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Jul 29

Deduction under Perturbed Evidence: Probing Student Simulation Capabilities of Large Language Models

We explore whether Large Language Models (LLMs) are capable of logical reasoning with distorted facts, which we call Deduction under Perturbed Evidence (DUPE). DUPE presents a unique challenge to LLMs since they typically rely on their parameters, which encode mostly accurate information, to reason and make inferences. However, in DUPE, LLMs must reason over manipulated or falsified evidence present in their prompts, which can result in false conclusions that are valid only under the manipulated evidence. Our goal with DUPE is to determine whether LLMs can arrive at these false conclusions and identify whether the dominant factor influencing the deduction process is the encoded data in the parameters or the manipulated evidence in the prompts. To evaluate the DUPE capabilities of LLMs, we create a DUPEd version of the StrategyQA dataset, where facts are manipulated to reverse the answer to the question. Our findings show that even the most advanced GPT models struggle to reason on manipulated facts - showcasing poor DUPE skills - with accuracy dropping by 45% compared to the original dataset. We also investigate prompt settings inspired from student simulation models, which mitigate the accuracy drop to some extent. Our findings have practical implications for understanding the performance of LLMs in real-world applications such as student simulation models that involve reasoning over inaccurate information.

Towards a Deeper Understanding of Reasoning Capabilities in Large Language Models

While large language models demonstrate impressive performance on static benchmarks, the true potential of large language models as self-learning and reasoning agents in dynamic environments remains unclear. This study systematically evaluates the efficacy of self-reflection, heuristic mutation, and planning as prompting techniques to test the adaptive capabilities of agents. We conduct experiments with various open-source language models in dynamic environments and find that larger models generally outperform smaller ones, but that strategic prompting can close this performance gap. Second, a too-long prompt can negatively impact smaller models on basic reactive tasks, while larger models show more robust behaviour. Third, advanced prompting techniques primarily benefit smaller models on complex games, but offer less improvement for already high-performing large language models. Yet, we find that advanced reasoning methods yield highly variable outcomes: while capable of significantly improving performance when reasoning and decision-making align, they also introduce instability and can lead to big performance drops. Compared to human performance, our findings reveal little evidence of true emergent reasoning. Instead, large language model performance exhibits persistent limitations in crucial areas such as planning, reasoning, and spatial coordination, suggesting that current-generation large language models still suffer fundamental shortcomings that may not be fully overcome through self-reflective prompting alone. Reasoning is a multi-faceted task, and while reasoning methods like Chain of thought improves multi-step reasoning on math word problems, our findings using dynamic benchmarks highlight important shortcomings in general reasoning capabilities, indicating a need to move beyond static benchmarks to capture the complexity of reasoning.

Language Models Are Capable of Metacognitive Monitoring and Control of Their Internal Activations

Large language models (LLMs) can sometimes report the strategies they actually use to solve tasks, but they can also fail to do so. This suggests some degree of metacognition -- the capacity to monitor one's own cognitive processes for subsequent reporting and self-control. Metacognitive abilities enhance AI capabilities but raise safety concerns, as models might obscure their internal processes to evade neural-activation-based oversight mechanisms designed to detect harmful behaviors. Given society's increased reliance on these models, it is critical that we understand the limits of their metacognitive abilities, particularly their ability to monitor their internal activations. To address this, we introduce a neuroscience-inspired neurofeedback paradigm designed to quantify the ability of LLMs to explicitly report and control their activation patterns. By presenting models with sentence-label pairs where labels correspond to sentence-elicited internal activations along specific directions in the neural representation space, we demonstrate that LLMs can learn to report and control these activations. The performance varies with several factors: the number of example pairs provided, the semantic interpretability of the target neural direction, and the variance explained by that direction. These results reveal a "metacognitive space" with dimensionality much lower than the model's neural space, suggesting LLMs can monitor only a subset of their neural mechanisms. Our findings provide empirical evidence quantifying metacognitive capabilities in LLMs, with significant implications for AI safety.

Retrieval Augmented Fact Verification by Synthesizing Contrastive Arguments

The rapid propagation of misinformation poses substantial risks to public interest. To combat misinformation, large language models (LLMs) are adapted to automatically verify claim credibility. Nevertheless, existing methods heavily rely on the embedded knowledge within LLMs and / or black-box APIs for evidence collection, leading to subpar performance with smaller LLMs or upon unreliable context. In this paper, we propose retrieval augmented fact verification through the synthesis of contrasting arguments (RAFTS). Upon input claims, RAFTS starts with evidence retrieval, where we design a retrieval pipeline to collect and re-rank relevant documents from verifiable sources. Then, RAFTS forms contrastive arguments (i.e., supporting or refuting) conditioned on the retrieved evidence. In addition, RAFTS leverages an embedding model to identify informative demonstrations, followed by in-context prompting to generate the prediction and explanation. Our method effectively retrieves relevant documents as evidence and evaluates arguments from varying perspectives, incorporating nuanced information for fine-grained decision-making. Combined with informative in-context examples as prior, RAFTS achieves significant improvements to supervised and LLM baselines without complex prompts. We demonstrate the effectiveness of our method through extensive experiments, where RAFTS can outperform GPT-based methods with a significantly smaller 7B LLM.

Can AI Validate Science? Benchmarking LLMs for Accurate Scientific Claim rightarrow Evidence Reasoning

Large language models (LLMs) are increasingly being used for complex research tasks such as literature review, idea generation, and scientific paper analysis, yet their ability to truly understand and process the intricate relationships within complex research papers, such as the logical links between claims and supporting evidence remains largely unexplored. In this study, we present CLAIM-BENCH, a comprehensive benchmark for evaluating LLMs' capabilities in scientific claim-evidence extraction and validation, a task that reflects deeper comprehension of scientific argumentation. We systematically compare three approaches which are inspired by divide and conquer approaches, across six diverse LLMs, highlighting model-specific strengths and weaknesses in scientific comprehension. Through evaluation involving over 300 claim-evidence pairs across multiple research domains, we reveal significant limitations in LLMs' ability to process complex scientific content. Our results demonstrate that closed-source models like GPT-4 and Claude consistently outperform open-source counterparts in precision and recall across claim-evidence identification tasks. Furthermore, strategically designed three-pass and one-by-one prompting approaches significantly improve LLMs' abilities to accurately link dispersed evidence with claims, although this comes at increased computational cost. CLAIM-BENCH sets a new standard for evaluating scientific comprehension in LLMs, offering both a diagnostic tool and a path forward for building systems capable of deeper, more reliable reasoning across full-length papers.

Retrieval-Augmented Generation by Evidence Retroactivity in LLMs

Retrieval-augmented generation has gained significant attention due to its ability to integrate relevant external knowledge, enhancing the accuracy and reliability of the LLMs' responses. Most of the existing methods apply a dynamic multiple retrieval-generating process, to address multi-hop complex questions by decomposing them into sub-problems. However, these methods rely on an unidirectional forward reasoning paradigm, where errors from insufficient reasoning steps or inherent flaws in current retrieval systems are irreversible, potentially derailing the entire reasoning chain. For the first time, this work introduces Retroactive Retrieval-Augmented Generation (RetroRAG), a novel framework to build a retroactive reasoning paradigm. RetroRAG revises and updates the evidence, redirecting the reasoning chain to the correct direction. RetroRAG constructs an evidence-collation-discovery framework to search, generate, and refine credible evidence. It synthesizes inferential evidence related to the key entities in the question from the existing source knowledge and formulates search queries to uncover additional information. As new evidence is found, RetroRAG continually updates and organizes this information, enhancing its ability to locate further necessary evidence. Paired with an Answerer to generate and evaluate outputs, RetroRAG is capable of refining its reasoning process iteratively until a reliable answer is obtained. Empirical evaluations show that RetroRAG significantly outperforms existing methods.

R2MED: A Benchmark for Reasoning-Driven Medical Retrieval

Current medical retrieval benchmarks primarily emphasize lexical or shallow semantic similarity, overlooking the reasoning-intensive demands that are central to clinical decision-making. In practice, physicians often retrieve authoritative medical evidence to support diagnostic hypotheses. Such evidence typically aligns with an inferred diagnosis rather than the surface form of a patient's symptoms, leading to low lexical or semantic overlap between queries and relevant documents. To address this gap, we introduce R2MED, the first benchmark explicitly designed for reasoning-driven medical retrieval. It comprises 876 queries spanning three tasks: Q&A reference retrieval, clinical evidence retrieval, and clinical case retrieval. These tasks are drawn from five representative medical scenarios and twelve body systems, capturing the complexity and diversity of real-world medical information needs. We evaluate 15 widely-used retrieval systems on R2MED and find that even the best model achieves only 31.4 nDCG@10, demonstrating the benchmark's difficulty. Classical re-ranking and generation-augmented retrieval methods offer only modest improvements. Although large reasoning models improve performance via intermediate inference generation, the best results still peak at 41.4 nDCG@10. These findings underscore a substantial gap between current retrieval techniques and the reasoning demands of real clinical tasks. We release R2MED as a challenging benchmark to foster the development of next-generation medical retrieval systems with enhanced reasoning capabilities. Data and code are available at https://github.com/R2MED/R2MED

Evidence Inference 2.0: More Data, Better Models

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

SemEval-2023 Task 7: Multi-Evidence Natural Language Inference for Clinical Trial Data

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

Tool Calling: Enhancing Medication Consultation via Retrieval-Augmented Large Language Models

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

The Ideation-Execution Gap: Execution Outcomes of LLM-Generated versus Human Research Ideas

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.

DetectiveQA: Evaluating Long-Context Reasoning on Detective Novels

With the rapid advancement of Large Language Models (LLMs), long-context information understanding and processing have become a hot topic in academia and industry. However, benchmarks for evaluating the ability of LLMs to handle long-context information do not seem to have kept pace with the development of LLMs. Despite the emergence of various long-context evaluation benchmarks, the types of capability assessed are still limited, without new capability dimensions. In this paper, we introduce DetectiveQA, a narrative reasoning benchmark featured with an average context length of over 100K tokens. DetectiveQA focuses on evaluating the long-context reasoning ability of LLMs, which not only requires a full understanding of context but also requires extracting important evidences from the context and reasoning according to extracted evidences to answer the given questions. This is a new dimension of capability evaluation, which is more in line with the current intelligence level of LLMs. We use detective novels as data sources, which naturally have various reasoning elements. Finally, we manually annotated 600 questions in Chinese and then also provided an English edition of the context information and questions. We evaluate many long-context LLMs on DetectiveQA, including commercial and open-sourced models, and the results indicate that existing long-context LLMs still require significant advancements to effectively process true long-context dependency questions.

ECtHR-PCR: A Dataset for Precedent Understanding and Prior Case Retrieval in the European Court of Human Rights

In common law jurisdictions, legal practitioners rely on precedents to construct arguments, in line with the doctrine of stare decisis. As the number of cases grow over the years, prior case retrieval (PCR) has garnered significant attention. Besides lacking real-world scale, existing PCR datasets do not simulate a realistic setting, because their queries use complete case documents while only masking references to prior cases. The query is thereby exposed to legal reasoning not yet available when constructing an argument for an undecided case as well as spurious patterns left behind by citation masks, potentially short-circuiting a comprehensive understanding of case facts and legal principles. To address these limitations, we introduce a PCR dataset based on judgements from the European Court of Human Rights (ECtHR), which explicitly separate facts from arguments and exhibit precedential practices, aiding us to develop this PCR dataset to foster systems' comprehensive understanding. We benchmark different lexical and dense retrieval approaches with various negative sampling strategies, adapting them to deal with long text sequences using hierarchical variants. We found that difficulty-based negative sampling strategies were not effective for the PCR task, highlighting the need for investigation into domain-specific difficulty criteria. Furthermore, we observe performance of the dense models degrade with time and calls for further research into temporal adaptation of retrieval models. Additionally, we assess the influence of different views , Halsbury's and Goodhart's, in practice in ECtHR jurisdiction using PCR task.

Toward Reliable Biomedical Hypothesis Generation: Evaluating Truthfulness and Hallucination in Large Language Models

Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful biomedical hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.

REAPER: Reasoning based Retrieval Planning for Complex RAG Systems

Complex dialog systems often use retrieved evidence to facilitate factual responses. Such RAG (Retrieval Augmented Generation) systems retrieve from massive heterogeneous data stores that are usually architected as multiple indexes or APIs instead of a single monolithic source. For a given query, relevant evidence needs to be retrieved from one or a small subset of possible retrieval sources. Complex queries can even require multi-step retrieval. For example, a conversational agent on a retail site answering customer questions about past orders will need to retrieve the appropriate customer order first and then the evidence relevant to the customer's question in the context of the ordered product. Most RAG Agents handle such Chain-of-Thought (CoT) tasks by interleaving reasoning and retrieval steps. However, each reasoning step directly adds to the latency of the system. For large models (>100B parameters) this latency cost is significant -- in the order of multiple seconds. Multi-agent systems may classify the query to a single Agent associated with a retrieval source, though this means that a (small) classification model dictates the performance of a large language model. In this work we present REAPER (REAsoning-based PlannER) - an LLM based planner to generate retrieval plans in conversational systems. We show significant gains in latency over Agent-based systems and are able to scale easily to new and unseen use cases as compared to classification-based planning. Though our method can be applied to any RAG system, we show our results in the context of Rufus -- Amazon's conversational shopping assistant.

MME-Reasoning: A Comprehensive Benchmark for Logical Reasoning in MLLMs

Logical reasoning is a fundamental aspect of human intelligence and an essential capability for multimodal large language models (MLLMs). Despite the significant advancement in multimodal reasoning, existing benchmarks fail to comprehensively evaluate their reasoning abilities due to the lack of explicit categorization for logical reasoning types and an unclear understanding of reasoning. To address these issues, we introduce MME-Reasoning, a comprehensive benchmark designed to evaluate the reasoning ability of MLLMs, which covers all three types of reasoning (i.e., inductive, deductive, and abductive) in its questions. We carefully curate the data to ensure that each question effectively evaluates reasoning ability rather than perceptual skills or knowledge breadth, and extend the evaluation protocols to cover the evaluation of diverse questions. Our evaluation reveals substantial limitations of state-of-the-art MLLMs when subjected to holistic assessments of logical reasoning capabilities. Even the most advanced MLLMs show limited performance in comprehensive logical reasoning, with notable performance imbalances across reasoning types. In addition, we conducted an in-depth analysis of approaches such as ``thinking mode'' and Rule-based RL, which are commonly believed to enhance reasoning abilities. These findings highlight the critical limitations and performance imbalances of current MLLMs in diverse logical reasoning scenarios, providing comprehensive and systematic insights into the understanding and evaluation of reasoning capabilities.

PRobELM: Plausibility Ranking Evaluation for Language Models

This paper introduces PRobELM (Plausibility Ranking Evaluation for Language Models), a benchmark designed to assess language models' ability to discern more plausible from less plausible scenarios through their parametric knowledge. While benchmarks such as TruthfulQA emphasise factual accuracy or truthfulness, and others such as COPA explore plausible scenarios without explicitly incorporating world knowledge, PRobELM seeks to bridge this gap by evaluating models' capabilities to prioritise plausible scenarios that leverage world knowledge over less plausible alternatives. This design allows us to assess the potential of language models for downstream use cases such as literature-based discovery where the focus is on identifying information that is likely but not yet known. Our benchmark is constructed from a dataset curated from Wikidata edit histories, tailored to align the temporal bounds of the training data for the evaluated models. PRobELM facilitates the evaluation of language models across multiple prompting types, including statement, text completion, and question-answering. Experiments with 10 models of various sizes and architectures on the relationship between model scales, training recency, and plausibility performance, reveal that factual accuracy does not directly correlate with plausibility performance and that up-to-date training data enhances plausibility assessment across different model architectures.

From Questions to Clinical Recommendations: Large Language Models Driving Evidence-Based Clinical Decision Making

Clinical evidence, derived from rigorous research and data analysis, provides healthcare professionals with reliable scientific foundations for informed decision-making. Integrating clinical evidence into real-time practice is challenging due to the enormous workload, complex professional processes, and time constraints. This highlights the need for tools that automate evidence synthesis to support more efficient and accurate decision making in clinical settings. This study introduces Quicker, an evidence-based clinical decision support system powered by large language models (LLMs), designed to automate evidence synthesis and generate clinical recommendations modeled after standard clinical guideline development processes. Quicker implements a fully automated chain that covers all phases, from questions to clinical recommendations, and further enables customized decision-making through integrated tools and interactive user interfaces. To evaluate Quicker's capabilities, we developed the Q2CRBench-3 benchmark dataset, based on clinical guideline development records for three different diseases. Experimental results highlighted Quicker's strong performance, with fine-grained question decomposition tailored to user preferences, retrieval sensitivities comparable to human experts, and literature screening performance approaching comprehensive inclusion of relevant studies. In addition, Quicker-assisted evidence assessment effectively supported human reviewers, while Quicker's recommendations were more comprehensive and logically coherent than those of clinicians. In system-level testing, collaboration between a single reviewer and Quicker reduced the time required for recommendation development to 20-40 minutes. In general, our findings affirm the potential of Quicker to help physicians make quicker and more reliable evidence-based clinical decisions.

EAIRA: Establishing a Methodology for Evaluating AI Models as Scientific Research Assistants

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

The Trilemma of Truth in Large Language Models

We often attribute human characteristics to large language models (LLMs) and claim that they "know" certain things. LLMs have an internal probabilistic knowledge that represents information retained during training. How can we assess the veracity of this knowledge? We examine two common methods for probing the veracity of LLMs and discover several assumptions that are flawed. To address these flawed assumptions, we introduce sAwMIL (short for Sparse Aware Multiple-Instance Learning), a probing method that utilizes the internal activations of LLMs to separate statements into true, false, and neither. sAwMIL is based on multiple-instance learning and conformal prediction. We evaluate sAwMIL on 5 validity criteria across 16 open-source LLMs, including both default and chat-based variants, as well as on 3 new datasets. Among the insights we provide are: (1) the veracity signal is often concentrated in the third quarter of an LLM's depth; (2) truth and falsehood signals are not always symmetric; (3) linear probes perform better on chat models than on default models; (4) nonlinear probes may be required to capture veracity signals for some LLMs with reinforcement learning from human feedback or knowledge distillation; and (5) LLMs capture a third type of signal that is distinct from true and false and is neither true nor false. These findings provide a reliable method for verifying what LLMs "know" and how certain they are of their probabilistic internal knowledge.

Pipeline and Dataset Generation for Automated Fact-checking in Almost Any Language

This article presents a pipeline for automated fact-checking leveraging publicly available Language Models and data. The objective is to assess the accuracy of textual claims using evidence from a ground-truth evidence corpus. The pipeline consists of two main modules -- the evidence retrieval and the claim veracity evaluation. Our primary focus is on the ease of deployment in various languages that remain unexplored in the field of automated fact-checking. Unlike most similar pipelines, which work with evidence sentences, our pipeline processes data on a paragraph level, simplifying the overall architecture and data requirements. Given the high cost of annotating language-specific fact-checking training data, our solution builds on the Question Answering for Claim Generation (QACG) method, which we adapt and use to generate the data for all models of the pipeline. Our strategy enables the introduction of new languages through machine translation of only two fixed datasets of moderate size. Subsequently, any number of training samples can be generated based on an evidence corpus in the target language. We provide open access to all data and fine-tuned models for Czech, English, Polish, and Slovak pipelines, as well as to our codebase that may be used to reproduce the results.We comprehensively evaluate the pipelines for all four languages, including human annotations and per-sample difficulty assessment using Pointwise V-information. The presented experiments are based on full Wikipedia snapshots to promote reproducibility. To facilitate implementation and user interaction, we develop the FactSearch application featuring the proposed pipeline and the preliminary feedback on its performance.

MOOSE-Chem: Large Language Models for Rediscovering Unseen Chemistry Scientific Hypotheses

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

Worse than Zero-shot? A Fact-Checking Dataset for Evaluating the Robustness of RAG Against Misleading Retrievals

Retrieval-augmented generation (RAG) has shown impressive capabilities in mitigating hallucinations in large language models (LLMs). However, LLMs struggle to handle misleading retrievals and often fail to maintain their own reasoning when exposed to conflicting or selectively-framed evidence, making them vulnerable to real-world misinformation. In such real-world retrieval scenarios, misleading and conflicting information is rampant, particularly in the political domain, where evidence is often selectively framed, incomplete, or polarized. However, existing RAG benchmarks largely assume a clean retrieval setting, where models succeed by accurately retrieving and generating answers from gold-standard documents. This assumption fails to align with real-world conditions, leading to an overestimation of RAG system performance. To bridge this gap, we introduce RAGuard, a fact-checking dataset designed to evaluate the robustness of RAG systems against misleading retrievals. Unlike prior benchmarks that rely on synthetic noise, our dataset constructs its retrieval corpus from Reddit discussions, capturing naturally occurring misinformation. It categorizes retrieved evidence into three types: supporting, misleading, and irrelevant, providing a realistic and challenging testbed for assessing how well RAG systems navigate different retrieval information. Our benchmark experiments reveal that when exposed to misleading retrievals, all tested LLM-powered RAG systems perform worse than their zero-shot baselines (i.e., no retrieval at all), highlighting their susceptibility to noisy environments. To the best of our knowledge, RAGuard is the first benchmark to systematically assess RAG robustness against misleading evidence. We expect this benchmark will drive future research toward improving RAG systems beyond idealized datasets, making them more reliable for real-world applications.

SUPER: Evaluating Agents on Setting Up and Executing Tasks from Research Repositories

Given that Large Language Models (LLMs) have made significant progress in writing code, can they now be used to autonomously reproduce results from research repositories? Such a capability would be a boon to the research community, helping researchers validate, understand, and extend prior work. To advance towards this goal, we introduce SUPER, the first benchmark designed to evaluate the capability of LLMs in setting up and executing tasks from research repositories. SUPERaims to capture the realistic challenges faced by researchers working with Machine Learning (ML) and Natural Language Processing (NLP) research repositories. Our benchmark comprises three distinct problem sets: 45 end-to-end problems with annotated expert solutions, 152 sub problems derived from the expert set that focus on specific challenges (e.g., configuring a trainer), and 602 automatically generated problems for larger-scale development. We introduce various evaluation measures to assess both task success and progress, utilizing gold solutions when available or approximations otherwise. We show that state-of-the-art approaches struggle to solve these problems with the best model (GPT-4o) solving only 16.3% of the end-to-end set, and 46.1% of the scenarios. This illustrates the challenge of this task, and suggests that SUPER can serve as a valuable resource for the community to make and measure progress.

Don't Take the Premise for Granted: Evaluating the Premise Critique Ability of Large Language Models

Large language models (LLMs) have witnessed rapid advancements, demonstrating remarkable capabilities. However, a notable vulnerability persists: LLMs often uncritically accept flawed or contradictory premises, leading to inefficient reasoning and unreliable outputs. This emphasizes the significance of possessing the Premise Critique Ability for LLMs, defined as the capacity to proactively identify and articulate errors in input premises. Most existing studies assess LLMs' reasoning ability in ideal settings, largely ignoring their vulnerabilities when faced with flawed premises. Thus, we introduce the Premise Critique Bench (PCBench), designed by incorporating four error types across three difficulty levels, paired with multi-faceted evaluation metrics. We conducted systematic evaluations of 15 representative LLMs. Our findings reveal: (1) Most models rely heavily on explicit prompts to detect errors, with limited autonomous critique; (2) Premise critique ability depends on question difficulty and error type, with direct contradictions being easier to detect than complex or procedural errors; (3) Reasoning ability does not consistently correlate with the premise critique ability; (4) Flawed premises trigger overthinking in reasoning models, markedly lengthening responses due to repeated attempts at resolving conflicts. These insights underscore the urgent need to enhance LLMs' proactive evaluation of input validity, positioning premise critique as a foundational capability for developing reliable, human-centric systems. The code is available at https://github.com/MLGroupJLU/Premise_Critique.

A Comprehensive Evaluation of GPT-4V on Knowledge-Intensive Visual Question Answering

The emergence of multimodal large models (MLMs) has significantly advanced the field of visual understanding, offering remarkable capabilities in the realm of visual question answering (VQA). Yet, the true challenge lies in the domain of knowledge-intensive VQA tasks, which necessitate not just recognition of visual elements, but also a deep comprehension of the visual information in conjunction with a vast repository of learned knowledge. To uncover such capabilities of MLMs, particularly the newly introduced GPT-4V and Gemini, we provide an in-depth evaluation from three perspectives: 1) Commonsense Knowledge, which assesses how well models can understand visual cues and connect to general knowledge; 2) Fine-grained World Knowledge, which tests the model's skill in reasoning out specific knowledge from images, showcasing their proficiency across various specialized fields; 3) Comprehensive Knowledge with Decision-making Rationales, which examines model's capability to provide logical explanations for its inference, facilitating a deeper analysis from the interpretability perspective. Additionally, we utilize a visual knowledge-enhanced training strategy and multimodal retrieval-augmented generation approach to enhance MLMs, highlighting the future need for advancements in this research direction. Extensive experiments indicate that: a) GPT-4V demonstrates enhanced explanation generation when using composite images as few-shots; b) GPT-4V and other MLMs produce severe hallucinations when dealing with world knowledge; c) Visual knowledge enhanced training and prompting technicals present potential to improve performance. Codes: https://github.com/HITsz-TMG/Cognitive-Visual-Language-Mapper

SciKnowEval: Evaluating Multi-level Scientific Knowledge of Large Language Models

The burgeoning utilization of Large Language Models (LLMs) in scientific research necessitates advanced benchmarks capable of evaluating their understanding and application of scientific knowledge comprehensively. To address this need, we introduce the SciKnowEval benchmark, a novel framework that systematically evaluates LLMs across five progressive levels of scientific knowledge: studying extensively, inquiring earnestly, thinking profoundly, discerning clearly, and practicing assiduously. These levels aim to assess the breadth and depth of scientific knowledge in LLMs, including knowledge coverage, inquiry and exploration capabilities, reflection and reasoning abilities, ethic and safety considerations, as well as practice proficiency. Specifically, we take biology and chemistry as the two instances of SciKnowEval and construct a dataset encompassing 50K multi-level scientific problems and solutions. By leveraging this dataset, we benchmark 20 leading open-source and proprietary LLMs using zero-shot and few-shot prompting strategies. The results reveal that despite achieving state-of-the-art performance, the proprietary LLMs still have considerable room for improvement, particularly in addressing scientific computations and applications. We anticipate that SciKnowEval will establish a comprehensive standard for benchmarking LLMs in science research and discovery, and promote the development of LLMs that integrate scientific knowledge with strong safety awareness. The dataset and code are publicly available at https://github.com/hicai-zju/sciknoweval .

Natural Logic-guided Autoregressive Multi-hop Document Retrieval for Fact Verification

A key component of fact verification is thevevidence retrieval, often from multiple documents. Recent approaches use dense representations and condition the retrieval of each document on the previously retrieved ones. The latter step is performed over all the documents in the collection, requiring storing their dense representations in an index, thus incurring a high memory footprint. An alternative paradigm is retrieve-and-rerank, where documents are retrieved using methods such as BM25, their sentences are reranked, and further documents are retrieved conditioned on these sentences, reducing the memory requirements. However, such approaches can be brittle as they rely on heuristics and assume hyperlinks between documents. We propose a novel retrieve-and-rerank method for multi-hop retrieval, that consists of a retriever that jointly scores documents in the knowledge source and sentences from previously retrieved documents using an autoregressive formulation and is guided by a proof system based on natural logic that dynamically terminates the retrieval process if the evidence is deemed sufficient. This method is competitive with current state-of-the-art methods on FEVER, HoVer and FEVEROUS-S, while using 5 to 10 times less memory than competing systems. Evaluation on an adversarial dataset indicates improved stability of our approach compared to commonly deployed threshold-based methods. Finally, the proof system helps humans predict model decisions correctly more often than using the evidence alone.

ScholarSearch: Benchmarking Scholar Searching Ability of LLMs

Large Language Models (LLMs)' search capabilities have garnered significant attention. Existing benchmarks, such as OpenAI's BrowseComp, primarily focus on general search scenarios and fail to adequately address the specific demands of academic search. These demands include deeper literature tracing and organization, professional support for academic databases, the ability to navigate long-tail academic knowledge, and ensuring academic rigor. Here, we proposed ScholarSearch, the first dataset specifically designed to evaluate the complex information retrieval capabilities of Large Language Models (LLMs) in academic research. ScholarSearch possesses the following key characteristics: Academic Practicality, where question content closely mirrors real academic learning and research environments, avoiding deliberately misleading models; High Difficulty, with answers that are challenging for single models (e.g., Grok DeepSearch or Gemini Deep Research) to provide directly, often requiring at least three deep searches to derive; Concise Evaluation, where limiting conditions ensure answers are as unique as possible, accompanied by clear sources and brief solution explanations, greatly facilitating subsequent audit and verification, surpassing the current lack of analyzed search datasets both domestically and internationally; and Broad Coverage, as the dataset spans at least 15 different academic disciplines. Through ScholarSearch, we expect to more precisely measure and promote the performance improvement of LLMs in complex academic information retrieval tasks. The data is available at: https://huggingface.co/datasets/PKU-DS-LAB/ScholarSearch

Combining Fact Extraction and Verification with Neural Semantic Matching Networks

The increasing concern with misinformation has stimulated research efforts on automatic fact checking. The recently-released FEVER dataset introduced a benchmark fact-verification task in which a system is asked to verify a claim using evidential sentences from Wikipedia documents. In this paper, we present a connected system consisting of three homogeneous neural semantic matching models that conduct document retrieval, sentence selection, and claim verification jointly for fact extraction and verification. For evidence retrieval (document retrieval and sentence selection), unlike traditional vector space IR models in which queries and sources are matched in some pre-designed term vector space, we develop neural models to perform deep semantic matching from raw textual input, assuming no intermediate term representation and no access to structured external knowledge bases. We also show that Pageview frequency can also help improve the performance of evidence retrieval results, that later can be matched by using our neural semantic matching network. For claim verification, unlike previous approaches that simply feed upstream retrieved evidence and the claim to a natural language inference (NLI) model, we further enhance the NLI model by providing it with internal semantic relatedness scores (hence integrating it with the evidence retrieval modules) and ontological WordNet features. Experiments on the FEVER dataset indicate that (1) our neural semantic matching method outperforms popular TF-IDF and encoder models, by significant margins on all evidence retrieval metrics, (2) the additional relatedness score and WordNet features improve the NLI model via better semantic awareness, and (3) by formalizing all three subtasks as a similar semantic matching problem and improving on all three stages, the complete model is able to achieve the state-of-the-art results on the FEVER test set.

ProcBench: Benchmark for Multi-Step Reasoning and Following Procedure

Reasoning is central to a wide range of intellectual activities, and while the capabilities of large language models (LLMs) continue to advance, their performance in reasoning tasks remains limited. The processes and mechanisms underlying reasoning are not yet fully understood, but key elements include path exploration, selection of relevant knowledge, and multi-step inference. Problems are solved through the synthesis of these components. In this paper, we propose a benchmark that focuses on a specific aspect of reasoning ability: the direct evaluation of multi-step inference. To this end, we design a special reasoning task where multi-step inference is specifically focused by largely eliminating path exploration and implicit knowledge utilization. Our dataset comprises pairs of explicit instructions and corresponding questions, where the procedures necessary for solving the questions are entirely detailed within the instructions. This setup allows models to solve problems solely by following the provided directives. By constructing problems that require varying numbers of steps to solve and evaluating responses at each step, we enable a thorough assessment of state-of-the-art LLMs' ability to follow instructions. To ensure the robustness of our evaluation, we include multiple distinct tasks. Furthermore, by comparing accuracy across tasks, utilizing step-aware metrics, and applying separately defined measures of complexity, we conduct experiments that offer insights into the capabilities and limitations of LLMs in reasoning tasks. Our findings have significant implications for the development of LLMs and highlight areas for future research in advancing their reasoning abilities. Our dataset is available at https://huggingface.co/datasets/ifujisawa/procbench and code at https://github.com/ifujisawa/proc-bench.

Rewarding Progress: Scaling Automated Process Verifiers for LLM Reasoning

A promising approach for improving reasoning in large language models is to use process reward models (PRMs). PRMs provide feedback at each step of a multi-step reasoning trace, potentially improving credit assignment over outcome reward models (ORMs) that only provide feedback at the final step. However, collecting dense, per-step human labels is not scalable, and training PRMs from automatically-labeled data has thus far led to limited gains. To improve a base policy by running search against a PRM or using it as dense rewards for reinforcement learning (RL), we ask: "How should we design process rewards?". Our key insight is that, to be effective, the process reward for a step should measure progress: a change in the likelihood of producing a correct response in the future, before and after taking the step, corresponding to the notion of step-level advantages in RL. Crucially, this progress should be measured under a prover policy distinct from the base policy. We theoretically characterize the set of good provers and our results show that optimizing process rewards from such provers improves exploration during test-time search and online RL. In fact, our characterization shows that weak prover policies can substantially improve a stronger base policy, which we also observe empirically. We validate our claims by training process advantage verifiers (PAVs) to predict progress under such provers, and show that compared to ORMs, test-time search against PAVs is >8% more accurate, and 1.5-5times more compute-efficient. Online RL with dense rewards from PAVs enables one of the first results with 5-6times gain in sample efficiency, and >6% gain in accuracy, over ORMs.

Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

WebThinker: Empowering Large Reasoning Models with Deep Research Capability

Large reasoning models (LRMs), such as OpenAI-o1 and DeepSeek-R1, demonstrate impressive long-horizon reasoning capabilities. However, their reliance on static internal knowledge limits their performance on complex, knowledge-intensive tasks and hinders their ability to produce comprehensive research reports requiring synthesis of diverse web information. To address this, we propose WebThinker, a deep research agent that empowers LRMs to autonomously search the web, navigate web pages, and draft research reports during the reasoning process. WebThinker integrates a Deep Web Explorer module, enabling LRMs to dynamically search, navigate, and extract information from the web when encountering knowledge gaps. It also employs an Autonomous Think-Search-and-Draft strategy, allowing the model to seamlessly interleave reasoning, information gathering, and report writing in real time. To further enhance research tool utilization, we introduce an RL-based training strategy via iterative online Direct Preference Optimization (DPO). Extensive experiments on complex reasoning benchmarks (GPQA, GAIA, WebWalkerQA, HLE) and scientific report generation tasks (Glaive) demonstrate that WebThinker significantly outperforms existing methods and strong proprietary systems. Our approach enhances LRM reliability and applicability in complex scenarios, paving the way for more capable and versatile deep research systems. The code is available at https://github.com/RUC-NLPIR/WebThinker.

B-STaR: Monitoring and Balancing Exploration and Exploitation in Self-Taught Reasoners

In the absence of extensive human-annotated data for complex reasoning tasks, self-improvement -- where models are trained on their own outputs -- has emerged as a primary method for enhancing performance. However, the critical factors underlying the mechanism of these iterative self-improving methods remain poorly understood, such as under what conditions self-improvement is effective, and what are the bottlenecks in the current iterations. In this work, we identify and propose methods to monitor two pivotal factors in this iterative process: (1) the model's ability to generate sufficiently diverse responses (exploration); and (2) the effectiveness of external rewards in distinguishing high-quality candidates from lower-quality ones (exploitation). Using mathematical reasoning as a case study, we begin with a quantitative analysis to track the dynamics of exploration and exploitation, discovering that a model's exploratory capabilities rapidly deteriorate over iterations, and the effectiveness of exploiting external rewards diminishes as well. Motivated by these findings, we introduce B-STaR, a Self-Taught Reasoning framework that autonomously adjusts configurations across iterations to Balance exploration and exploitation, thereby optimizing the self-improving effectiveness based on the current policy model and available rewards. Our experiments on mathematical reasoning, coding, and commonsense reasoning demonstrate that B-STaR not only enhances the model's exploratory capabilities throughout training but also achieves a more effective balance between exploration and exploitation, leading to superior performance.

LeCaRDv2: A Large-Scale Chinese Legal Case Retrieval Dataset

As an important component of intelligent legal systems, legal case retrieval plays a critical role in ensuring judicial justice and fairness. However, the development of legal case retrieval technologies in the Chinese legal system is restricted by three problems in existing datasets: limited data size, narrow definitions of legal relevance, and naive candidate pooling strategies used in data sampling. To alleviate these issues, we introduce LeCaRDv2, a large-scale Legal Case Retrieval Dataset (version 2). It consists of 800 queries and 55,192 candidates extracted from 4.3 million criminal case documents. To the best of our knowledge, LeCaRDv2 is one of the largest Chinese legal case retrieval datasets, providing extensive coverage of criminal charges. Additionally, we enrich the existing relevance criteria by considering three key aspects: characterization, penalty, procedure. This comprehensive criteria enriches the dataset and may provides a more holistic perspective. Furthermore, we propose a two-level candidate set pooling strategy that effectively identify potential candidates for each query case. It's important to note that all cases in the dataset have been annotated by multiple legal experts specializing in criminal law. Their expertise ensures the accuracy and reliability of the annotations. We evaluate several state-of-the-art retrieval models at LeCaRDv2, demonstrating that there is still significant room for improvement in legal case retrieval. The details of LeCaRDv2 can be found at the anonymous website https://github.com/anonymous1113243/LeCaRDv2.

Evidence-Driven Retrieval Augmented Response Generation for Online Misinformation

The proliferation of online misinformation has posed significant threats to public interest. While numerous online users actively participate in the combat against misinformation, many of such responses can be characterized by the lack of politeness and supporting facts. As a solution, text generation approaches are proposed to automatically produce counter-misinformation responses. Nevertheless, existing methods are often trained end-to-end without leveraging external knowledge, resulting in subpar text quality and excessively repetitive responses. In this paper, we propose retrieval augmented response generation for online misinformation (RARG), which collects supporting evidence from scientific sources and generates counter-misinformation responses based on the evidences. In particular, our RARG consists of two stages: (1) evidence collection, where we design a retrieval pipeline to retrieve and rerank evidence documents using a database comprising over 1M academic articles; (2) response generation, in which we align large language models (LLMs) to generate evidence-based responses via reinforcement learning from human feedback (RLHF). We propose a reward function to maximize the utilization of the retrieved evidence while maintaining the quality of the generated text, which yields polite and factual responses that clearly refutes misinformation. To demonstrate the effectiveness of our method, we study the case of COVID-19 and perform extensive experiments with both in- and cross-domain datasets, where RARG consistently outperforms baselines by generating high-quality counter-misinformation responses.

Large Language Models as Biomedical Hypothesis Generators: A Comprehensive Evaluation

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

LitLLMs, LLMs for Literature Review: Are we there yet?

Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially due to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Our project page including a demonstration system and toolkit can be accessed here: https://litllm.github.io.

LitSearch: A Retrieval Benchmark for Scientific Literature Search

Literature search questions, such as "where can I find research on the evaluation of consistency in generated summaries?" pose significant challenges for modern search engines and retrieval systems. These questions often require a deep understanding of research concepts and the ability to reason over entire articles. In this work, we introduce LitSearch, a retrieval benchmark comprising 597 realistic literature search queries about recent ML and NLP papers. LitSearch is constructed using a combination of (1) questions generated by GPT-4 based on paragraphs containing inline citations from research papers and (2) questions about recently published papers, manually written by their authors. All LitSearch questions were manually examined or edited by experts to ensure high quality. We extensively benchmark state-of-the-art retrieval models and also evaluate two LLM-based reranking pipelines. We find a significant performance gap between BM25 and state-of-the-art dense retrievers, with a 24.8% difference in absolute recall@5. The LLM-based reranking strategies further improve the best-performing dense retriever by 4.4%. Additionally, commercial search engines and research tools like Google Search perform poorly on LitSearch, lagging behind the best dense retriever by 32 points. Taken together, these results show that LitSearch is an informative new testbed for retrieval systems while catering to a real-world use case.

SciPIP: An LLM-based Scientific Paper Idea Proposer

The exponential growth of knowledge and the increasing complexity of interdisciplinary research pose significant challenges for researchers, including information overload and difficulties in exploring novel ideas. The advancements in large language models (LLMs), such as GPT-4, have shown great potential in enhancing idea proposals, but how to effectively utilize large models for reasonable idea proposal has not been thoroughly explored. This paper proposes a scientific paper idea proposer (SciPIP). Based on a user-provided research background, SciPIP retrieves helpful papers from a literature database while leveraging the capabilities of LLMs to generate more novel and feasible ideas. To this end, 1) we construct a literature retrieval database, extracting lots of papers' multi-dimension information for fast access. Then, a literature retrieval method based on semantics, entity, and citation co-occurrences is proposed to search relevant literature from multiple aspects based on the user-provided background. 2) After literature retrieval, we introduce dual-path idea proposal strategies, where one path infers solutions from the retrieved literature and the other path generates original ideas through model brainstorming. We then combine the two to achieve a good balance between feasibility and originality. Through extensive experiments on the natural language processing (NLP) field, we demonstrate that SciPIP can retrieve citations similar to those of existing top conference papers and generate many ideas consistent with them. Additionally, we evaluate the originality of other ideas generated by SciPIP using large language models, further validating the effectiveness of our proposed method. The code and the database are released at https://github.com/cheerss/SciPIP.

m1: Unleash the Potential of Test-Time Scaling for Medical Reasoning with Large Language Models

Test-time scaling has emerged as a powerful technique for enhancing the reasoning capabilities of large language models. However, its effectiveness in medical reasoning remains uncertain, as the medical domain fundamentally differs from mathematical tasks in terms of knowledge representation and decision-making processes. In this paper, we provide the first comprehensive investigation of test-time scaling for medical reasoning and present m1, a simple yet effective approach that increases a model's medical reasoning capability at inference. Our evaluation across diverse medical tasks demonstrates that test-time scaling consistently enhances medical reasoning, enabling lightweight fine-tuned models under 10B parameters to establish new state-of-the-art performance, while our 32B model rivals previous 70B-scale medical LLMs. However, we identify an optimal reasoning token budget of approximately 4K, beyond which performance may degrade due to overthinking. Budget forcing, which extends test-time computation through iterative prompts, helps models double-check answers but does not necessarily improve the overall medical QA performance and, in some cases, even introduces errors into previously correct responses. Our case-by-case analysis identifies insufficient medical knowledge as a key bottleneck that prevents further performance gains through test-time scaling. We find that increasing data scale, improving data quality, and expanding model capacity consistently enhance medical knowledge grounding, enabling continued performance improvements, particularly on challenging medical benchmarks where smaller models reach saturation. These findings underscore fundamental differences between medical and mathematical reasoning in LLMs, highlighting that enriched medical knowledge, other than increased reasoning depth alone, is essential for realizing the benefits of test-time scaling.

LeanDojo: Theorem Proving with Retrieval-Augmented Language Models

Large language models (LLMs) have shown promise in proving formal theorems using proof assistants such as Lean. However, existing methods are difficult to reproduce or build on, due to private code, data, and large compute requirements. This has created substantial barriers to research on machine learning methods for theorem proving. This paper removes these barriers by introducing LeanDojo: an open-source Lean playground consisting of toolkits, data, models, and benchmarks. LeanDojo extracts data from Lean and enables interaction with the proof environment programmatically. It contains fine-grained annotations of premises in proofs, providing valuable data for premise selection: a key bottleneck in theorem proving. Using this data, we develop ReProver (Retrieval-Augmented Prover): the first LLM-based prover that is augmented with retrieval for selecting premises from a vast math library. It is inexpensive and needs only one GPU week of training. Our retriever leverages LeanDojo's program analysis capability to identify accessible premises and hard negative examples, which makes retrieval much more effective. Furthermore, we construct a new benchmark consisting of 96,962 theorems and proofs extracted from Lean's math library. It features challenging data split requiring the prover to generalize to theorems relying on novel premises that are never used in training. We use this benchmark for training and evaluation, and experimental results demonstrate the effectiveness of ReProver over non-retrieval baselines and GPT-4. We thus provide the first set of open-source LLM-based theorem provers without any proprietary datasets and release it under a permissive MIT license to facilitate further research.

Science Hierarchography: Hierarchical Organization of Science Literature

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

PRISMA-DFLLM: An Extension of PRISMA for Systematic Literature Reviews using Domain-specific Finetuned Large Language Models

With the proliferation of open-sourced Large Language Models (LLMs) and efficient finetuning techniques, we are on the cusp of the emergence of numerous domain-specific LLMs that have been finetuned for expertise across specialized fields and applications for which the current general-purpose LLMs are unsuitable. In academia, this technology has the potential to revolutionize the way we conduct systematic literature reviews (SLRs), access knowledge and generate new insights. This paper proposes an AI-enabled methodological framework that combines the power of LLMs with the rigorous reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). By finetuning LLMs on domain-specific academic papers that have been selected as a result of a rigorous SLR process, the proposed PRISMA-DFLLM (for Domain-specific Finetuned LLMs) reporting guidelines offer the potential to achieve greater efficiency, reusability and scalability, while also opening the potential for conducting incremental living systematic reviews with the aid of LLMs. Additionally, the proposed approach for leveraging LLMs for SLRs enables the dissemination of finetuned models, empowering researchers to accelerate advancements and democratize cutting-edge research. This paper presents the case for the feasibility of finetuned LLMs to support rigorous SLRs and the technical requirements for realizing this. This work then proposes the extended PRISMA-DFLLM checklist of reporting guidelines as well as the advantages, challenges, and potential implications of implementing PRISMA-DFLLM. Finally, a future research roadmap to develop this line of AI-enabled SLRs is presented, paving the way for a new era of evidence synthesis and knowledge discovery.

Satori: Reinforcement Learning with Chain-of-Action-Thought Enhances LLM Reasoning via Autoregressive Search

Large language models (LLMs) have demonstrated remarkable reasoning capabilities across diverse domains. Recent studies have shown that increasing test-time computation enhances LLMs' reasoning capabilities. This typically involves extensive sampling at inference time guided by an external LLM verifier, resulting in a two-player system. Despite external guidance, the effectiveness of this system demonstrates the potential of a single LLM to tackle complex tasks. Thus, we pose a new research problem: Can we internalize the searching capabilities to fundamentally enhance the reasoning abilities of a single LLM? This work explores an orthogonal direction focusing on post-training LLMs for autoregressive searching (i.e., an extended reasoning process with self-reflection and self-exploration of new strategies). To achieve this, we propose the Chain-of-Action-Thought (COAT) reasoning and a two-stage training paradigm: 1) a small-scale format tuning stage to internalize the COAT reasoning format and 2) a large-scale self-improvement stage leveraging reinforcement learning. Our approach results in Satori, a 7B LLM trained on open-source models and data. Extensive empirical evaluations demonstrate that Satori achieves state-of-the-art performance on mathematical reasoning benchmarks while exhibits strong generalization to out-of-domain tasks. Code, data, and models will be fully open-sourced.

Unleashing Reasoning Capability of LLMs via Scalable Question Synthesis from Scratch

The availability of high-quality data is one of the most important factors in improving the reasoning capability of LLMs. Existing works have demonstrated the effectiveness of creating more instruction data from seed questions or knowledge bases. Recent research indicates that continually scaling up data synthesis from strong models (e.g., GPT-4) can further elicit reasoning performance. Though promising, the open-sourced community still lacks high-quality data at scale and scalable data synthesis methods with affordable costs. To address this, we introduce ScaleQuest, a scalable and novel data synthesis method that utilizes "small-size" (e.g., 7B) open-source models to generate questions from scratch without the need for seed data with complex augmentation constraints. With the efficient ScaleQuest, we automatically constructed a mathematical reasoning dataset consisting of 1 million problem-solution pairs, which are more effective than existing open-sourced datasets. It can universally increase the performance of mainstream open-source models (i.e., Mistral, Llama3, DeepSeekMath, and Qwen2-Math) by achieving 29.2% to 46.4% gains on MATH. Notably, simply fine-tuning the Qwen2-Math-7B-Base model with our dataset can even surpass Qwen2-Math-7B-Instruct, a strong and well-aligned model on closed-source data, and proprietary models such as GPT-4-Turbo and Claude-3.5 Sonnet.

Accelerating Clinical Evidence Synthesis with Large Language Models

Synthesizing clinical evidence largely relies on systematic reviews of clinical trials and retrospective analyses from medical literature. However, the rapid expansion of publications presents challenges in efficiently identifying, summarizing, and updating clinical evidence. Here, we introduce TrialMind, a generative artificial intelligence (AI) pipeline for facilitating human-AI collaboration in three crucial tasks for evidence synthesis: study search, screening, and data extraction. To assess its performance, we chose published systematic reviews to build the benchmark dataset, named TrialReviewBench, which contains 100 systematic reviews and the associated 2,220 clinical studies. Our results show that TrialMind excels across all three tasks. In study search, it generates diverse and comprehensive search queries to achieve high recall rates (Ours 0.711-0.834 v.s. Human baseline 0.138-0.232). For study screening, TrialMind surpasses traditional embedding-based methods by 30% to 160%. In data extraction, it outperforms a GPT-4 baseline by 29.6% to 61.5%. We further conducted user studies to confirm its practical utility. Compared to manual efforts, human-AI collaboration using TrialMind yielded a 71.4% recall lift and 44.2% time savings in study screening and a 23.5% accuracy lift and 63.4% time savings in data extraction. Additionally, when comparing synthesized clinical evidence presented in forest plots, medical experts favored TrialMind's outputs over GPT-4's outputs in 62.5% to 100% of cases. These findings show the promise of LLM-based approaches like TrialMind to accelerate clinical evidence synthesis via streamlining study search, screening, and data extraction from medical literature, with exceptional performance improvement when working with human experts.

SciClaimHunt: A Large Dataset for Evidence-based Scientific Claim Verification

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.

Search-in-the-Chain: Towards Accurate, Credible and Traceable Large Language Models for Knowledge-intensive Tasks

Making the contents generated by Large Language Model (LLM) such as ChatGPT, accurate, credible and traceable is crucial, especially in complex knowledge-intensive tasks that require multi-step reasoning and each of which needs knowledge to solve. Introducing Information Retrieval (IR) to provide LLM with external knowledge is good potential to solve this problem. However, where and how to introduce IR into LLM is a big challenge. Previous work has the disadvantage that the wrong knowledge retrieved by IR misleads the LLM or breaks the reasoning chain of LLM. In this paper, we propose a novel framework called Search-in-the-Chain (SearChain) for the interaction between LLM and IR to solve the challenges. First, LLM generates the global reasoning chain called Chain-of-Query (CoQ) where each node consists of an IR-oriented query and the answer to the query. Second, IR verifies the answer of each node of CoQ, it corrects the answer that is not consistent with the retrieved information when IR gives high confidence, which improves the credibility. Third, LLM can mark its missing knowledge in CoQ and IR can provide this knowledge to LLM. These three operations improve the accuracy of LLM for complex knowledge-intensive tasks in terms of reasoning ability and knowledge. Finally, SearChain generates the reasoning process and marks references to supporting documents for each reasoning step, which improves traceability. SearChain transforms the topology of reasoning from chain to tree, which can modify the reasoning direction. Experiment shows that SearChain outperforms baselines on complex knowledge-intensive tasks including multi-hop question-answering, slot filling, fact checking, and long-form question-answering.

One Example Shown, Many Concepts Known! Counterexample-Driven Conceptual Reasoning in Mathematical LLMs

Leveraging mathematical Large Language Models (LLMs) for proof generation is a fundamental topic in LLMs research. We argue that the ability of current LLMs to prove statements largely depends on whether they have encountered the relevant proof process during training. This reliance limits their deeper understanding of mathematical theorems and related concepts. Inspired by the pedagogical method of "proof by counterexamples" commonly used in human mathematics education, our work aims to enhance LLMs' ability to conduct mathematical reasoning and proof through counterexamples. Specifically, we manually create a high-quality, university-level mathematical benchmark, CounterMATH, which requires LLMs to prove mathematical statements by providing counterexamples, thereby assessing their grasp of mathematical concepts. Additionally, we develop a data engineering framework to automatically obtain training data for further model improvement. Extensive experiments and detailed analyses demonstrate that CounterMATH is challenging, indicating that LLMs, such as OpenAI o1, have insufficient counterexample-driven proof capabilities. Moreover, our exploration into model training reveals that strengthening LLMs' counterexample-driven conceptual reasoning abilities is crucial for improving their overall mathematical capabilities. We believe that our work offers new perspectives on the community of mathematical LLMs.

AI-Driven Scholarly Peer Review via Persistent Workflow Prompting, Meta-Prompting, and Meta-Reasoning

Critical peer review of scientific manuscripts presents a significant challenge for Large Language Models (LLMs), partly due to data limitations and the complexity of expert reasoning. This report introduces Persistent Workflow Prompting (PWP), a potentially broadly applicable prompt engineering methodology designed to bridge this gap using standard LLM chat interfaces (zero-code, no APIs). We present a proof-of-concept PWP prompt for the critical analysis of experimental chemistry manuscripts, featuring a hierarchical, modular architecture (structured via Markdown) that defines detailed analysis workflows. We develop this PWP prompt through iterative application of meta-prompting techniques and meta-reasoning aimed at systematically codifying expert review workflows, including tacit knowledge. Submitted once at the start of a session, this PWP prompt equips the LLM with persistent workflows triggered by subsequent queries, guiding modern reasoning LLMs through systematic, multimodal evaluations. Demonstrations show the PWP-guided LLM identifying major methodological flaws in a test case while mitigating LLM input bias and performing complex tasks, including distinguishing claims from evidence, integrating text/photo/figure analysis to infer parameters, executing quantitative feasibility checks, comparing estimates against claims, and assessing a priori plausibility. To ensure transparency and facilitate replication, we provide full prompts, detailed demonstration analyses, and logs of interactive chats as supplementary resources. Beyond the specific application, this work offers insights into the meta-development process itself, highlighting the potential of PWP, informed by detailed workflow formalization, to enable sophisticated analysis using readily available LLMs for complex scientific tasks.

Eureka: Evaluating and Understanding Large Foundation Models

Rigorous and reproducible evaluation is critical for assessing the state of the art and for guiding scientific advances in Artificial Intelligence. Evaluation is challenging in practice due to several reasons, including benchmark saturation, lack of transparency in methods used for measurement, development challenges in extracting measurements for generative tasks, and, more generally, the extensive number of capabilities required for a well-rounded comparison across models. We make three contributions to alleviate the above challenges. First, we present Eureka, an open-source framework for standardizing evaluations of large foundation models beyond single-score reporting and rankings. Second, we introduce Eureka-Bench as an extensible collection of benchmarks testing capabilities that (i) are still challenging for state-of-the-art models and (ii) represent fundamental but overlooked language and multimodal capabilities. The inherent space for improvement in non-saturated benchmarks enables us to discover meaningful differences between models at a capability level. Third, using Eureka, we conduct an analysis of 12 state-of-the-art models, providing in-depth insights into failure understanding and model comparison, which can be leveraged to plan targeted improvements. In contrast to recent trends in reports and leaderboards showing absolute rankings and claims for one model or another to be the best, our analysis shows that there is no such best model. Different models have different strengths, but there are models that appear more often than others as best performers for some capabilities. Despite the recent improvements, current models still struggle with several fundamental capabilities including detailed image understanding, benefiting from multimodal input when available rather than fully relying on language, factuality and grounding for information retrieval, and over refusals.

MediQ: Question-Asking LLMs and a Benchmark for Reliable Interactive Clinical Reasoning

Users typically engage with LLMs interactively, yet most existing benchmarks evaluate them in a static, single-turn format, posing reliability concerns in interactive scenarios. We identify a key obstacle towards reliability: LLMs are trained to answer any question, even with incomplete context or insufficient knowledge. In this paper, we propose to change the static paradigm to an interactive one, develop systems that proactively ask questions to gather more information and respond reliably, and introduce an benchmark - MediQ - to evaluate question-asking ability in LLMs. MediQ simulates clinical interactions consisting of a Patient System and an adaptive Expert System; with potentially incomplete initial information, the Expert refrains from making diagnostic decisions when unconfident, and instead elicits missing details via follow-up questions. We provide a pipeline to convert single-turn medical benchmarks into an interactive format. Our results show that directly prompting state-of-the-art LLMs to ask questions degrades performance, indicating that adapting LLMs to proactive information-seeking settings is nontrivial. We experiment with abstention strategies to better estimate model confidence and decide when to ask questions, improving diagnostic accuracy by 22.3%; however, performance still lags compared to an (unrealistic in practice) upper bound with complete information upfront. Further analyses show improved interactive performance with filtering irrelevant contexts and reformatting conversations. Overall, we introduce a novel problem towards LLM reliability, an interactive MediQ benchmark and a novel question-asking system, and highlight directions to extend LLMs' information-seeking abilities in critical domains.

Reasoning Capacity in Multi-Agent Systems: Limitations, Challenges and Human-Centered Solutions

Remarkable performance of large language models (LLMs) in a variety of tasks brings forth many opportunities as well as challenges of utilizing them in production settings. Towards practical adoption of LLMs, multi-agent systems hold great promise to augment, integrate, and orchestrate LLMs in the larger context of enterprise platforms that use existing proprietary data and models to tackle complex real-world tasks. Despite the tremendous success of these systems, current approaches rely on narrow, single-focus objectives for optimization and evaluation, often overlooking potential constraints in real-world scenarios, including restricted budgets, resources and time. Furthermore, interpreting, analyzing, and debugging these systems requires different components to be evaluated in relation to one another. This demand is currently not feasible with existing methodologies. In this postion paper, we introduce the concept of reasoning capacity as a unifying criterion to enable integration of constraints during optimization and establish connections among different components within the system, which also enable a more holistic and comprehensive approach to evaluation. We present a formal definition of reasoning capacity and illustrate its utility in identifying limitations within each component of the system. We then argue how these limitations can be addressed with a self-reflective process wherein human-feedback is used to alleviate shortcomings in reasoning and enhance overall consistency of the system.

CORE-MM: Complex Open-Ended Reasoning Evaluation For Multi-Modal Large Language Models

Multi-modal Large Language Models (MLLMs) are increasingly prominent in the field of artificial intelligence. These models not only excel in traditional vision-language tasks but also demonstrate impressive performance in contemporary multi-modal benchmarks. Although many of these benchmarks attempt to holistically evaluate MLLMs, they typically concentrate on basic reasoning tasks, often yielding only simple yes/no or multi-choice responses. These methods naturally lead to confusion and difficulties in conclusively determining the reasoning capabilities of MLLMs. To mitigate this issue, we manually curate a benchmark dataset specifically designed for MLLMs, with a focus on complex reasoning tasks. Our benchmark comprises three key reasoning categories: deductive, abductive, and analogical reasoning. The queries in our dataset are intentionally constructed to engage the reasoning capabilities of MLLMs in the process of generating answers. For a fair comparison across various MLLMs, we incorporate intermediate reasoning steps into our evaluation criteria. In instances where an MLLM is unable to produce a definitive answer, its reasoning ability is evaluated by requesting intermediate reasoning steps. If these steps align with our manual annotations, appropriate scores are assigned. This evaluation scheme resembles methods commonly used in human assessments, such as exams or assignments, and represents what we consider a more effective assessment technique compared with existing benchmarks. We evaluate a selection of representative MLLMs using this rigorously developed open-ended multi-step elaborate reasoning benchmark, designed to challenge and accurately measure their reasoning capabilities. The code and data will be released at https://core-mm.github.io/

Adaptive Chameleon or Stubborn Sloth: Unraveling the Behavior of Large Language Models in Knowledge Clashes

By providing external information to large language models (LLMs), tool augmentation (including retrieval augmentation) has emerged as a promising solution for addressing the limitations of LLMs' static parametric memory. However, how receptive are LLMs to such external evidence, especially when the evidence conflicts with their parametric memory? We present the first comprehensive and controlled investigation into the behavior of LLMs when encountering knowledge conflicts. We propose a systematic framework to elicit high-quality parametric memory from LLMs and construct the corresponding counter-memory, which enables us to conduct a series of controlled experiments. Our investigation reveals seemingly contradicting behaviors of LLMs. On the one hand, different from prior wisdom, we find that LLMs can be highly receptive to external evidence even when that conflicts with their parametric memory, given that the external evidence is coherent and convincing. On the other hand, LLMs also demonstrate a strong confirmation bias when the external evidence contains some information that is consistent with their parametric memory, despite being presented with conflicting evidence at the same time. These results pose important implications that are worth careful consideration for the further development and deployment of tool- and retrieval-augmented LLMs.

MechGPT, a language-based strategy for mechanics and materials modeling that connects knowledge across scales, disciplines and modalities

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Discovering Hierarchical Latent Capabilities of Language Models via Causal Representation Learning

Faithful evaluation of language model capabilities is crucial for deriving actionable insights that can inform model development. However, rigorous causal evaluations in this domain face significant methodological challenges, including complex confounding effects and prohibitive computational costs associated with extensive retraining. To tackle these challenges, we propose a causal representation learning framework wherein observed benchmark performance is modeled as a linear transformation of a few latent capability factors. Crucially, these latent factors are identified as causally interrelated after appropriately controlling for the base model as a common confounder. Applying this approach to a comprehensive dataset encompassing over 1500 models evaluated across six benchmarks from the Open LLM Leaderboard, we identify a concise three-node linear causal structure that reliably explains the observed performance variations. Further interpretation of this causal structure provides substantial scientific insights beyond simple numerical rankings: specifically, we reveal a clear causal direction starting from general problem-solving capabilities, advancing through instruction-following proficiency, and culminating in mathematical reasoning ability. Our results underscore the essential role of carefully controlling base model variations during evaluation, a step critical to accurately uncovering the underlying causal relationships among latent model capabilities.

BLADE: Benchmarking Language Model Agents for Data-Driven Science

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.

LLM The Genius Paradox: A Linguistic and Math Expert's Struggle with Simple Word-based Counting Problems

Interestingly, LLMs yet struggle with some basic tasks that humans find trivial to handle, e.g., counting the number of character r's in the word "strawberry". There are several popular conjectures (e.g., tokenization, architecture and training data) regarding the reason for deficiency of LLMs in simple word-based counting problems, sharing the similar belief that such failure stems from model pretraining hence probably inevitable during deployment. In this paper, we carefully design multiple evaluation settings to investigate validity of prevalent conjectures. Meanwhile, we measure transferability of advanced mathematical and coding reasoning capabilities from specialized LLMs to simple counting tasks. Although specialized LLMs suffer from counting problems as well, we find conjectures about inherent deficiency of LLMs invalid and further seek opportunities to elicit knowledge and capabilities from LLMs that are beneficial to counting tasks. Compared with strategies such as finetuning and in-context learning that are commonly adopted to enhance performance on new or challenging tasks, we show that engaging reasoning is the most robust and efficient way to help LLMs better perceive tasks with more accurate responses. We hope our conjecture validation design could provide insights into the study of future critical failure modes of LLMs. Based on challenges in transferring advanced capabilities to much simpler tasks, we call for more attention to model capability acquisition and evaluation. We also highlight the importance of cultivating consciousness of "reasoning before responding" during model pretraining.

MedAgent-Pro: Towards Multi-modal Evidence-based Medical Diagnosis via Reasoning Agentic Workflow

Developing reliable AI systems to assist human clinicians in multi-modal medical diagnosis has long been a key objective for researchers. Recently, Multi-modal Large Language Models (MLLMs) have gained significant attention and achieved success across various domains. With strong reasoning capabilities and the ability to perform diverse tasks based on user instructions, they hold great potential for enhancing medical diagnosis. However, directly applying MLLMs to the medical domain still presents challenges. They lack detailed perception of visual inputs, limiting their ability to perform quantitative image analysis, which is crucial for medical diagnostics. Additionally, MLLMs often exhibit hallucinations and inconsistencies in reasoning, whereas clinical diagnoses must adhere strictly to established criteria. To address these challenges, we propose MedAgent-Pro, an evidence-based reasoning agentic system designed to achieve reliable, explainable, and precise medical diagnoses. This is accomplished through a hierarchical workflow: at the task level, knowledge-based reasoning generate reliable diagnostic plans for specific diseases following retrieved clinical criteria. While at the case level, multiple tool agents process multi-modal inputs, analyze different indicators according to the plan, and provide a final diagnosis based on both quantitative and qualitative evidence. Comprehensive experiments on both 2D and 3D medical diagnosis tasks demonstrate the superiority and effectiveness of MedAgent-Pro, while case studies further highlight its reliability and interpretability. The code is available at https://github.com/jinlab-imvr/MedAgent-Pro.

LLMAuditor: A Framework for Auditing Large Language Models Using Human-in-the-Loop

As Large Language Models (LLMs) become more pervasive across various users and scenarios, identifying potential issues when using these models becomes essential. Examples of such issues include: bias, inconsistencies, and hallucination. Although auditing the LLM for these problems is often warranted, such a process is neither easy nor accessible for most. An effective method is to probe the LLM using different versions of the same question. This could expose inconsistencies in its knowledge or operation, indicating potential for bias or hallucination. However, to operationalize this auditing method at scale, we need an approach to create those probes reliably and automatically. In this paper we propose the LLMAuditor framework which is an automatic, and scalable solution, where one uses a different LLM along with human-in-the-loop (HIL). This approach offers verifiability and transparency, while avoiding circular reliance on the same LLM, and increasing scientific rigor and generalizability. Specifically, LLMAuditor includes two phases of verification using humans: standardized evaluation criteria to verify responses, and a structured prompt template to generate desired probes. A case study using questions from the TruthfulQA dataset demonstrates that we can generate a reliable set of probes from one LLM that can be used to audit inconsistencies in a different LLM. This process is enhanced by our structured prompt template with HIL, which not only boosts the reliability of our approach in auditing but also yields the delivery of less hallucinated results. The novelty of our research stems from the development of a comprehensive, general-purpose framework that includes a HIL verified prompt template for auditing responses generated by LLMs.

Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

LegalVis: Exploring and Inferring Precedent Citations in Legal Documents

To reduce the number of pending cases and conflicting rulings in the Brazilian Judiciary, the National Congress amended the Constitution, allowing the Brazilian Supreme Court (STF) to create binding precedents (BPs), i.e., a set of understandings that both Executive and lower Judiciary branches must follow. The STF's justices frequently cite the 58 existing BPs in their decisions, and it is of primary relevance that judicial experts could identify and analyze such citations. To assist in this problem, we propose LegalVis, a web-based visual analytics system designed to support the analysis of legal documents that cite or could potentially cite a BP. We model the problem of identifying potential citations (i.e., non-explicit) as a classification problem. However, a simple score is not enough to explain the results; that is why we use an interpretability machine learning method to explain the reason behind each identified citation. For a compelling visual exploration of documents and BPs, LegalVis comprises three interactive visual components: the first presents an overview of the data showing temporal patterns, the second allows filtering and grouping relevant documents by topic, and the last one shows a document's text aiming to interpret the model's output by pointing out which paragraphs are likely to mention the BP, even if not explicitly specified. We evaluated our identification model and obtained an accuracy of 96%; we also made a quantitative and qualitative analysis of the results. The usefulness and effectiveness of LegalVis were evaluated through two usage scenarios and feedback from six domain experts.

A Reliable Knowledge Processing Framework for Combustion Science using Foundation Models

This research explores the integration of large language models (LLMs) into scientific data assimilation, focusing on combustion science as a case study. Leveraging foundational models integrated with Retrieval-Augmented Generation (RAG) framework, the study introduces an approach to process diverse combustion research data, spanning experimental studies, simulations, and literature. The multifaceted nature of combustion research emphasizes the critical role of knowledge processing in navigating and extracting valuable information from a vast and diverse pool of sources. The developed approach minimizes computational and economic expenses while optimizing data privacy and accuracy. It incorporates prompt engineering and offline open-source LLMs, offering user autonomy in selecting base models. The study provides a thorough examination of text segmentation strategies, conducts comparative studies between LLMs, and explores various optimized prompts to demonstrate the effectiveness of the framework. By incorporating an external database, the framework outperforms a conventional LLM in generating accurate responses and constructing robust arguments. Additionally, the study delves into the investigation of optimized prompt templates for the purpose of efficient extraction of scientific literature. The research addresses concerns related to hallucinations and false research articles by introducing a custom workflow developed with a detection algorithm to filter out inaccuracies. Despite identified areas for improvement, the framework consistently delivers accurate domain-specific responses with minimal human oversight. The prompt-agnostic approach introduced holds promise for future deliberations. The study underscores the significance of integrating LLMs and knowledge processing techniques in scientific research, providing a foundation for advancements in data assimilation and utilization.

Evidence to Generate (E2G): A Single-agent Two-step Prompting for Context Grounded and Retrieval Augmented Reasoning

While chain-of-thought (CoT) prompting has revolutionized how LLMs perform reasoning tasks, its current methods and variations (e.g, Self-consistency, ReACT, Reflexion, Tree-of-Thoughts (ToT), Cumulative Reasoning (CR)) suffer from limitations like slowness, limited context grounding, hallucination and inconsistent outputs. To overcome these challenges, we introduce Evidence to Generate (E2G), a novel single-agent, two-step prompting framework. Instead of unverified reasoning claims, this innovative approach leverages the power of "evidence for decision making" by first focusing exclusively on the thought sequences (the series of intermediate steps) explicitly mentioned in the context which then serve as extracted evidence, guiding the LLM's output generation process with greater precision and efficiency. This simple yet powerful approach unlocks the true potential of chain-of-thought like prompting, paving the way for faster, more reliable, and more contextually aware reasoning in LLMs. \tool achieves remarkable results robustly across a wide range of knowledge-intensive reasoning and generation tasks, surpassing baseline approaches with state-of-the-art LLMs. For example, (i) on LogiQA benchmark using GPT-4 as backbone model, \tool achieves a new state-of-the Accuracy of 53.8% exceeding CoT by 18%, ToT by 11%, CR by 9% (ii) a variant of E2G with PaLM2 outperforms the variable-shot performance of Gemini Ultra by 0.9 F1 points, reaching an F1 score of 83.3 on a subset of DROP.

Reinforced Internal-External Knowledge Synergistic Reasoning for Efficient Adaptive Search Agent

Retrieval-augmented generation (RAG) is a common strategy to reduce hallucinations in Large Language Models (LLMs). While reinforcement learning (RL) can enable LLMs to act as search agents by activating retrieval capabilities, existing ones often underutilize their internal knowledge. This can lead to redundant retrievals, potential harmful knowledge conflicts, and increased inference latency. To address these limitations, an efficient and adaptive search agent capable of discerning optimal retrieval timing and synergistically integrating parametric (internal) and retrieved (external) knowledge is in urgent need. This paper introduces the Reinforced Internal-External Knowledge Synergistic Reasoning Agent (IKEA), which could indentify its own knowledge boundary and prioritize the utilization of internal knowledge, resorting to external search only when internal knowledge is deemed insufficient. This is achieved using a novel knowledge-boundary aware reward function and a knowledge-boundary aware training dataset. These are designed for internal-external knowledge synergy oriented RL, incentivizing the model to deliver accurate answers, minimize unnecessary retrievals, and encourage appropriate external searches when its own knowledge is lacking. Evaluations across multiple knowledge reasoning tasks demonstrate that IKEA significantly outperforms baseline methods, reduces retrieval frequency significantly, and exhibits robust generalization capabilities.

MedCaseReasoning: Evaluating and learning diagnostic reasoning from clinical case reports

Doctors and patients alike increasingly use Large Language Models (LLMs) to diagnose clinical cases. However, unlike domains such as math or coding, where correctness can be objectively defined by the final answer, medical diagnosis requires both the outcome and the reasoning process to be accurate. Currently, widely used medical benchmarks like MedQA and MMLU assess only accuracy in the final answer, overlooking the quality and faithfulness of the clinical reasoning process. To address this limitation, we introduce MedCaseReasoning, the first open-access dataset for evaluating LLMs on their ability to align with clinician-authored diagnostic reasoning. The dataset includes 14,489 diagnostic question-and-answer cases, each paired with detailed reasoning statements derived from open-access medical case reports. We evaluate state-of-the-art reasoning LLMs on MedCaseReasoning and find significant shortcomings in their diagnoses and reasoning: for instance, the top-performing open-source model, DeepSeek-R1, achieves only 48% 10-shot diagnostic accuracy and mentions only 64% of the clinician reasoning statements (recall). However, we demonstrate that fine-tuning LLMs on the reasoning traces derived from MedCaseReasoning significantly improves diagnostic accuracy and clinical reasoning recall by an average relative gain of 29% and 41%, respectively. The open-source dataset, code, and models are available at https://github.com/kevinwu23/Stanford-MedCaseReasoning.

Are Large Language Models Really Good Logical Reasoners? A Comprehensive Evaluation and Beyond

Logical reasoning consistently plays a fundamental and significant role in the domains of knowledge engineering and artificial intelligence. Recently, Large Language Models (LLMs) have emerged as a noteworthy innovation in natural language processing (NLP), exhibiting impressive achievements across various classic NLP tasks. However, the question of whether LLMs can effectively address the task of logical reasoning, which requires gradual cognitive inference similar to human intelligence, remains unanswered. To this end, we aim to bridge this gap and provide comprehensive evaluations in this paper. Firstly, to offer systematic evaluations, we select fifteen typical logical reasoning datasets and organize them into deductive, inductive, abductive and mixed-form reasoning settings. Considering the comprehensiveness of evaluations, we include three representative LLMs (i.e., text-davinci-003, ChatGPT and BARD) and evaluate them on all selected datasets under zero-shot, one-shot and three-shot settings. Secondly, different from previous evaluations relying only on simple metrics (e.g., accuracy), we propose fine-level evaluations from objective and subjective manners, covering both answers and explanations. Additionally, to uncover the logical flaws of LLMs, problematic cases will be attributed to five error types from two dimensions, i.e., evidence selection process and reasoning process. Thirdly, to avoid the influences of knowledge bias and purely focus on benchmarking the logical reasoning capability of LLMs, we propose a new dataset with neutral content. It contains 3,000 samples and covers deductive, inductive and abductive settings. Based on the in-depth evaluations, this paper finally forms a general evaluation scheme of logical reasoning capability from six dimensions. It reflects the pros and cons of LLMs and gives guiding directions for future works.

Causal Reasoning and Large Language Models: Opening a New Frontier for Causality

The causal capabilities of large language models (LLMs) are a matter of significant debate, with critical implications for the use of LLMs in societally impactful domains such as medicine, science, law, and policy. We conduct a "behavorial" study of LLMs to benchmark their capability in generating causal arguments. Across a wide range of tasks, we find that LLMs can generate text corresponding to correct causal arguments with high probability, surpassing the best-performing existing methods. Algorithms based on GPT-3.5 and 4 outperform existing algorithms on a pairwise causal discovery task (97%, 13 points gain), counterfactual reasoning task (92%, 20 points gain) and event causality (86% accuracy in determining necessary and sufficient causes in vignettes). We perform robustness checks across tasks and show that the capabilities cannot be explained by dataset memorization alone, especially since LLMs generalize to novel datasets that were created after the training cutoff date. That said, LLMs exhibit unpredictable failure modes, and we discuss the kinds of errors that may be improved and what are the fundamental limits of LLM-based answers. Overall, by operating on the text metadata, LLMs bring capabilities so far understood to be restricted to humans, such as using collected knowledge to generate causal graphs or identifying background causal context from natural language. As a result, LLMs may be used by human domain experts to save effort in setting up a causal analysis, one of the biggest impediments to the widespread adoption of causal methods. Given that LLMs ignore the actual data, our results also point to a fruitful research direction of developing algorithms that combine LLMs with existing causal techniques. Code and datasets are available at https://github.com/py-why/pywhy-llm.

Does Reinforcement Learning Really Incentivize Reasoning Capacity in LLMs Beyond the Base Model?

Reinforcement Learning with Verifiable Rewards (RLVR) has recently demonstrated notable success in enhancing the reasoning capabilities of LLMs, particularly in mathematics and programming tasks. It is widely believed that RLVR enables LLMs to continuously self-improve, thus acquiring novel reasoning abilities that exceed corresponding base models' capacity. In this study, however, we critically re-examines this assumption by measuring the pass@k metric with large values of k to explore the reasoning capability boundary of the models across a wide range of model families and benchmarks. Surprisingly, the RL does not, in fact, elicit fundamentally new reasoning patterns. While RL-trained models outperform their base models at smaller values of k (\eg, k=1), base models can achieve a comparable or even higher pass@k score compared to their RL counterparts at large k values. The reasoning paths generated by RL-trained models are already included in the base models' sampling distribution, suggesting that most reasoning abilities manifested in RL-trained models are already obtained by base models. Further analysis shows that RL training boosts the performance by biasing the model's output distribution toward paths that are more likely to yield rewards, therefore sampling correct responses more efficiently. But this also results in a narrower reasoning capability boundary compared to base models. Similar results are observed in visual reasoning tasks trained with RLVR. Moreover, we find that distillation can genuinely introduce new knowledge into the model, different from RLVR. These findings underscore a critical limitation of RLVR in advancing LLM reasoning abilities which requires us to fundamentally rethink the impact of RL training in reasoning LLMs and the need of a better paradigm. Project Page: https://limit-of-RLVR.github.io

Application of NotebookLM, a Large Language Model with Retrieval-Augmented Generation, for Lung Cancer Staging

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

Investigating the Factual Knowledge Boundary of Large Language Models with Retrieval Augmentation

Knowledge-intensive tasks (e.g., open-domain question answering (QA)) require a substantial amount of factual knowledge and often rely on external information for assistance. Recently, large language models (LLMs) (e.g., ChatGPT), have demonstrated impressive prowess in solving a wide range of tasks with world knowledge, including knowledge-intensive tasks. However, it remains unclear how well LLMs are able to perceive their factual knowledge boundaries, particularly how they behave when incorporating retrieval augmentation. In this study, we present an initial analysis of the factual knowledge boundaries of LLMs and how retrieval augmentation affects LLMs on open-domain QA. Specially, we focus on three primary research questions and analyze them by examining QA performance, priori judgement and posteriori judgement of LLMs. We show evidence that LLMs possess unwavering confidence in their capabilities to respond to questions and the accuracy of their responses. Furthermore, retrieval augmentation proves to be an effective approach in enhancing LLMs' awareness of knowledge boundaries, thereby improving their judgemental abilities. Additionally, we also find that LLMs have a propensity to rely on the provided retrieval results when formulating answers, while the quality of these results significantly impacts their reliance. The code to reproduce this work is available at https://github.com/RUCAIBox/LLM-Knowledge-Boundary.

The Evolving Role of Large Language Models in Scientific Innovation: Evaluator, Collaborator, and Scientist

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

Knowledge-Aware Iterative Retrieval for Multi-Agent Systems

We introduce a novel large language model (LLM)-driven agent framework, which iteratively refines queries and filters contextual evidence by leveraging dynamically evolving knowledge. A defining feature of the system is its decoupling of external sources from an internal knowledge cache that is progressively updated to guide both query generation and evidence selection. This design mitigates bias-reinforcement loops and enables dynamic, trackable search exploration paths, thereby optimizing the trade-off between exploring diverse information and maintaining accuracy through autonomous agent decision-making. Our approach is evaluated on a broad range of open-domain question answering benchmarks, including multi-step tasks that mirror real-world scenarios where integrating information from multiple sources is critical, especially given the vulnerabilities of LLMs that lack explicit reasoning or planning capabilities. The results show that the proposed system not only outperforms single-step baselines regardless of task difficulty but also, compared to conventional iterative retrieval methods, demonstrates pronounced advantages in complex tasks through precise evidence-based reasoning and enhanced efficiency. The proposed system supports both competitive and collaborative sharing of updated context, enabling multi-agent extension. The benefits of multi-agent configurations become especially prominent as task difficulty increases. The number of convergence steps scales with task difficulty, suggesting cost-effective scalability.

Ranking Free RAG: Replacing Re-ranking with Selection in RAG for Sensitive Domains

Traditional Retrieval-Augmented Generation (RAG) pipelines rely on similarity-based retrieval and re-ranking, which depend on heuristics such as top-k, and lack explainability, interpretability, and robustness against adversarial content. To address this gap, we propose a novel method METEORA that replaces re-ranking in RAG with a rationale-driven selection approach. METEORA operates in two stages. First, a general-purpose LLM is preference-tuned to generate rationales conditioned on the input query using direct preference optimization. These rationales guide the evidence chunk selection engine, which selects relevant chunks in three stages: pairing individual rationales with corresponding retrieved chunks for local relevance, global selection with elbow detection for adaptive cutoff, and context expansion via neighboring chunks. This process eliminates the need for top-k heuristics. The rationales are also used for consistency check using a Verifier LLM to detect and filter poisoned or misleading content for safe generation. The framework provides explainable and interpretable evidence flow by using rationales consistently across both selection and verification. Our evaluation across six datasets spanning legal, financial, and academic research domains shows that METEORA improves generation accuracy by 33.34% while using approximately 50% fewer chunks than state-of-the-art re-ranking methods. In adversarial settings, METEORA significantly improves the F1 score from 0.10 to 0.44 over the state-of-the-art perplexity-based defense baseline, demonstrating strong resilience to poisoning attacks. Code available at: https://anonymous.4open.science/r/METEORA-DC46/README.md