Literature Meets Data: A Synergistic Approach to Hypothesis Generation

Can AI Agents Synthesize Scientific Conclusions?

Scientific AI agents increasingly retrieve evidence, reason across sources, and synthesize conclusions used in consequential decisions. Yet, their ability to do so in high-stakes domains such as health remains unclear. We introduce SciConBench, a large-scale live benchmark of 9.11K questions and expert-written conclusions from systematic reviews to evaluate open-domain scientific conclusion synthesis. The benchmark draws on an expert-validated automated evaluation pipeline that decomposes conclusions into atomic facts and measures correctness and comprehensiveness via factual precision and recall. To mitigate data leakage, we further introduce SciConHarness, a clean-room evaluation harness that equips agents with controlled web interaction to ensure valid measurement. Evaluating 8 frontier models and deep research agents, we find that factual quality remains low: under clean-room settings, the best agent achieves only a factual F1 of 0.337. Our clean-room setting consistently reduces performance relative to unconstrained evaluation, suggesting that leakage inflates estimates of models' true synthesis capabilities. Finally, we audit consumer-facing agents (e.g., Google AI Overview, OpenEvidence) and find they frequently generate incomplete and sometimes contradictory conclusions, even when the ground-truth answer is available. Overall, our results show that reliable synthesis of scientific conclusions remains an open challenge, and that clean-room evaluation is essential for assessing open-domain AI agents.

AI Research Agents Narrow Scientific Exploration

AI research agents can now generate research ideas, design experiments, run code, and draft papers, raising the possibility of large-scale AI-assisted scientific discovery. Many current agent frameworks explicitly encourage the generation of novel and high-impact ideas. Yet it remains unclear whether AI-assisted ideation broadens scientific exploration or mainly concentrates around existing work. We study AI research agents as scientific search systems. Using four AI research-agent frameworks and six large language models, we generate 37,802 scientific ideas from shared seed literature across citation-defined research areas in AI and machine learning. We then compare the resulting AI ideas against human-authored papers from the same research areas, follow-on human research emerging from the same seed literature, and the seed literature itself. Across experiments, four consistent patterns emerge. First, AI-generated ideas are substantially more concentrated than human-authored papers from the same research areas. Second, AI-generated ideas remain much closer to their starting literature than later human follow-on work does. Third, papers most similar to AI-generated ideas tend to receive lower subsequent citations. Fourth, when AI-generated ideas differ from prior work, the differences arise primarily from recombining existing technical methods rather than introducing fundamentally new research questions. Overall, current AI research agents appear better suited to local elaboration than to broadening scientific exploration.

Sparse Autoencoders for Hypothesis Generation

We describe HypotheSAEs, a general method to hypothesize interpretable relationships between text data (e.g., headlines) and a target variable (e.g., clicks). HypotheSAEs has three steps: (1) train a sparse autoencoder on text embeddings to produce interpretable features describing the data distribution, (2) select features that predict the target variable, and (3) generate a natural language interpretation of each feature (e.g., "mentions being surprised or shocked") using an LLM. Each interpretation serves as a hypothesis about what predicts the target variable. Compared to baselines, our method better identifies reference hypotheses on synthetic datasets (at least +0.06 in F1) and produces more predictive hypotheses on real datasets (~twice as many significant findings), despite requiring 1-2 orders of magnitude less compute than recent LLM-based methods. HypotheSAEs also produces novel discoveries on two well-studied tasks: explaining partisan differences in Congressional speeches and identifying drivers of engagement with online headlines.

Language agents achieve superhuman synthesis of scientific knowledge

Language models are known to hallucinate incorrect information, and it is unclear if they are sufficiently accurate and reliable for use in scientific research. We developed a rigorous human-AI comparison methodology to evaluate language model agents on real-world literature search tasks covering information retrieval, summarization, and contradiction detection tasks. We show that PaperQA2, a frontier language model agent optimized for improved factuality, matches or exceeds subject matter expert performance on three realistic literature research tasks without any restrictions on humans (i.e., full access to internet, search tools, and time). PaperQA2 writes cited, Wikipedia-style summaries of scientific topics that are significantly more accurate than existing, human-written Wikipedia articles. We also introduce a hard benchmark for scientific literature research called LitQA2 that guided design of PaperQA2, leading to it exceeding human performance. Finally, we apply PaperQA2 to identify contradictions within the scientific literature, an important scientific task that is challenging for humans. PaperQA2 identifies 2.34 +/- 1.99 contradictions per paper in a random subset of biology papers, of which 70% are validated by human experts. These results demonstrate that language model agents are now capable of exceeding domain experts across meaningful tasks on scientific literature.

Accelerating Scientific Research with Gemini: Case Studies and Common Techniques

Recent advances in large language models (LLMs) have opened new avenues for accelerating scientific research. While models are increasingly capable of assisting with routine tasks, their ability to contribute to novel, expert-level mathematical discovery is less understood. We present a collection of case studies demonstrating how researchers have successfully collaborated with advanced AI models, specifically Google's Gemini-based models (in particular Gemini Deep Think and its advanced variants), to solve open problems, refute conjectures, and generate new proofs across diverse areas in theoretical computer science, as well as other areas such as economics, optimization, and physics. Based on these experiences, we extract common techniques for effective human-AI collaboration in theoretical research, such as iterative refinement, problem decomposition, and cross-disciplinary knowledge transfer. While the majority of our results stem from this interactive, conversational methodology, we also highlight specific instances that push beyond standard chat interfaces. These include deploying the model as a rigorous adversarial reviewer to detect subtle flaws in existing proofs, and embedding it within a "neuro-symbolic" loop that autonomously writes and executes code to verify complex derivations. Together, these examples highlight the potential of AI not just as a tool for automation, but as a versatile, genuine partner in the creative process of scientific discovery.

Towards Automating Scientific Review with Google's Paper Assistant Tool

Artificial intelligence is driving a revolution in scientific discovery, accelerating everything from hypothesis generation to mathematical theorem proving. However, this rapid acceleration is creating a systemic challenge: traditional human peer review cannot scale to match the influx of AI-assisted science. Ultimately, to resolve this tension, we must also deploy AI to accelerate the verification and review process itself. To frame the discussion around this transition, we propose a taxonomy consisting of four progressive levels of AI-human collaboration in scientific evaluation, and discuss various trade-offs involved with each. As a step toward this future, we introduce the Paper Assistant Tool (PAT), an agentic AI framework built for deep scientific review and verification. PAT ingests full scientific manuscripts and produces a comprehensive evaluation, checking theoretical results, validating experiments, suggesting improvements, and identifying potential flaws. By utilizing inference scaling techniques, PAT is able to identify deeper issues than a single model call alone, achieving a 34% improvement over zero-shot recall on mathematical errors in the SPOT benchmark. Pilot deployments of PAT as a pre-submission tool for authors at two major Computer Science conferences -- STOC and ICML -- demonstrate its ability to identify critical errors and suggest substantive improvements to research papers. By catching errors early, PAT eases the cognitive burden placed on referees, while preserving their control over the outcomes of the review process.

Words that Work: Using Large Language Models to Generate and Refine Hypotheses from Text

In this paper, we introduce a data-driven framework for generating and refining hypotheses from text. Our three-step approach–Hypothesize, Intervene, and Predic

Generative AI Meets Open-Ended Survey Responses: Research Participant Use of AI and Homogenization

The growing popularity of generative artificial intelligence (AI) tools presents new challenges for data quality in online surveys and experiments. This study examines participants’ use of large language models to answer open-ended survey questions and describes empirical tendencies in human versus large language model (LLM)-generated text responses. In an original survey of research participants recruited from a popular online platform for sourcing social science research subjects, 34 percent reported using LLMs to help them answer open-ended survey questions. Simulations comparing human-written responses from three pre-ChatGPT studies with LLM-generated text reveal that LLM responses are more homogeneous and positive, particularly when they describe social groups in sensitive questions. These homogenization patterns may mask important underlying social variation in attitudes and beliefs among human subjects, raising concerns about data validity. Our findings shed light on the scope and potential consequences of participants’ LLM use in online research.

How LLMs Distort Our Written Language

Large language models (LLMs) are used by over a billion people globally, most often to assist with writing. In this work, we demonstrate that LLMs not only alter the voice and tone of human writing but also consistently alter the intended meaning. First, we conduct a human user study to understand how people actually interact with LLMs when using them for writing. Our findings reveal that extensive LLM use led to a nearly 70% increase in essays that remained neutral in answering the topic question. Significantly more heavy LLM users reported that the writing was less creative and not in their voice. Next, using a dataset of human-written essays that was collected in 2021 before the widespread release of LLMs, we study how asking an LLM to revise the essay based on the human-written feedback in the dataset induces large changes in the resulting content and meaning. We find that even when LLMs are prompted with expert feedback and asked to only make grammar edits, they still change the text in a way that significantly alters its semantic meaning. We then examine LLM-generated text in the wild, specifically focusing on the 21% of AI-generated scientific peer reviews at a recent top AI conference. We find that LLM-generated reviews place significantly less weight on clarity and significance of the research, and assign scores that, on average, are a full point higher. These findings highlight a misalignment between the perceived benefit of AI use and an implicit, consistent effect on the semantics of human writing, motivating future work on how widespread AI writing will affect our cultural and scientific institutions.

How LLMs Distort Our Written Language

Large language models (LLMs) are used by over a billion people globally, most often to assist with writing. In this work, we demonstrate that LLMs not only alter the voice and tone of human writing but also consistently alter the intended meaning. First, we conduct a human user study to understand how people actually interact with LLMs when using them for writing. Our findings reveal that extensive LLM use led to a nearly 70% increase in essays that remained neutral in answering the topic question. Significantly more heavy LLM users reported that the writing was less creative and not in their voice. Next, using a dataset of human-written essays that was collected in 2021 before the widespread release of LLMs, we study how asking an LLM to revise the essay based on the human-written feedback in the dataset induces large changes in the resulting content and meaning. We find that even when LLMs are prompted with expert feedback and asked to only make grammar edits, they still change the text in a way that significantly alters its semantic meaning. We then examine LLM-generated text in the wild, specifically focusing on the 21% of AI-generated scientific peer reviews at a recent top AI conference. We find that LLM-generated reviews place significantly less weight on clarity and significance of the research, and assign scores that, on average, are a full point higher. These findings highlight a misalignment between the perceived benefit of AI use and an implicit, consistent effect on the semantics of human writing, motivating future work on how widespread AI writing will affect our cultural and scientific institutions.

Believe It or Not: How Deeply do LLMs Believe Implanted Facts?

Knowledge editing techniques promise to implant new factual knowledge into large language models (LLMs). But do LLMs really believe these facts? We develop a framework to measure belief depth and use it to evaluate the success of knowledge editing techniques. We operationalize belief depth as the extent to which implanted knowledge 1) generalizes to related contexts (e.g. Fermi estimates several logical steps removed), 2) is robust to self-scrutiny and direct challenge, and 3) is represented similarly to genuine knowledge (as measured by linear probes). Our evaluations show that simple prompting and mechanistic editing techniques fail to implant knowledge deeply. In contrast, Synthetic Document Finetuning (SDF) - where models are trained on LLM-generated documents consistent with a fact - often succeeds at implanting beliefs that behave similarly to genuine knowledge. However, SDF's success is not universal, as implanted beliefs that contradict basic world knowledge are brittle and representationally distinct from genuine knowledge. Overall, our work introduces measurable criteria for belief depth and enables the rigorous evaluation necessary for deploying knowledge editing in real-world applications.

Believe It or Not: How Deeply do LLMs Believe Implanted Facts?

Knowledge editing techniques promise to implant new factual knowledge into large language models (LLMs). But do LLMs really believe these facts? We develop a framework to measure belief depth and use it to evaluate the success of knowledge editing techniques. We operationalize belief depth as the extent to which implanted knowledge 1) generalizes to related contexts (e.g. Fermi estimates several logical steps removed), 2) is robust to self-scrutiny and direct challenge, and 3) is represented similarly to genuine knowledge (as measured by linear probes). Our evaluations show that simple prompting and mechanistic editing techniques fail to implant knowledge deeply. In contrast, Synthetic Document Finetuning (SDF) - where models are trained on LLM-generated documents consistent with a fact - often succeeds at implanting beliefs that behave similarly to genuine knowledge. However, SDF's success is not universal, as implanted beliefs that contradict basic world knowledge are brittle and representationally distinct from genuine knowledge. Overall, our work introduces measurable criteria for belief depth and enables the rigorous evaluation necessary for deploying knowledge editing in real-world applications.

Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting

Large Language Models (LLMs) can achieve strong performance on many tasks by producing step-by-step reasoning before giving a final output, often referred to as chain-of-thought reasoning (CoT). It is tempting to interpret these CoT explanations as the LLM's process for solving a task. This level of transparency into LLMs' predictions would yield significant safety benefits. However, we find that CoT explanations can systematically misrepresent the true reason for a model's prediction. We demonstrate that CoT explanations can be heavily influenced by adding biasing features to model inputs--e.g., by reordering the multiple-choice options in a few-shot prompt to make the answer always "(A)"--which models systematically fail to mention in their explanations. When we bias models toward incorrect answers, they frequently generate CoT explanations rationalizing those answers. This causes accuracy to drop by as much as 36% on a suite of 13 tasks from BIG-Bench Hard, when testing with GPT-3.5 from OpenAI and Claude 1.0 from Anthropic. On a social-bias task, model explanations justify giving answers in line with stereotypes without mentioning the influence of these social biases. Our findings indicate that CoT explanations can be plausible yet misleading, which risks increasing our trust in LLMs without guaranteeing their safety. Building more transparent and explainable systems will require either improving CoT faithfulness through targeted efforts or abandoning CoT in favor of alternative methods.

Language Models Don't Always Say What They Think: Unfaithful Explanations in Chain-of-Thought Prompting

Large Language Models (LLMs) can achieve strong performance on many tasks by producing step-by-step reasoning before giving a final output, often referred to as chain-of-thought reasoning (CoT). It is tempting to interpret these CoT explanations as the LLM's process for solving a task. This level of transparency into LLMs' predictions would yield significant safety benefits. However, we find that CoT explanations can systematically misrepresent the true reason for a model's prediction. We demonstrate that CoT explanations can be heavily influenced by adding biasing features to model inputs--e.g., by reordering the multiple-choice options in a few-shot prompt to make the answer always "(A)"--which models systematically fail to mention in their explanations. When we bias models toward incorrect answers, they frequently generate CoT explanations rationalizing those answers. This causes accuracy to drop by as much as 36% on a suite of 13 tasks from BIG-Bench Hard, when testing with GPT-3.5 from OpenAI and Claude 1.0 from Anthropic. On a social-bias task, model explanations justify giving answers in line with stereotypes without mentioning the influence of these social biases. Our findings indicate that CoT explanations can be plausible yet misleading, which risks increasing our trust in LLMs without guaranteeing their safety. Building more transparent and explainable systems will require either improving CoT faithfulness through targeted efforts or abandoning CoT in favor of alternative methods.

Knowledge Collapse in LLMs: When Fluency Survives but Facts Fail under Recursive Synthetic Training

Large language models increasingly rely on synthetic data due to human-written content scarcity, yet recursive training on model-generated outputs leads to model collapse, a degenerative process threatening factual reliability. We define knowledge collapse as a distinct three-stage phenomenon where factual accuracy deteriorates while surface fluency persists, creating "confidently wrong" outputs that pose critical risks in accuracy-dependent domains. Through controlled experiments with recursive synthetic training, we demonstrate that collapse trajectory and timing depend critically on instruction format, distinguishing instruction-following collapse from traditional model collapse through its conditional, prompt-dependent nature. We propose domain-specific synthetic training as a targeted mitigation strategy that achieves substantial improvements in collapse resistance while maintaining computational efficiency. Our evaluation framework combines model-centric indicators with task-centric metrics to detect distinct degradation phases, enabling reproducible assessment of epistemic deterioration across different language models. These findings provide both theoretical insights into collapse dynamics and practical guidance for sustainable AI training in knowledge-intensive applications where accuracy is paramount.

Knowledge Collapse in LLMs: When Fluency Survives but Facts Fail under Recursive Synthetic Training

Large language models increasingly rely on synthetic data due to human-written content scarcity, yet recursive training on model-generated outputs leads to model collapse, a degenerative process threatening factual reliability. We define knowledge collapse as a distinct three-stage phenomenon where factual accuracy deteriorates while surface fluency persists, creating "confidently wrong" outputs that pose critical risks in accuracy-dependent domains. Through controlled experiments with recursive synthetic training, we demonstrate that collapse trajectory and timing depend critically on instruction format, distinguishing instruction-following collapse from traditional model collapse through its conditional, prompt-dependent nature. We propose domain-specific synthetic training as a targeted mitigation strategy that achieves substantial improvements in collapse resistance while maintaining computational efficiency. Our evaluation framework combines model-centric indicators with task-centric metrics to detect distinct degradation phases, enabling reproducible assessment of epistemic deterioration across different language models. These findings provide both theoretical insights into collapse dynamics and practical guidance for sustainable AI training in knowledge-intensive applications where accuracy is paramount.