. In this direction, we propose an on-device architecture that aims to exploit the functionality of carry-on devices by using small models from the Hugging Face community. We examine the effectiveness of these approaches on real-world applications of various domains, including the generation of a piano sheet. Through an extensive analysis of the literature and available technologies, this thesis aims to set a compass for researchers and practitioners to harness the full potential of LLMs augmented with external tool capabilities, thus paving the way for more autonomous, robust, and context-aware AI agents.

Despite recent advances in multimodal content generation enabled by vision-language models (VLMs), their ability to reason about and generate structured 3D scenes remains largely underexplored. This limitation constrains their utility in spatially grounded tasks such as embodied AI, immersive simulations, and interactive 3D applications. We introduce a new paradigm that enables VLMs to generate, understand, and edit complex 3D environments by injecting a continually evolving spatial context. Constructed from multimodal input, this context consists of three components: a scene portrait that provides a high-level semantic blueprint, a semantically labeled point cloud capturing object-level geometry, and a scene hypergraph that encodes rich spatial relationships, including unary, binary, and higher-order constraints. Together, these components provide the VLM with a structured, geometry-aware working memory that integrates its inherent multimodal reasoning capabilities with structured 3D understanding for effective spatial reasoning. Building on this foundation, we develop an agentic 3D scene generation pipeline in which the VLM iteratively reads from and updates the spatial context. The pipeline features high-quality asset generation with geometric restoration, environment setup with automatic verification, and ergonomic adjustment guided by the scene hypergraph. Experiments show that our framework can handle diverse and challenging inputs, achieving a level of generalization not observed in prior work. Further results demonstrate that injecting spatial context enables VLMs to perform downstream tasks such as interactive scene editing and path planning, suggesting strong potential for spatially intelligent systems in computer graphics, 3D vision, and embodied applications.

Retrieval-augmented generation (RAG) enhances the capabilities of large language models (LLMs) by incorporating external knowledge into their input prompts. However, when the retrieved context contradicts the LLM's parametric knowledge, it often fails to resolve the conflict between incorrect external context and correct parametric knowledge, known as context-memory conflict. To tackle this problem, we introduce Conflict-Aware REtrieval-Augmented Generation (CARE), consisting of a context assessor and a base LLM. The context assessor encodes compact memory token embeddings from raw context tokens. Through grounded/adversarial soft prompting, the context assessor is trained to discern unreliable context and capture a guidance signal that directs reasoning toward the more reliable knowledge source. Extensive experiments show that CARE effectively mitigates context-memory conflicts, leading to an average performance gain of 5.0\% on QA and fact-checking benchmarks, establishing a promising direction for trustworthy and adaptive RAG systems.

The Model Context Protocol has emerged as a transformative standard for connecting large language models to external data sources and tools, rapidly gaining adoption across major AI providers and development platforms. However, existing benchmarks are overly simplistic and fail to capture real application challenges such as long-horizon reasoning and large, unfamiliar tool spaces. To address this critical gap, we introduce MCP-Universe, the first comprehensive benchmark specifically designed to evaluate LLMs in realistic and hard tasks through interaction with real-world MCP servers. Our benchmark encompasses 6 core domains spanning 11 different MCP servers: Location Navigation, Repository Management, Financial Analysis, 3D Design, Browser Automation, and Web Searching. To ensure rigorous evaluation, we implement execution-based evaluators, including format evaluators for agent format compliance, static evaluators for time-invariant content matching, and dynamic evaluators that automatically retrieve real-time ground truth for temporally sensitive tasks. Through extensive evaluation of leading LLMs, we find that even SOTA models such as GPT-5 (43.72%), Grok-4 (33.33%) and Claude-4.0-Sonnet (29.44%) exhibit significant performance limitations. In addition, our benchmark poses a significant long-context challenge for LLM agents, as the number of input tokens increases rapidly with the number of interaction steps. Moreover, it introduces an unknown-tools challenge, as LLM agents often lack familiarity with the precise usage of the MCP servers. Notably, enterprise-level agents like Cursor cannot achieve better performance than standard ReAct frameworks. Beyond evaluation, we open-source our extensible evaluation framework with UI support, enabling researchers and practitioners to seamlessly integrate new agents and MCP servers while fostering innovation in the rapidly evolving MCP ecosystem.

Histopathology and transcriptomics are fundamental modalities in oncology, encapsulating the morphological and molecular aspects of the disease. Multi-modal self-supervised learning has demonstrated remarkable potential in learning pathological representations by integrating diverse data sources. Conventional multi-modal integration methods primarily emphasize modality alignment, while paying insufficient attention to retaining the modality-specific structures. However, unlike conventional scenarios where multi-modal inputs share highly overlapping features, histopathology and transcriptomics exhibit pronounced heterogeneity, offering orthogonal yet complementary insights. Histopathology provides morphological and spatial context, elucidating tissue architecture and cellular topology, whereas transcriptomics delineates molecular signatures through gene expression patterns. This inherent disparity introduces a major challenge in aligning them while maintaining modality-specific fidelity. To address these challenges, we present MIRROR, a novel multi-modal representation learning method designed to foster both modality alignment and retention. MIRROR employs dedicated encoders to extract comprehensive features for each modality, which is further complemented by a modality alignment module to achieve seamless integration between phenotype patterns and molecular profiles. Furthermore, a modality retention module safeguards unique attributes from each modality, while a style clustering module mitigates redundancy and enhances disease-relevant information by modeling and aligning consistent pathological signatures within a clustering space. Extensive evaluations on TCGA cohorts for cancer subtyping and survival analysis highlight MIRROR's superior performance, demonstrating its effectiveness in constructing comprehensive oncological feature representations and benefiting the cancer diagnosis.

Large language models (LLMs) have achieved remarkable success in text-based tasks but often struggle to provide actionable guidance in real-world physical environments. This is because of their inability to recognize their limited understanding of the user's physical context. We present SituationalLLM, a novel approach that integrates structured scene information into an LLM to deliver proactive, context-aware assistance. By encoding objects, attributes, and relationships in a custom Scene Graph Language, SituationalLLM actively identifies gaps in environmental context and seeks clarifications during user interactions. This behavior emerges from training on the Situational Awareness Database for Instruct-Tuning (SAD-Instruct), which combines diverse, scenario-specific scene graphs with iterative, dialogue-based refinements. Experimental results indicate that SituationalLLM outperforms generic LLM baselines in task specificity, reliability, and adaptability, paving the way for environment-aware AI assistants capable of delivering robust, user-centric guidance under real-world constraints.

Context utilisation, the ability of Language Models (LMs) to incorporate relevant information from the provided context when generating responses, remains largely opaque to users, who cannot determine whether models draw from parametric memory or provided context, nor identify which specific context pieces inform the response. Highlight explanations (HEs) offer a natural solution as they can point the exact context pieces and tokens that influenced model outputs. However, no existing work evaluates their effectiveness in accurately explaining context utilisation. We address this gap by introducing the first gold standard HE evaluation framework for context attribution, using controlled test cases with known ground-truth context usage, which avoids the limitations of existing indirect proxy evaluations. To demonstrate the framework's broad applicability, we evaluate four HE methods -- three established techniques and MechLight, a mechanistic interpretability approach we adapt for this task -- across four context scenarios, four datasets, and five LMs. Overall, we find that MechLight performs best across all context scenarios. However, all methods struggle with longer contexts and exhibit positional biases, pointing to fundamental challenges in explanation accuracy that require new approaches to deliver reliable context utilisation explanations at scale.

A central challenge in sequence modeling is efficiently handling tasks with extended contexts. While recent state-space models (SSMs) have made significant progress in this area, they often lack input-dependent filtering or require substantial increases in model complexity to handle input variability. We address this gap by introducing S7, a simplified yet powerful SSM that can handle input dependence while incorporating stable reparameterization and specific design choices to dynamically adjust state transitions based on input content, maintaining efficiency and performance. We prove that this reparameterization ensures stability in long-sequence modeling by keeping state transitions well-behaved over time. Additionally, it controls the gradient norm, enabling efficient training and preventing issues like exploding or vanishing gradients. S7 significantly outperforms baselines across various sequence modeling tasks, including neuromorphic event-based datasets, Long Range Arena benchmarks, and various physical and biological time series. Overall, S7 offers a more straightforward approach to sequence modeling without relying on complex, domain-specific inductive biases, achieving significant improvements across key benchmarks.

Recent advancements in long-context Large Language Models (LLMs) have primarily concentrated on processing extended input contexts, resulting in significant strides in long-context comprehension. However, the equally critical aspect of generating long-form outputs has received comparatively less attention. This paper advocates for a paradigm shift in NLP research toward addressing the challenges of long-output generation. Tasks such as novel writing, long-term planning, and complex reasoning require models to understand extensive contexts and produce coherent, contextually rich, and logically consistent extended text. These demands highlight a critical gap in current LLM capabilities. We underscore the importance of this under-explored domain and call for focused efforts to develop foundational LLMs tailored for generating high-quality, long-form outputs, which hold immense potential for real-world applications.

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

In static monitoring cameras, useful contextual information can stretch far beyond the few seconds typical video understanding models might see: subjects may exhibit similar behavior over multiple days, and background objects remain static. Due to power and storage constraints, sampling frequencies are low, often no faster than one frame per second, and sometimes are irregular due to the use of a motion trigger. In order to perform well in this setting, models must be robust to irregular sampling rates. In this paper we propose a method that leverages temporal context from the unlabeled frames of a novel camera to improve performance at that camera. Specifically, we propose an attention-based approach that allows our model, Context R-CNN, to index into a long term memory bank constructed on a per-camera basis and aggregate contextual features from other frames to boost object detection performance on the current frame. We apply Context R-CNN to two settings: (1) species detection using camera traps, and (2) vehicle detection in traffic cameras, showing in both settings that Context R-CNN leads to performance gains over strong baselines. Moreover, we show that increasing the contextual time horizon leads to improved results. When applied to camera trap data from the Snapshot Serengeti dataset, Context R-CNN with context from up to a month of images outperforms a single-frame baseline by 17.9% mAP, and outperforms S3D (a 3d convolution based baseline) by 11.2% mAP.

Karl Marx once wrote that ``the human essence is the ensemble of social relations'', suggesting that individuals are not isolated entities but are fundamentally shaped by their interactions with other entities, within which contexts play a constitutive and essential role. With the advent of computers and artificial intelligence, these contexts are no longer limited to purely human--human interactions: human--machine interactions are included as well. Then a central question emerges: How can machines better understand our situations and purposes? To address this challenge, researchers have recently introduced the concept of context engineering. Although it is often regarded as a recent innovation of the agent era, we argue that related practices can be traced back more than twenty years. Since the early 1990s, the field has evolved through distinct historical phases, each shaped by the intelligence level of machines: from early human--computer interaction frameworks built around primitive computers, to today's human--agent interaction paradigms driven by intelligent agents, and potentially to human--level or superhuman intelligence in the future. In this paper, we situate context engineering, provide a systematic definition, outline its historical and conceptual landscape, and examine key design considerations for practice. By addressing these questions, we aim to offer a conceptual foundation for context engineering and sketch its promising future. This paper is a stepping stone for a broader community effort toward systematic context engineering in AI systems.

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

The emerging zero-shot capabilities of Large Language Models (LLMs) have led to their applications in areas extending well beyond natural language processing tasks. In reinforcement learning, while LLMs have been extensively used in text-based environments, their integration with continuous state spaces remains understudied. In this paper, we investigate how pre-trained LLMs can be leveraged to predict in context the dynamics of continuous Markov decision processes. We identify handling multivariate data and incorporating the control signal as key challenges that limit the potential of LLMs' deployment in this setup and propose Disentangled In-Context Learning (DICL) to address them. We present proof-of-concept applications in two reinforcement learning settings: model-based policy evaluation and data-augmented off-policy reinforcement learning, supported by theoretical analysis of the proposed methods. Our experiments further demonstrate that our approach produces well-calibrated uncertainty estimates. We release the code at https://github.com/abenechehab/dicl.

Large Language Models (LLMs) have become an essential infrastructure for Artificial General Intelligence (AGI), yet their lack of well-defined memory management systems hinders the development of long-context reasoning, continual personalization, and knowledge consistency.Existing models mainly rely on static parameters and short-lived contextual states, limiting their ability to track user preferences or update knowledge over extended periods.While Retrieval-Augmented Generation (RAG) introduces external knowledge in plain text, it remains a stateless workaround without lifecycle control or integration with persistent representations.Recent work has modeled the training and inference cost of LLMs from a memory hierarchy perspective, showing that introducing an explicit memory layer between parameter memory and external retrieval can substantially reduce these costs by externalizing specific knowledge. Beyond computational efficiency, LLMs face broader challenges arising from how information is distributed over time and context, requiring systems capable of managing heterogeneous knowledge spanning different temporal scales and sources. To address this challenge, we propose MemOS, a memory operating system that treats memory as a manageable system resource. It unifies the representation, scheduling, and evolution of plaintext, activation-based, and parameter-level memories, enabling cost-efficient storage and retrieval. As the basic unit, a MemCube encapsulates both memory content and metadata such as provenance and versioning. MemCubes can be composed, migrated, and fused over time, enabling flexible transitions between memory types and bridging retrieval with parameter-based learning. MemOS establishes a memory-centric system framework that brings controllability, plasticity, and evolvability to LLMs, laying the foundation for continual learning and personalized modeling.

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

Large language models (LLMs) have advanced the field of artificial intelligence (AI) and are a powerful enabler for interactive systems. However, they still face challenges in long-term interactions that require adaptation towards the user as well as contextual knowledge and understanding of the ever-changing environment. To overcome these challenges, holistic memory modeling is required to efficiently retrieve and store relevant information across interaction sessions for suitable responses. Cognitive AI, which aims to simulate the human thought process in a computerized model, highlights interesting aspects, such as thoughts, memory mechanisms, and decision-making, that can contribute towards improved memory modeling for LLMs. Inspired by these cognitive AI principles, we propose our memory framework CAIM. CAIM consists of three modules: 1.) The Memory Controller as the central decision unit; 2.) the Memory Retrieval, which filters relevant data for interaction upon request; and 3.) the Post-Thinking, which maintains the memory storage. We compare CAIM against existing approaches, focusing on metrics such as retrieval accuracy, response correctness, contextual coherence, and memory storage. The results demonstrate that CAIM outperforms baseline frameworks across different metrics, highlighting its context-awareness and potential to improve long-term human-AI interactions.

Recent advances in context optimization (CoOp) guided by large language model (LLM)-distilled medical semantic priors offer a scalable alternative to manual prompt engineering and full fine-tuning for adapting biomedical CLIP-based vision-language models (VLMs). However, prompt learning in this context is challenged by semantic misalignment between LLMs and CLIP variants due to divergent training corpora and model architectures; it further lacks scalability across continuously evolving families of foundation models. More critically, pairwise multimodal alignment via conventional Euclidean-space optimization lacks the capacity to model unified representations or apply localized geometric constraints, which tends to amplify modality gaps in complex biomedical imaging and destabilize few-shot adaptation. In this work, we propose vMFCoOp, a framework that inversely estimates von Mises-Fisher (vMF) distributions on a shared Hyperspherical Manifold, aligning semantic biases between arbitrary LLMs and CLIP backbones via Unified Semantic Anchors to achieve robust biomedical prompting and superior few-shot classification. Grounded in three complementary constraints, vMFCoOp demonstrates consistent improvements across 14 medical datasets, 12 medical imaging modalities, and 13 anatomical regions, outperforming state-of-the-art methods in accuracy, generalization, and clinical applicability. This work will be continuously expanded to encompass more downstream applications, and the corresponding resources are intended to be shared through https://github.com/VinyehShaw/UniEqui.

In the era of Large Language Models (LLMs), human-computer interaction has evolved towards natural language, offering unprecedented flexibility. Despite this, LLMs are heavily reliant on well-structured prompts to function efficiently within the realm of In-Context Learning. Vanilla In-Context Learning relies on human-provided contexts, such as labeled examples, explicit instructions, or other guiding mechanisms that shape the model's outputs. To address this challenge, our study presents a universal framework named Automatic In-Context Learning. Upon receiving a user's request, we ask the model to independently generate examples, including labels, instructions, or reasoning pathways. The model then leverages this self-produced context to tackle the given problem. Our approach is universally adaptable and can be implemented in any setting where vanilla In-Context Learning is applicable. We demonstrate that our method yields strong performance across a range of tasks, standing up well when compared to existing methods.

The ability of large language models (LLMs) to process and reason over long textual inputs is critical for a wide range of real-world applications. However, progress in this area is significantly constrained by the absence of high-quality, diverse, and verifiable long-context datasets suitable for both training and evaluation. This work introduces a modular, extensible framework for synthetic long-context data generation via prompt-based interaction with LLMs. The framework supports multiple training and alignment objectives, including Supervised Fine-Tuning (SFT), Direct Preference Optimization (DPO), and Group Relative Policy Optimization (GRPO). It encompasses four core generation paradigms: multi-turn conversational dialogues, document-grounded input-output pairs, verifiable instruction-response tasks, and long-context reasoning examples. Through templated prompting, a model-agnostic architecture, and metadata-enriched outputs, the proposed approach facilitates scalable, controllable, and purpose-aligned dataset creation for advancing long-context capabilities in LLMs.

Agents centered around Large Language Models (LLMs) are now capable of automating mobile device operations for users. After fine-tuning to learn a user's mobile operations, these agents can adhere to high-level user instructions online. They execute tasks such as goal decomposition, sequencing of sub-goals, and interactive environmental exploration, until the final objective is achieved. However, privacy concerns related to personalized user data arise during mobile operations, requiring user confirmation. Moreover, users' real-world operations are exploratory, with action data being complex and redundant, posing challenges for agent learning. To address these issues, in our practical application, we have designed interactive tasks between agents and humans to identify sensitive information and align with personalized user needs. Additionally, we integrated Standard Operating Procedure (SOP) information within the model's in-context learning to enhance the agent's comprehension of complex task execution. Our approach is evaluated on the new device control benchmark AitW, which encompasses 30K unique instructions across multi-step tasks, including application operation, web searching, and web shopping. Experimental results show that the SOP-based agent achieves state-of-the-art performance in LLMs without incurring additional inference costs, boasting an overall action success rate of 66.92\%. The code and data examples are available at https://github.com/alipay/mobile-agent.

Large language models (LLMs) achieved remarkable performance across various tasks. However, they face challenges in managing long documents and extended conversations, due to significantly increased computational requirements, both in memory and inference time, and potential context truncation when the input exceeds the LLM's fixed context length. This paper proposes a method called Selective Context that enhances the inference efficiency of LLMs by identifying and pruning redundancy in the input context to make the input more compact. We test our approach using common data sources requiring long context processing: arXiv papers, news articles, and long conversations, on tasks of summarisation, question answering, and response generation. Experimental results show that Selective Context significantly reduces memory cost and decreases generation latency while maintaining comparable performance compared to that achieved when full context is used. Specifically, we achieve a 50\% reduction in context cost, resulting in a 36\% reduction in inference memory usage and a 32\% reduction in inference time, while observing only a minor drop of .023 in BERTscore and .038 in faithfulness on four downstream applications, indicating that our method strikes a good balance between efficiency and performance.

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

In AI research, the optimization of Large Language Models (LLMs) remains a significant challenge, crucial for advancing the field's practical applications and sustainability. Building upon the foundational work of Professor Song Han's lab at MIT, this paper introduces a novel approach in developing Mini-GPTs via contextual pruning. Our methodology strategically prunes the computational architecture of traditional LLMs, like Phi-1.5, focusing on retaining core functionalities while drastically reducing model sizes. We employ the technique across diverse and complex datasets, including US law, Medical Q&A, Skyrim dialogue, English-Taiwanese translation, and Economics articles. The results underscore the efficiency and effectiveness of contextual pruning, not merely as a theoretical concept but as a practical tool in developing domain-specific, resource-efficient LLMs. Contextual pruning is a promising method for building domain-specific LLMs, and this research is a building block towards future development with more hardware compute, refined fine-tuning, and quantization.

This paper presents Dynamic Context Prompting/Programming (DCP/P), a novel framework for interacting with LLMs to generate graph-based content with a dynamic context window history. While there is an existing study utilizing LLMs to generate a visual novel game, the previous study involved a manual process of output extraction and did not provide flexibility in generating a longer, coherent story. We evaluate DCP/P against our baseline, which does not provide context history to an LLM and only relies on the initial story data. Through objective evaluation, we show that simply providing the LLM with a summary leads to a subpar story compared to additionally providing the LLM with the proper context of the story. We also provide an extensive qualitative analysis and discussion. We qualitatively examine the quality of the objectively best-performing generated game from each approach. In addition, we examine biases in word choices and word sentiment of the generated content. We find a consistent observation with previous studies that LLMs are biased towards certain words, even with a different LLM family. Finally, we provide a comprehensive discussion on opportunities for future studies.

Large Language Models (LLMs) exhibit strong general-purpose reasoning abilities but lack access to wireless environment information due to the absence of native sensory input and domain-specific priors. Previous attempts to apply LLMs in wireless systems either depend on retraining with network-specific data, which compromises language generalization, or rely on manually scripted interfaces, which hinder scalability. To overcome these limitations, we propose a Model Context Protocol (MCP)-based Internet of Experts (IoX) framework that equips LLMs with wireless environment-aware reasoning capabilities. The framework incorporates a set of lightweight expert models, each trained to solve a specific deterministic task in wireless communications, such as detecting a specific wireless attribute, e.g., line-of-sight propagation, Doppler effects, or fading conditions. Through MCP, the LLM can selectively query and interpret expert outputs at inference time, without modifying its own parameters. This architecture enables modular, extensible, and interpretable reasoning over wireless contexts. Evaluated across multiple mainstream LLMs, the proposed wireless environment-aware LLM agents achieve 40%-50% improvements in classification tasks over LLM-only baselines. More broadly, the MCP-based design offers a viable paradigm for future LLMs to inherit structured wireless network management capabilities.

Segmenting cells and tracking their motion over time is a common task in biomedical applications. However, predicting accurate instance-wise segmentation and cell motions from microscopy imagery remains a challenging task. Using microstructured environments for analyzing single cells in a constant flow of media adds additional complexity. While large-scale labeled microscopy datasets are available, we are not aware of any large-scale dataset, including both cells and microstructures. In this paper, we introduce the trapped yeast cell (TYC) dataset, a novel dataset for understanding instance-level semantics and motions of cells in microstructures. We release 105 dense annotated high-resolution brightfield microscopy images, including about 19k instance masks. We also release 261 curated video clips composed of 1293 high-resolution microscopy images to facilitate unsupervised understanding of cell motions and morphology. TYC offers ten times more instance annotations than the previously largest dataset, including cells and microstructures. Our effort also exceeds previous attempts in terms of microstructure variability, resolution, complexity, and capturing device (microscopy) variability. We facilitate a unified comparison on our novel dataset by introducing a standardized evaluation strategy. TYC and evaluation code are publicly available under CC BY 4.0 license.

In order for large language models to achieve true conversational continuity and benefit from experiential learning, they need memory. While research has focused on the development of complex memory systems, it remains unclear which types of memory are most effective for long-context conversational tasks. We present a systematic evaluation of memory-augmented methods using LoCoMo, a benchmark of synthetic long-context dialogues annotated for question-answering tasks that require diverse reasoning strategies. We analyse full-context prompting, semantic memory through retrieval-augmented generation and agentic memory, episodic memory through in-context learning, and procedural memory through prompt optimization. Our findings show that memory-augmented approaches reduce token usage by over 90% while maintaining competitive accuracy. Memory architecture complexity should scale with model capability, with small foundation models benefitting most from RAG, and strong instruction-tuned reasoning model gaining from episodic learning through reflections and more complex agentic semantic memory. In particular, episodic memory can help LLMs recognise the limits of their own knowledge.

This paper is an opinion paper that looks at the future of computing in the age of Generative \& Agentic AI. Current software systems are static and inflexible, leading to significant challenges in translating human goals into computational actions. "Living software systems" powered by generative AI offer a solution to this fundamental problem in computing. Traditional software development involves multiple layers of imperfect translation, from business requirements to code, resulting in rigid systems that struggle to adapt to changing user needs and contexts. Generative AI, particularly large language models, can serve as a universal translator between human intent and computer operations. This approach enables the creation of more flexible, context-aware systems that can dynamically evolve to meet user goals. Two pathways for implementing living software systems are explored: using generative AI to accelerate traditional software development, and leveraging agentic AI to create truly adaptive systems. New skills like Prompt Engineering are necessary. By reimagining software as a living, adaptable entity, we can create computing interfaces that are more intuitive, powerful, and responsive to human needs.

Handling long input contexts remains a significant challenge for Large Language Models (LLMs), particularly in resource-constrained environments such as mobile devices. Our work aims to address this limitation by introducing InfiniPot, a novel KV cache control framework designed to enable pre-trained LLMs to manage extensive sequences within fixed memory constraints efficiently, without requiring additional training. InfiniPot leverages Continual Context Distillation (CCD), an iterative process that compresses and retains essential information through novel importance metrics, effectively maintaining critical data even without access to future context. Our comprehensive evaluations indicate that InfiniPot significantly outperforms models trained for long contexts in various NLP tasks, establishing its efficacy and versatility. This work represents a substantial advancement toward making LLMs applicable to a broader range of real-world scenarios.

Pre-trained Large Language Models (LLMs) require post-training methods such as supervised fine-tuning (SFT) on instruction-response pairs to enable instruction following. However, this process can potentially harm existing capabilities learned during pre-training. In this paper, we investigate the loss of context awareness after SFT, where context awareness is defined as the ability to extract and understand information from user-provided context and respond accordingly. We identify and demonstrate that the loss of context awareness, particularly in open-source models, occurs in instruction fine-tuned LLMs when the chat template is applied to input prompts. We identify that the performance decline is associated with a bias toward different roles learned during conversational instruction fine-tuning. We demonstrate this correlation by visualizing changes in attention allocation after the chat template is applied and manually steering the attention heads. The bias can be learned from training examples that align with the model's internal knowledge and rely less on the user-provided context to generate correct responses. Based on these observations, we propose a metric to identify context-dependent examples from general instruction fine-tuning datasets. We then apply conditional instruction fine-tuning with a context-dependency indicator, enabling the model to preserve context awareness after SFT. Empirical experiments on four context-dependent downstream tasks and three pre-trained LLMs of different sizes show that our method effectively mitigates the loss of context awareness without compromising general instruction-following capabilities.

Despite significant progress, existing research on Multimodal Large Language Models (MLLMs) mainly focuses on general visual understanding, overlooking the ability to integrate textual context associated with objects for a more context-aware multimodal understanding -- an ability we refer to as Region-level Context-aware Multimodal Understanding (RCMU). To address this limitation, we first formulate the RCMU task, which requires models to respond to user instructions by integrating both image content and textual information of regions or objects. To equip MLLMs with RCMU capabilities, we propose Region-level Context-aware Visual Instruction Tuning (RCVIT), which incorporates object information into the model input and enables the model to utilize bounding box coordinates to effectively associate objects' visual content with their textual information. To address the lack of datasets, we introduce the RCMU dataset, a large-scale visual instruction tuning dataset that covers multiple RCMU tasks. We also propose RC\&P-Bench, a comprehensive benchmark that can evaluate the performance of MLLMs in RCMU and multimodal personalized understanding tasks. Additionally, we propose a reference-free evaluation metric to perform a comprehensive and fine-grained evaluation of the region-level context-aware image descriptions. By performing RCVIT on Qwen2-VL models with the RCMU dataset, we developed RC-Qwen2-VL models. Experimental results indicate that RC-Qwen2-VL models not only achieve outstanding performance on multiple RCMU tasks but also demonstrate successful applications in multimodal RAG and personalized conversation. Our data, model and benchmark are available at https://github.com/hongliang-wei/RC-MLLM

Following the success of the in-context learning paradigm in large-scale language and computer vision models, the recently emerging field of in-context reinforcement learning is experiencing a rapid growth. However, its development has been held back by the lack of challenging benchmarks, as all the experiments have been carried out in simple environments and on small-scale datasets. We present XLand-100B, a large-scale dataset for in-context reinforcement learning based on the XLand-MiniGrid environment, as a first step to alleviate this problem. It contains complete learning histories for nearly 30,000 different tasks, covering 100B transitions and 2.5B episodes. It took 50,000 GPU hours to collect the dataset, which is beyond the reach of most academic labs. Along with the dataset, we provide the utilities to reproduce or expand it even further. With this substantial effort, we aim to democratize research in the rapidly growing field of in-context reinforcement learning and provide a solid foundation for further scaling. The code is open-source and available under Apache 2.0 licence at https://github.com/dunno-lab/xland-minigrid-datasets.

This study explores the capabilities of multimodal large language models (LLMs) in handling challenging multistep tasks that integrate language and vision, focusing on model steerability, composability, and the application of long-term memory and context understanding. The problem addressed is the LLM's ability (Nov 2023 GPT-4 Vision Preview) to manage tasks that require synthesizing visual and textual information, especially where stepwise instructions and sequential logic are paramount. The research presents a series of 14 creatively and constructively diverse tasks, ranging from AI Lego Designing to AI Satellite Image Analysis, designed to test the limits of current LLMs in contexts that previously proved difficult without extensive memory and contextual understanding. Key findings from evaluating 800 guided dialogs include notable disparities in task completion difficulty. For instance, 'Image to Ingredient AI Bartender' (Low difficulty) contrasted sharply with 'AI Game Self-Player' (High difficulty), highlighting the LLM's varying proficiency in processing complex visual data and generating coherent instructions. Tasks such as 'AI Genetic Programmer' and 'AI Negotiator' showed high completion difficulty, emphasizing challenges in maintaining context over multiple steps. The results underscore the importance of developing LLMs that combine long-term memory and contextual awareness to mimic human-like thought processes in complex problem-solving scenarios.

Creating a vivid video from the event or scenario in our imagination is a truly fascinating experience. Recent advancements in text-to-video synthesis have unveiled the potential to achieve this with prompts only. While text is convenient in conveying the overall scene context, it may be insufficient to control precisely. In this paper, we explore customized video generation by utilizing text as context description and motion structure (e.g. frame-wise depth) as concrete guidance. Our method, dubbed Make-Your-Video, involves joint-conditional video generation using a Latent Diffusion Model that is pre-trained for still image synthesis and then promoted for video generation with the introduction of temporal modules. This two-stage learning scheme not only reduces the computing resources required, but also improves the performance by transferring the rich concepts available in image datasets solely into video generation. Moreover, we use a simple yet effective causal attention mask strategy to enable longer video synthesis, which mitigates the potential quality degradation effectively. Experimental results show the superiority of our method over existing baselines, particularly in terms of temporal coherence and fidelity to users' guidance. In addition, our model enables several intriguing applications that demonstrate potential for practical usage.

With the rapid rise of large language models (LLMs), phone automation has undergone transformative changes. This paper systematically reviews LLM-driven phone GUI agents, highlighting their evolution from script-based automation to intelligent, adaptive systems. We first contextualize key challenges, (i) limited generality, (ii) high maintenance overhead, and (iii) weak intent comprehension, and show how LLMs address these issues through advanced language understanding, multimodal perception, and robust decision-making. We then propose a taxonomy covering fundamental agent frameworks (single-agent, multi-agent, plan-then-act), modeling approaches (prompt engineering, training-based), and essential datasets and benchmarks. Furthermore, we detail task-specific architectures, supervised fine-tuning, and reinforcement learning strategies that bridge user intent and GUI operations. Finally, we discuss open challenges such as dataset diversity, on-device deployment efficiency, user-centric adaptation, and security concerns, offering forward-looking insights into this rapidly evolving field. By providing a structured overview and identifying pressing research gaps, this paper serves as a definitive reference for researchers and practitioners seeking to harness LLMs in designing scalable, user-friendly phone GUI agents.

In the age of mobile internet, user data, often referred to as memories, is continuously generated on personal devices. Effectively managing and utilizing this data to deliver services to users is a compelling research topic. In this paper, we introduce a novel task of crafting personalized agents powered by large language models (LLMs), which utilize a user's smartphone memories to enhance downstream applications with advanced LLM capabilities. To achieve this goal, we introduce EMG-RAG, a solution that combines Retrieval-Augmented Generation (RAG) techniques with an Editable Memory Graph (EMG). This approach is further optimized using Reinforcement Learning to address three distinct challenges: data collection, editability, and selectability. Extensive experiments on a real-world dataset validate the effectiveness of EMG-RAG, achieving an improvement of approximately 10% over the best existing approach. Additionally, the personalized agents have been transferred into a real smartphone AI assistant, which leads to enhanced usability.

A high-performance image compression algorithm is crucial for real-time information transmission across numerous fields. Despite rapid progress in image compression, computational inefficiency and poor redundancy modeling still pose significant bottlenecks, limiting practical applications. Inspired by the effectiveness of state space models (SSMs) in capturing long-range dependencies, we leverage SSMs to address computational inefficiency in existing methods and improve image compression from multiple perspectives. In this paper, we integrate the advantages of SSMs for better efficiency-performance trade-off and propose an enhanced image compression approach through refined context modeling, which we term MambaIC. Specifically, we explore context modeling to adaptively refine the representation of hidden states. Additionally, we introduce window-based local attention into channel-spatial entropy modeling to reduce potential spatial redundancy during compression, thereby increasing efficiency. Comprehensive qualitative and quantitative results validate the effectiveness and efficiency of our approach, particularly for high-resolution image compression. Code is released at https://github.com/AuroraZengfh/MambaIC.

Understanding context is key to understanding human language, an ability which Large Language Models (LLMs) have been increasingly seen to demonstrate to an impressive extent. However, though the evaluation of LLMs encompasses various domains within the realm of Natural Language Processing, limited attention has been paid to probing their linguistic capability of understanding contextual features. This paper introduces a context understanding benchmark by adapting existing datasets to suit the evaluation of generative models. This benchmark comprises of four distinct tasks and nine datasets, all featuring prompts designed to assess the models' ability to understand context. First, we evaluate the performance of LLMs under the in-context learning pretraining scenario. Experimental results indicate that pre-trained dense models struggle with understanding more nuanced contextual features when compared to state-of-the-art fine-tuned models. Second, as LLM compression holds growing significance in both research and real-world applications, we assess the context understanding of quantized models under in-context-learning settings. We find that 3-bit post-training quantization leads to varying degrees of performance reduction on our benchmark. We conduct an extensive analysis of these scenarios to substantiate our experimental results.

Recently, image-to-video (I2V) diffusion models have demonstrated impressive scene understanding and generative quality, incorporating image conditions to guide generation. However, these models primarily animate static images without extending beyond their provided context. Introducing additional constraints, such as camera trajectories, can enhance diversity but often degrades visual quality, limiting their applicability for tasks requiring faithful scene representation. We propose CamContextI2V, an I2V model that integrates multiple image conditions with 3D constraints alongside camera control to enrich both global semantics and fine-grained visual details. This enables more coherent and context-aware video generation. Moreover, we motivate the necessity of temporal awareness for an effective context representation. Our comprehensive study on the RealEstate10K dataset demonstrates improvements in visual quality and camera controllability. We make our code and models publicly available at: https://github.com/LDenninger/CamContextI2V.

Interactive programming with interleaved code snippet cells and natural language markdown is recently gaining popularity in the form of Jupyter notebooks, which accelerate prototyping and collaboration. To study code generation conditioned on a long context history, we present JuICe, a corpus of 1.5 million examples with a curated test set of 3.7K instances based on online programming assignments. Compared with existing contextual code generation datasets, JuICe provides refined human-curated data, open-domain code, and an order of magnitude more training data. Using JuICe, we train models for two tasks: (1) generation of the API call sequence in a code cell, and (2) full code cell generation, both conditioned on the NL-Code history up to a particular code cell. Experiments using current baseline code generation models show that both context and distant supervision aid in generation, and that the dataset is challenging for current systems.

Large language models (LLMs) with decoder-only architectures demonstrate remarkable in-context learning (ICL) capabilities. This feature enables them to effectively handle both familiar and novel tasks by utilizing examples provided within their input context. Recognizing the potential of this capability, we propose leveraging the ICL feature in LLMs to enhance the process of text embedding generation. To this end, we introduce a novel model bge-en-icl, which employs few-shot examples to produce high-quality text embeddings. Our approach integrates task-related examples directly into the query side, resulting in significant improvements across various tasks. Additionally, we have investigated how to effectively utilize LLMs as embedding models, including various attention mechanisms, pooling methods, etc. Our findings suggest that retaining the original framework often yields the best results, underscoring that simplicity is best. Experimental results on the MTEB and AIR-Bench benchmarks demonstrate that our approach sets new state-of-the-art (SOTA) performance. Our model, code and dataset are freely available at https://github.com/FlagOpen/FlagEmbedding .

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

Emerging world models autoregressively generate video frames in response to actions, such as camera movements and text prompts, among other control signals. Due to limited temporal context window sizes, these models often struggle to maintain scene consistency during revisits, leading to severe forgetting of previously generated environments. Inspired by the mechanisms of human memory, we introduce a novel framework to enhancing long-term consistency of video world models through a geometry-grounded long-term spatial memory. Our framework includes mechanisms to store and retrieve information from the long-term spatial memory and we curate custom datasets to train and evaluate world models with explicitly stored 3D memory mechanisms. Our evaluations show improved quality, consistency, and context length compared to relevant baselines, paving the way towards long-term consistent world generation.

Recent advances in unified multimodal models (UMMs) have enabled impressive progress in visual comprehension and generation. However, existing datasets and benchmarks focus primarily on single-turn interactions, failing to capture the multi-turn, context-dependent nature of real-world image creation and editing. To address this gap, we present WEAVE, the first suite for in-context interleaved cross-modality comprehension and generation. Our suite consists of two complementary parts. WEAVE-100k is a large-scale dataset of 100K interleaved samples spanning over 370K dialogue turns and 500K images, covering comprehension, editing, and generation tasks that require reasoning over historical context. WEAVEBench is a human-annotated benchmark with 100 tasks based on 480 images, featuring a hybrid VLM judger evaluation framework based on both the reference image and the combination of the original image with editing instructions that assesses models' abilities in multi-turn generation, visual memory, and world-knowledge reasoning across diverse domains. Experiments demonstrate that training on WEAVE-100k enables vision comprehension, image editing, and comprehension-generation collaboration capabilities. Furthermore, it facilitates UMMs to develop emergent visual-memory capabilities, while extensive evaluations on WEAVEBench expose the persistent limitations and challenges of current approaches in multi-turn, context-aware image generation and editing. We believe WEAVE provides a view and foundation for studying in-context interleaved comprehension and generation for multi-modal community.

The current trend to improve language model performance seems to be based on scaling up with the number of parameters (e.g. the state of the art GPT4 model has approximately 1.7 trillion parameters) or the amount of training data fed into the model. However this comes at significant costs in terms of computational resources and energy costs that compromise the sustainability of AI solutions, as well as risk relating to privacy and misuse. In this paper we present the Erasmian Language Model (ELM) a small context specific, 900 million parameter model, pre-trained and fine-tuned by and for Erasmus University Rotterdam. We show how the model performs adequately in a classroom context for essay writing, and how it achieves superior performance in subjects that are part of its context. This has implications for a wide range of institutions and organizations, showing that context specific language models may be a viable alternative for resource constrained, privacy sensitive use cases.

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 proliferation of harmful online content--e.g., toxicity, spam, and negative sentiment--demands robust and adaptable moderation systems. However, prevailing moderation systems are centralized and task-specific, offering limited transparency and neglecting diverse user preferences--an approach ill-suited for privacy-sensitive or decentralized environments. We propose a novel framework that leverages in-context learning (ICL) with foundation models to unify the detection of toxicity, spam, and negative sentiment across binary, multi-class, and multi-label settings. Crucially, our approach enables lightweight personalization, allowing users to easily block new categories, unblock existing ones, or extend detection to semantic variations through simple prompt-based interventions--all without model retraining. Extensive experiments on public benchmarks (TextDetox, UCI SMS, SST2) and a new, annotated Mastodon dataset reveal that: (i) foundation models achieve strong cross-task generalization, often matching or surpassing task-specific fine-tuned models; (ii) effective personalization is achievable with as few as one user-provided example or definition; and (iii) augmenting prompts with label definitions or rationales significantly enhances robustness to noisy, real-world data. Our work demonstrates a definitive shift beyond one-size-fits-all moderation, establishing ICL as a practical, privacy-preserving, and highly adaptable pathway for the next generation of user-centric content safety systems. To foster reproducibility and facilitate future research, we publicly release our code on GitHub and the annotated Mastodon dataset on Hugging Face.

While small language models (SLMs) show promises for mobile deployment, their real-world performance and applications on smartphones remains underexplored. We present SlimLM, a series of SLMs optimized for document assistance tasks on mobile devices. Through extensive experiments on a Samsung Galaxy S24, we identify the optimal trade-offs between model size (ranging from 125M to 7B parameters), context length, and inference time for efficient on-device processing. SlimLM is pre-trained on SlimPajama-627B and fine-tuned on DocAssist, our constructed dataset for summarization, question answering and suggestion tasks. Our smallest model demonstrates efficient performance on S24, while larger variants offer enhanced capabilities within mobile constraints. We evaluate SlimLM against existing SLMs, showing comparable or superior performance and offering a benchmark for future research in on-device language models. We also provide an Android application, offering practical insights into SLM deployment. Our findings provide valuable insights and illuminate the capabilities of running advanced language models on high-end smartphones, potentially reducing server costs and enhancing privacy through on-device processing.

Large language models (LLMs) have recently emerged as promising tools for solving challenging robotic tasks, even in the presence of action and observation uncertainties. Recent LLM-based decision-making methods (also referred to as LLM-based agents), when paired with appropriate critics, have demonstrated potential in solving complex, long-horizon tasks with relatively few interactions. However, most existing LLM-based agents lack the ability to retain and learn from past interactions - an essential trait of learning-based robotic systems. We propose RAG-Modulo, a framework that enhances LLM-based agents with a memory of past interactions and incorporates critics to evaluate the agents' decisions. The memory component allows the agent to automatically retrieve and incorporate relevant past experiences as in-context examples, providing context-aware feedback for more informed decision-making. Further by updating its memory, the agent improves its performance over time, thereby exhibiting learning. Through experiments in the challenging BabyAI and AlfWorld domains, we demonstrate significant improvements in task success rates and efficiency, showing that the proposed RAG-Modulo framework outperforms state-of-the-art baselines.

Large language models (LLMs) have had a huge impact on society due to their impressive capabilities and vast knowledge of the world. Various applications and tools have been created that allow users to interact with these models in a black-box scenario. However, one limitation of this scenario is that users cannot modify the internal knowledge of the model, and the only way to add or modify internal knowledge is by explicitly mentioning it to the model during the current interaction. This learning process is called in-context training, and it refers to training that is confined to the user's current session or context. In-context learning has significant applications, but also has limitations that are seldom studied. In this paper, we present a study that shows how the model can suffer from interference between information that continually flows in the context, causing it to forget previously learned knowledge, which can reduce the model's performance. Along with showing the problem, we propose an evaluation benchmark based on the bAbI dataset.

This paper presents a novel context compression method for Transformer language models in online scenarios such as ChatGPT, where the context continually expands. As the context lengthens, the attention process requires more memory and computational resources, which in turn reduces the throughput of the language model. To this end, we propose a compressed context memory system that continually compresses the growing context into a compact memory space. The compression process simply involves integrating a lightweight conditional LoRA into the language model's forward pass during inference. Based on the compressed context memory, the language model can perform inference with reduced memory and attention operations. Through evaluations on conversation, personalization, and multi-task learning, we demonstrate that our approach achieves the performance level of a full context model with 5times smaller context memory space. Codes are available at https://github.com/snu-mllab/context-memory.

Detecting and classifying cells in histopathology H\&E stained whole-slide images is a core task in computational pathology, as it provides valuable insight into the tumor microenvironment. In this work we investigate the impact of ground truth formats on the models performance. Additionally, cell-tissue interactions are considered by providing tissue segmentation predictions as input to the cell detection model. We find that a "soft", probability-map instance segmentation ground truth leads to best model performance. Combined with cell-tissue interaction and test-time augmentation our Soft Cell-Tissue-Model (SoftCTM) achieves 0.7172 mean F1-Score on the Overlapped Cell On Tissue (OCELOT) test set, achieving the third best overall score in the OCELOT 2023 Challenge. The source code for our approach is made publicly available at https://github.com/lely475/ocelot23algo.

One of the key challenges in deploying RL to real-world applications is to adapt to variations of unknown environment contexts, such as changing terrains in robotic tasks and fluctuated bandwidth in congestion control. Existing works on adaptation to unknown environment contexts either assume the contexts are the same for the whole episode or assume the context variables are Markovian. However, in many real-world applications, the environment context usually stays stable for a stochastic period and then changes in an abrupt and unpredictable manner within an episode, resulting in a segment structure, which existing works fail to address. To leverage the segment structure of piecewise stable context in real-world applications, in this paper, we propose a \textbf{Segmented Context Belief Augmented Deep~(SeCBAD)} RL method. Our method can jointly infer the belief distribution over latent context with the posterior over segment length and perform more accurate belief context inference with observed data within the current context segment. The inferred belief context can be leveraged to augment the state, leading to a policy that can adapt to abrupt variations in context. We demonstrate empirically that SeCBAD can infer context segment length accurately and outperform existing methods on a toy grid world environment and Mujuco tasks with piecewise-stable context.

Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to converge on best practices and limits the reproducibility of insights across studies. We present BMFM-RNA, an open-source, modular software package that unifies diverse TFM pretraining and fine-tuning objectives within a single framework. Leveraging this capability, we introduce a novel training objective, whole cell expression decoder (WCED), which captures global expression patterns using an autoencoder-like CLS bottleneck representation. In this paper, we describe the framework, supported input representations, and training objectives. We evaluated four model checkpoints pretrained on CELLxGENE using combinations of masked language modeling (MLM), WCED and multitask learning. Using the benchmarking capabilities of BMFM-RNA, we show that WCED-based models achieve performance that matches or exceeds state-of-the-art approaches like scGPT across more than a dozen datasets in both zero-shot and fine-tuning tasks. BMFM-RNA, available as part of the biomed-multi-omics project ( https://github.com/BiomedSciAI/biomed-multi-omic ), offers a reproducible foundation for systematic benchmarking and community-driven exploration of optimal TFM training strategies, enabling the development of more effective tools to leverage the latest advances in AI for understanding cell biology.