Daily Papers

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

Large Language Models (LLMs) have shown promise in accelerating the scientific research pipeline. A key capability for this process is the ability to generate novel research ideas, and prior studies have found settings in which LLM-generated research ideas were judged as more novel than human-expert ideas. However, a good idea should not simply appear to be novel, it should also result in better research after being executed. To test whether AI-generated ideas lead to better research outcomes, we conduct an execution study by recruiting 43 expert researchers to execute randomly-assigned ideas, either written by experts or generated by an LLM. Each expert spent over 100 hours implementing the idea and wrote a 4-page short paper to document the experiments. All the executed projects are then reviewed blindly by expert NLP researchers. Comparing the review scores of the same ideas before and after execution, the scores of the LLM-generated ideas decrease significantly more than expert-written ideas on all evaluation metrics (novelty, excitement, effectiveness, and overall; p < 0.05), closing the gap between LLM and human ideas observed at the ideation stage. When comparing the aggregated review scores from the execution study, we even observe that for many metrics there is a flip in rankings where human ideas score higher than LLM ideas. This ideation-execution gap highlights the limitations of current LLMs in generating truly effective research ideas and the challenge of evaluating research ideas in the absence of execution outcomes.

Recent advancements in large language models (LLMs) have sparked optimism about their potential to accelerate scientific discovery, with a growing number of works proposing research agents that autonomously generate and validate new ideas. Despite this, no evaluations have shown that LLM systems can take the very first step of producing novel, expert-level ideas, let alone perform the entire research process. We address this by establishing an experimental design that evaluates research idea generation while controlling for confounders and performs the first head-to-head comparison between expert NLP researchers and an LLM ideation agent. By recruiting over 100 NLP researchers to write novel ideas and blind reviews of both LLM and human ideas, we obtain the first statistically significant conclusion on current LLM capabilities for research ideation: we find LLM-generated ideas are judged as more novel (p < 0.05) than human expert ideas while being judged slightly weaker on feasibility. Studying our agent baselines closely, we identify open problems in building and evaluating research agents, including failures of LLM self-evaluation and their lack of diversity in generation. Finally, we acknowledge that human judgements of novelty can be difficult, even by experts, and propose an end-to-end study design which recruits researchers to execute these ideas into full projects, enabling us to study whether these novelty and feasibility judgements result in meaningful differences in research outcome.

Large Language Models (LLMs) generalize well across language tasks, but suffer from hallucinations and uninterpretability, making it difficult to assess their accuracy without ground-truth. Retrieval-Augmented Generation (RAG) models have been proposed to reduce hallucinations and provide provenance for how an answer was generated. Applying such models to the scientific literature may enable large-scale, systematic processing of scientific knowledge. We present PaperQA, a RAG agent for answering questions over the scientific literature. PaperQA is an agent that performs information retrieval across full-text scientific articles, assesses the relevance of sources and passages, and uses RAG to provide answers. Viewing this agent as a question answering model, we find it exceeds performance of existing LLMs and LLM agents on current science QA benchmarks. To push the field closer to how humans perform research on scientific literature, we also introduce LitQA, a more complex benchmark that requires retrieval and synthesis of information from full-text scientific papers across the literature. Finally, we demonstrate PaperQA's matches expert human researchers on LitQA.

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

Due to the remarkable capabilities of powerful Large Language Models (LLMs) in effectively following instructions, there has been a growing number of assistants in the community to assist humans. Recently, significant progress has been made in the development of Vision Language Models (VLMs), expanding the capabilities of LLMs and enabling them to execute more diverse instructions. However, it is foreseeable that models will likely need to handle tasks involving additional modalities such as speech, video, and others. This poses a particularly prominent challenge of dealing with the complexity of mixed modalities. To address this, we introduce a novel architecture called PILL: Plug Into LLM with adapter expert and attention gate to better decouple these complex modalities and leverage efficient fine-tuning. We introduce two modules: Firstly, utilizing Mixture-of-Modality-Adapter-Expert to independently handle different modalities, enabling better adaptation to downstream tasks while preserving the expressive capability of the original model. Secondly, by introducing Modality-Attention-Gating, which enables adaptive control of the contribution of modality tokens to the overall representation. In addition, we have made improvements to the Adapter to enhance its learning and expressive capabilities. Experimental results demonstrate that our approach exhibits competitive performance compared to other mainstream methods for modality fusion. For researchers interested in our work, we provide free access to the code and models at https://github.com/DsaltYfish/PILL.

Training a large and state-of-the-art machine learning model typically necessitates the use of large-scale datasets, which, in turn, makes the training and parameter-tuning process expensive and time-consuming. Some researchers opt to distil information from real-world datasets into tiny and compact synthetic datasets while maintaining their ability to train a well-performing model, hence proposing a data-efficient method known as Dataset Distillation (DD). Despite recent progress in this field, existing methods still underperform and cannot effectively replace large datasets. In this paper, unlike previous methods that focus solely on improving the efficacy of student distillation, we are the first to recognize the important interplay between expert and student. We argue the significant impact of expert smoothness when employing more potent expert trajectories in subsequent dataset distillation. Based on this, we introduce the integration of clipping loss and gradient penalty to regulate the rate of parameter changes in expert trajectories. Furthermore, in response to the sensitivity exhibited towards randomly initialized variables during distillation, we propose representative initialization for synthetic dataset and balanced inner-loop loss. Finally, we present two enhancement strategies, namely intermediate matching loss and weight perturbation, to mitigate the potential occurrence of cumulative errors. We conduct extensive experiments on datasets of different scales, sizes, and resolutions. The results demonstrate that the proposed method significantly outperforms prior methods.

Reading comprehension of legal text can be a particularly challenging task due to the length and complexity of legal clauses and a shortage of expert-annotated datasets. To address this challenge, we introduce the Merger Agreement Understanding Dataset (MAUD), an expert-annotated reading comprehension dataset based on the American Bar Association's 2021 Public Target Deal Points Study, with over 39,000 examples and over 47,000 total annotations. Our fine-tuned Transformer baselines show promising results, with models performing well above random on most questions. However, on a large subset of questions, there is still room for significant improvement. As the only expert-annotated merger agreement dataset, MAUD is valuable as a benchmark for both the legal profession and the NLP community.

Breast cancer is a major cause of cancer death among women, emphasising the importance of early detection for improved treatment outcomes and quality of life. Mammography, the primary diagnostic imaging test, poses challenges due to the high variability and patterns in mammograms. Double reading of mammograms is recommended in many screening programs to improve diagnostic accuracy but increases radiologists' workload. Researchers explore Machine Learning models to support expert decision-making. Stand-alone models have shown comparable or superior performance to radiologists, but some studies note decreased sensitivity with multiple datasets, indicating the need for high generalisation and robustness models. This work devises MammoDG, a novel deep-learning framework for generalisable and reliable analysis of cross-domain multi-center mammography data. MammoDG leverages multi-view mammograms and a novel contrastive mechanism to enhance generalisation capabilities. Extensive validation demonstrates MammoDG's superiority, highlighting the critical importance of domain generalisation for trustworthy mammography analysis in imaging protocol variations.

Large language models (LLMs) offer an inexpensive yet powerful way to annotate text, but are often inconsistent when compared with experts. These errors can bias downstream estimates of population parameters such as regression coefficients and causal effects. To mitigate this bias, researchers have developed debiasing methods such as Design-based Supervised Learning (DSL) and Prediction-Powered Inference (PPI), which promise valid estimation by combining LLM annotations with a limited number of expensive expert annotations. Although these methods produce consistent estimates under theoretical assumptions, it is unknown how they compare in finite samples of sizes encountered in applied research. We make two contributions: First, we study how each method's performance scales with the number of expert annotations, highlighting regimes where LLM bias or limited expert labels significantly affect results. Second, we compare DSL and PPI across a range of tasks, finding that although both achieve low bias with large datasets, DSL often outperforms PPI on bias reduction and empirical efficiency, but its performance is less consistent across datasets. Our findings indicate that there is a bias-variance tradeoff at the level of debiasing methods, calling for more research on developing metrics for quantifying their efficiency in finite samples.

Recent large language models such as Gemini-1.5, DeepSeek-V3, and Llama-4 increasingly adopt Mixture-of-Experts (MoE) architectures, which offer strong efficiency-performance trade-offs by activating only a fraction of the model per token. Yet academic researchers still lack a fully open, end-to-end MoE platform for investigating scaling, routing, and expert behavior. We release FLAME-MoE, a completely open-source research suite composed of seven decoder-only models, ranging from 38M to 1.7B active parameters, whose architecture--64 experts with top-8 gating and 2 shared experts--closely reflects modern production LLMs. All training data pipelines, scripts, logs, and checkpoints are publicly available to enable reproducible experimentation. Across six evaluation tasks, FLAME-MoE improves average accuracy by up to 3.4 points over dense baselines trained with identical FLOPs. Leveraging full training trace transparency, we present initial analyses showing that (i) experts increasingly specialize on distinct token subsets, (ii) co-activation matrices remain sparse, reflecting diverse expert usage, and (iii) routing behavior stabilizes early in training. All code, training logs, and model checkpoints are available at https://github.com/cmu-flame/FLAME-MoE.

We present Welzijn.AI as new digital solution for monitoring (mental) well-being in elderly populations, and illustrate how development of systems like Welzijn.AI can align with guidelines on responsible AI development. Three evaluations with different stakeholders were designed to disclose new perspectives on the strengths, weaknesses, design characteristics, and value requirements of Welzijn.AI. Evaluations concerned expert panels and involved patient federations, general practitioners, researchers, and the elderly themselves. Panels concerned interviews, a co-creation session, and feedback on a proof-of-concept implementation. Interview results were summarized in terms of Welzijn.AI's strengths, weaknesses, opportunities and threats. The co-creation session ranked a variety of value requirements of Welzijn.AI with the Hundred Dollar Method. User evaluation comprised analysing proportions of (dis)agreement on statements targeting Welzijn.AI's design characteristics, and ranking desired social characteristics. Experts in the panel interviews acknowledged Welzijn.AI's potential to combat loneliness and extract patterns from elderly behaviour. The proof-of-concept evaluation complemented the design characteristics most appealing to the elderly to potentially achieve this: empathetic and varying interactions. Stakeholders also link the technology to the implementation context: it could help activate an individual's social network, but support should also be available to empower users. Yet, non-elderly and elderly experts also disclose challenges in properly understanding the application; non-elderly experts also highlight issues concerning privacy. In sum, incorporating all stakeholder perspectives in system development remains challenging. Still, our results benefit researchers, policy makers, and health professionals that aim to improve elderly care with technology.

Evaluating long-form responses to research queries heavily relies on expert annotators, restricting attention to areas like AI where researchers can conveniently enlist colleagues. Yet, research expertise is widespread: survey articles synthesize knowledge distributed across the literature. We introduce ResearchQA, a resource for evaluating LLM systems by distilling survey articles from 75 research fields into 21K queries and 160K rubric items. Each rubric, derived jointly with queries from survey sections, lists query-specific answer evaluation criteria, i.e., citing papers, making explanations, and describing limitations. Assessments by 31 Ph.D. annotators in 8 fields indicate 96% of queries support Ph.D. information needs and 87% of rubric items should be addressed in system responses by a sentence or more. Using our rubrics, we are able to construct an automatic pairwise judge obtaining 74% agreement with expert judgments. We leverage ResearchQA to analyze competency gaps in 18 systems in over 7.6K pairwise evaluations. No parametric or retrieval-augmented system we evaluate exceeds 70% on covering rubric items, and the highest-ranking agentic system shows 75% coverage. Error analysis reveals that the highest-ranking system fully addresses less than 11% of citation rubric items, 48% of limitation items, and 49% of comparison items. We release our data to facilitate more comprehensive multi-field evaluations.

Self-supervised learning has brought about a revolutionary paradigm shift in various computing domains, including NLP, vision, and biology. Recent approaches involve pre-training transformer models on vast amounts of unlabeled data, serving as a starting point for efficiently solving downstream tasks. In the realm of reinforcement learning, researchers have recently adapted these approaches by developing models pre-trained on expert trajectories, enabling them to address a wide range of tasks, from robotics to recommendation systems. However, existing methods mostly rely on intricate pre-training objectives tailored to specific downstream applications. This paper presents a comprehensive investigation of models we refer to as Pretrained Action-State Transformer Agents (PASTA). Our study uses a unified methodology and covers an extensive set of general downstream tasks including behavioral cloning, offline RL, sensor failure robustness, and dynamics change adaptation. Our goal is to systematically compare various design choices and provide valuable insights to practitioners for building robust models. Key highlights of our study include tokenization at the action and state component level, using fundamental pre-training objectives like next token prediction, training models across diverse domains simultaneously, and using parameter efficient fine-tuning (PEFT). The developed models in our study contain fewer than 10 million parameters and the application of PEFT enables fine-tuning of fewer than 10,000 parameters during downstream adaptation, allowing a broad community to use these models and reproduce our experiments. We hope that this study will encourage further research into the use of transformers with first-principles design choices to represent RL trajectories and contribute to robust policy learning.

Data-driven scientific discovery requires the iterative integration of scientific domain knowledge, statistical expertise, and an understanding of data semantics to make nuanced analytical decisions, e.g., about which variables, transformations, and statistical models to consider. LM-based agents equipped with planning, memory, and code execution capabilities have the potential to support data-driven science. However, evaluating agents on such open-ended tasks is challenging due to multiple valid approaches, partially correct steps, and different ways to express the same decisions. To address these challenges, we present BLADE, a benchmark to automatically evaluate agents' multifaceted approaches to open-ended research questions. BLADE consists of 12 datasets and research questions drawn from existing scientific literature, with ground truth collected from independent analyses by expert data scientists and researchers. To automatically evaluate agent responses, we developed corresponding computational methods to match different representations of analyses to this ground truth. Though language models possess considerable world knowledge, our evaluation shows that they are often limited to basic analyses. However, agents capable of interacting with the underlying data demonstrate improved, but still non-optimal, diversity in their analytical decision making. Our work enables the evaluation of agents for data-driven science and provides researchers deeper insights into agents' analysis approaches.

International institutions may have an important role to play in ensuring advanced AI systems benefit humanity. International collaborations can unlock AI's ability to further sustainable development, and coordination of regulatory efforts can reduce obstacles to innovation and the spread of benefits. Conversely, the potential dangerous capabilities of powerful and general-purpose AI systems create global externalities in their development and deployment, and international efforts to further responsible AI practices could help manage the risks they pose. This paper identifies a set of governance functions that could be performed at an international level to address these challenges, ranging from supporting access to frontier AI systems to setting international safety standards. It groups these functions into four institutional models that exhibit internal synergies and have precedents in existing organizations: 1) a Commission on Frontier AI that facilitates expert consensus on opportunities and risks from advanced AI, 2) an Advanced AI Governance Organization that sets international standards to manage global threats from advanced models, supports their implementation, and possibly monitors compliance with a future governance regime, 3) a Frontier AI Collaborative that promotes access to cutting-edge AI, and 4) an AI Safety Project that brings together leading researchers and engineers to further AI safety research. We explore the utility of these models and identify open questions about their viability.