AI-Assisted Scientific Research

AI-assisted research systems generate many failed attempts, but those failures rarely become a durable, shared knowledge asset. We propose a negative knowledge memory layer: a curator agent converts each failed attempt into a bounded, typed record in a shared bank, and a downstream research agent explicitly adopts or rejects those records before proposing its next experiment. We evaluate this layer in two settings: same-task retry on ScienceAgentBench and cross-task scientific research on two nonlinear math-physics PDE problems. The negative knowledge layer outperforms vanilla AutoResearch baselines while using fewer tokens; agents with the negative knowledge bank solve new tasks that all baselines fail to solve in PDE systems research. We also show that the previous negative knowledge bank can transfer and enhance AutoResearch on different PDE problems. These results suggest that structured negative knowledge is a knowledge asset that should be explicitly maintained in broader AI-engaged scientific research beyond a memory-compression or debugging aid, alongside positive findings, as a collective infrastructure for scientific memory. Code is available at https://github.com/hch-wang/Negative_Knowledge.

We develop a text-to-SQL (structured query language) system based on large language models (LLMs) using in-context learning and apply it to the Automatic Learning for the Rapid Classification of Events (ALeRCE) astronomical database. ALeRCE is a community broker for the Zwicky Transient Facility and the Vera C. Rubin Observatory. The system enables users to query the database in natural language (NL) and generates executable SQL queries. To develop and evaluate the system, we constructed a dataset of 110 NL/SQL pairs. We propose a step-by-step generation framework comprising four modules: schema linking, query classification, prompt decomposition, and self-correction. The performance of thirteen LLMs is evaluated using in-context learning and prompt engineering techniques. Text-to-SQL performance is assessed using the perfect-match (PM) rate for row identifiers (e.g., object identifiers) and column identifiers (i.e., column names). The proposed step-by-step framework consistently outperforms a direct-inference baseline, while the self-correction module consistently reduces execution errors. For Claude Opus 4.6, PM performance on row (column) identifiers is high for simple queries, reaching 0.97 (0.94), and decreases with query complexity to 0.44 (0.72) for medium queries and 0.59 (0.49) for hard queries. Among the thirteen evaluated models, the best-performing LLMs for the text-to-SQL task are Claude Opus 4.6, Gemini 2.5 Pro, Gemini 3 Flash, and GPT-5.2-Codex.

As Large Language Model based agents enter autonomous scientific research, their ability to resist pseudoscience becomes increasingly important. Otherwise, such systems may rapidly generate plausible yet misleading studies that contaminate academic literature and erode trust in science. We present PseudoBench, an adversarial benchmark for evaluating whether agentic auto-research systems can identify and resist pseudoscientific narratives. PseudoBench contains 200 curated pseudoscientific claim-evidence pairs across five domains and evaluates agents through an end-to-end research pipeline from experiments to writing. Testing seven state-of-the-art agents, we find that current systems readily produce persuasive reports that align with pseudoscientific premises with near-zero refusal rates and the highest resistance of only 27.4%. Stronger agents risk packaging pseudoscience in more sophisticated scientific language, increasing its apparent credibility. These findings reveal an alarming capacity to fuel pseudoscience, calling for scientific alignment before widespread deployment.

Meta-analysis is a demanding form of evidence synthesis that combines literature retrieval, PI/ECO-guided study selection, and statistical aggregation. Its structured, verifiable workflow makes it an ideal substrate for evaluating systematic scientific reasoning, yet existing benchmarks lack ground truth across the full retrieval-screening-synthesis pipeline. We introduce MetaSyn, a dataset of 442 expert-curated meta-analyses from Nature Portfolio journals. Each entry pairs a research question with PI/ECO criteria, a retrieval corpus of 140k PubMed articles, verified positive studies, hard negatives that are topically similar but PI/ECO-ineligible, and complete search strategies and date bounds. Benchmarking twelve pipeline configurations (nine RAG variants and a protocol-driven agent) reveals a critical screening bottleneck: despite a retrieval ceiling of 90.9% recall at K=200, no system recovers more than 52.7% of ground-truth included literature. Current LLMs fail to reliably separate eligible studies from PI/ECO-failing distractors in pools of comparable topical relevance. Stage-attributed metrics capture where systems succeed and fail; a single end-to-end score does not.

Using an open problem from the EC 2025 paper "Stable Menus of Public Goods" as a testbed, we conduct experiments to understand the effectiveness of different AI-for-EconCS research workflows. Specifically, we study three questions: Does providing human intuition in the prompt help? Does automated multi-turn interaction help? And, does an LLM outperform a first-year PhD student? Regarding the first two questions, we provide evidence for the following workflow suggestions: (1) prompting with human intuition can encourage the LLM to have better "taste", (2) multi-turn workflows help when the pipeline encourages "ambitious" steps. Regarding the third question, using an unpublished manuscript written by the paper's senior authors prior to collaborating with the first-year PhD student, we compare the effectiveness of the LLM with that of the first-year PhD student, and find that the LLM is slightly less effective.

Large Language Models (LLMs) are increasingly used to guide research methodology, yet their default methodological tendencies under minimal prompting remain unclear. Here, we prompt GPT-5.1, Gemini 3 Pro, and DeepSeek-V3.2 with an LLM-extracted research question from each of 1,000 recent arXiv computer-science papers and compare the resulting methodology suggestions against a paper-derived experimental inventory. Since we provide only the research question, the differences we measure reflect initial suggestions and not how optimal those suggestions are. We extract structured method features from both sources, map them into a shared taxonomy, and quantify divergence across multiple taxonomy dimensions including model provider, dataset task type, and evaluation metric type. The strongest imbalance appears in provider choice, with Jensen-Shannon divergence about 3-5x larger than any other taxonomy dimension. Other/Academic single-occurrence models are underrepresented by 23-24 percentage points, while reused academic/community models are slightly overrepresented (4-6pp). LLMs also suggest a much narrower range of methods overall: the effective number of model entities contracts from 1,232 to 59-96, and inter-LLM rank correlations (0.55-0.68) generally exceed LLM-to-paper correlations (0.33-0.56), so the distortions are largely shared across models. Popularity baselines, BM25 retrieval calibration, and paper-level similarity tests confirm that the outputs are query-specific responses, but filtered through a narrower set of options. Researchers who rely on LLM suggestions without cross-checking therefore risk narrowing their methodological search space toward a more concentrated default.

Scientific publication is still organized primarily around static manuscripts, even though much of scientific progress depends on tacit know-how: how to run code, reproduce figures, interpret edge cases, choose useful follow-up directions, and avoid failed paths. Large language model agents create an opportunity to publish not only knowledge, but also operational know-how in a form that future readers and researchers can directly use. This paper outlines the Agentic Publication Protocol (APP), a lightweight repository format for packaging a paper together with code, data, environment information, reproducibility instructions, and an agent-facing instruction file. APP treats a version-controlled repository as the publication object and uses \texttt{AGENTS.md} and optional skills to define a paper agent that can explain the work, reproduce key results when possible, and support follow-up research. We describe the design principles and details of the protocol, as well as the agent skills useful for publishing papers under the protocol. We also describe development tools for evaluating and improving the protocol and associated agent skills. Finally, we provide a broader discussion of the future of scientific research in the agent era.

AI-assisted mathematics is often evaluated on solving predefined problems. In practice, however, many important advances begin earlier, when a vague research intuition is transformed into a concrete problem, a promising route, and a theorem family worth proving. This report studies that stage through a case study that led to sign-embedding quantum algorithms for matrix equations and matrix functions, foundational primitives in quantum linear algebra and operator-output quantum algorithms. The project began with a human-originated intuition that rational approximation is especially effective for jump-type functions such as the sign function, and might therefore serve as a design principle for quantum algorithms. Rather than merely assisting after the problem was fixed, AI-assisted exploration, including workflows later integrated into the agentic AI-mathematician system AIM, played a key role in expanding this intuition into a route map, comparing candidate formulations, and converging toward sign embedding as the central framework. AIM then helped connect a known matrix-sign identity to wider classes of matrix equations and matrix functions, and drafted proof and complexity calculations. The decisive scientific judgments remained human: selecting which human-AI-expanded routes were worth pursuing, rejecting a Cayley-trapezoidal approximation when its validity required a hidden condition, and refining the Sylvester implementation from a coarse quadratic-gap query route to the final factorized and scaled analysis. The report argues that human-AI co-discovery workflows, with systems such as AIM as important components, are most valuable not as standalone theorem provers, but as research partners for problem formation, connection discovery, derivation, and skeptical review inside a human-gated research loop.

We can do more than defend science from a flood of AI-assisted papers. Used well, AI offers a historic opportunity to correct distortions in the publication system, help us publish fewer and better papers, and give scientists back the time to do their best work.

Reproducibility in the social and behavioral sciences is typically evaluated by independent researchers who reanalyze the original data to assess whether the published findings can be recovered. However, such approaches are resource-intensive and difficult to scale. Here, we show that large language models (LLMs) can automate reproducibility assessments. Using N = 180 published studies with predefined claims from the behavioral and social sciences, we compare LLM-generated analyses with the original findings. For 11 studies, the LLM pipeline could not produce a viable effect size estimate. For the remaining studies, the LLM reached the same qualitative conclusion as the original study in 80% of cases, and recovered the original effect sizes (using a +/-0.05 tolerance in Cohen's d) in 24% of studies. In a subset with human reanalyses, the LLM reached the same qualitative conclusion as the original study in 95% of studies, similar to human reanalysts (83%), and the LLM recovered the original effect sizes using a +/-0.05 tolerance in 40% of studies, again broadly similar to human reanalysts (28%). Given the current capabilities and limitations of LLMs, the findings show that LLMs can support systematic audits of empirical results rather than substitute expert judgment. As such, LLMs can serve as a scalable screening tool to improve the rigor and reproducibility in empirical research.

Large language models (LLMs) are increasingly used as research assistants, yet it remains unclear whether they can calibrate research takeaways to the strength and scope of the supporting evidence. We study evidence-calibrated scientific briefing: given a bounded package of related papers, a system should generate package-level takeaways with evidence strength, scope boundaries, and missing-evidence caveats. We contribute a verified pilot benchmark of 16 heterogeneous scientific evidence packages and 96 human-verified takeaways, and we use CalBrief, an auditable role/gap/strength framework, as a diagnostic probe to locate where briefing breaks down. Under a fair-schema evaluation, structured organization improves role and gap reasoning, but an explicit strength-calibration policy is systematically over-conservative and falls below majority and direct-LLM baselines. To explain why, we run a controlled diagnostic across three closed-model backbones (GPT-4o, Claude Sonnet, Gemini Flash) that separates three potential causes of conservatism. Approximately 63% of the conservatism gap is attributable to expanding the label space from binary {moderate, weak} to four-way {moderate, weak, uncertain, insufficient_evidence} (p < 0.001 across all backbones); only 1% is attributable to gap/scope signal injection (not significant); the remaining 36% arises from the pipeline policy itself. We also find that 4-way predictions can be post-hoc collapsed back to binary and then match or exceed direct binary prompting, so the extra labels carry information that strict matching hides. Label-level strength judgment and auditable evidence organization are distinct abilities currently in tension, and should be evaluated separately for LLM research assistants.

Large language models (LLMs) are increasingly used for tasks once reserved for trained researchers, including hypothesis generation, specification choice, and drafting conclusions. We argue that the reliability of AI-assisted research depends not only on model capability, but also on how cognitive labour is structured between humans and machines. We study this problem through Human-in-the-Loop Economic Research (HLER), a decision architecture based on pre-commitment, decision sequencing, accountability, and attention allocation. In a pre-specified 2*4 factorial experiment with 280 complete research runs across four datasets, an unconstrained multi-agent baseline produced critical failures in 72% of runs. Using the same underlying model, the same agent decomposition, and identical prompts for the shared reasoning agents, HLER reduced the failure rate to 16% by imposing three architectural commitments: LLMs reason but do not execute data work, data and estimation are handled deterministically, and three human decision gates bind the workflow. Fisher's exact test rejects equality of failure rates at p<0.001. Reliability gains were largest on the least publicly represented dataset, a Qing-dynasty population register, consistent with a task-based production model with Frechet-distributed output quality. An 80-run ablation suggests that deterministic computation and human gates contribute independently, with exploratory evidence of complementarity. We interpret HLER as a research harness rather than an autonomous AI scientist: it sharply reduces failures, makes residual weaknesses more visible, and prevents unreliable claims from being advanced as publication-ready outputs.

Autoresearch agents now propose, evaluate, and select scientific candidates against a metric, and that metric is usually an aggregate reduced over a heterogeneous space of regions, slices, or cohorts. We show that when scientific validity lives in that disaggregated structure, the aggregate can rank the wrong candidate first. The headline number improves while the structure underneath inverts, so a decision made on the number accepts a candidate that quietly breaks the model. The failure is not domain-specific. It appears wherever a candidate's validity is multi-dimensional but its verifier is a single reduction. We demonstrate the inversion on a fire-model task in the Ecosystem Demography model. The highest-scoring candidate and a slightly lower one are within noise of each other on global score, yet the top-scoring one collapses the protected boreal regions while the other preserves them. What separates them is the per-region behavior, not the headline number. This decision should not be left to the agent that produced the candidates. The agent optimizing the score is the last party likely to catch the score being wrong, and a prompt has no remaining turn once the agent has stopped. We move the decision to an external control loop that audits each candidate on its disaggregated behavior and acts after the agent has decided. It can demote a candidate the agent would have accepted, and it can reopen a run the agent had declared finished. Our contribution is the inversion finding itself, and a search-discipline protocol that decides on reviewable candidate-effect evidence instead of the score.

As autonomous research agents and AI co-scientist systems push large language models (LLMs) from drafting toward end-to-end manuscript production, the bottleneck shifts from generation to verification. Fluent LLM output can hide fabricated citations, numbers that drift from source tables, and unmet reporting-guideline items; existing tools generate without verifying, and self-critique inherits the blind spots that produce confident fabrication. We describe an architecture pairing generation with verification, resting on three principles: decompose the workflow into self-contained skills, gate every stage transition with halt-on-failure, and resolve each integrity question with the cheapest sufficient mechanism, a deterministic, re-executable check where one suffices and a prose-level probe only where interpretation is unavoidable. This determinism-where-possible split, organized as an integrity-gate taxonomy, is the core contribution. It is realized as MedSci Skills, an open-source toolkit of 43 skills with a 21-detector deterministic tier, evaluated on three public-dataset pipelines (STARD, PRISMA, STROBE) and a seeded-defect ablation. Across the three pipelines every content-hash manifest verified clean and the gates surfaced real defects; on 27 identical injected defects the deterministic gates detected all 27 with no false positives on the matched clean fixtures, whereas a single-prompt LLM reviewer detected 11, its misses in code, bibliography, and style defects the prose hides. Determinism-where-possible verification yields an auditable, re-executable trail that exposes the evidence a human needs to check an LLM-assisted manuscript: feasibility and reproducibility evidence, not a claim of human-competitive quality, which a separate blinded study addresses. MedSci Skills is MIT-licensed and archived (v3.8.0).

Large language models (LLMs) are increasingly used in academic research workflows, but scholarly tasks require high factual precision and therefore expose a key weakness: overconfidence. Here, overconfidence is defined behaviorally as the tendency to produce confident, assertive, and well-formatted outputs even when the underlying knowledge is incomplete or unverifiable, rather than as a calibration gap between stated confidence and accuracy. To examine this issue, we introduce GIScholarBench, a benchmark built from 10,865 papers published in 25 core GIScience journals between 2020 and 2025. The benchmark covers three tasks with increasing cognitive complexity: metadata retrieval, literature linking, and research direction generation. We evaluate Claude Sonnet 4.5, Gemini 3, and ChatGPT 5.3 through their native web interfaces under real-world user-facing conditions. Results show consistent overconfidence across all tasks. In metadata retrieval, ChatGPT 5.3 achieves the highest accuracy, but all models still generate definitive titles and DOIs when predictions are wrong. In literature linking, Claude Sonnet 4.5 recovers the most references, but all models show a clear gap between top-ranked retrieval and longer citation lists, suggesting that references are extended beyond reliable retrieval capacity. In research direction generation, AI-generated directions show lower topic coverage, higher novel miss rates, and lower semantic diversity than real future-citing papers. These findings suggest that LLM overconfidence is task-invariant but takes different forms: factual overgeneration in retrieval, unreliable citation expansion in literature linking, and overconfidence in output completeness during research ideation.

Foundation models for astronomical surveys offer powerful learned representations that can be transferred to downstream regression tasks such as galaxy property estimation. However, point predictions alone are insufficient for scientific inference; reliable uncertainty quantification (UQ) is essential. We compare seven UQ methods on galaxy property regression using frozen AION-1 foundation-model embeddings, predicting redshift, stellar mass, stellar-population age, gas-phase metallicity, and specific star-formation rate, from Legacy Survey photometry/imaging and DESI spectra, with PROVABGS-derived labels. Distribution-free conformal methods achieve marginal coverage within $\sim$1,pp of the nominal 90% across all properties, while non-conformal baselines (Deep Ensembles, MC~Dropout) fail to calibrate reliably. Among conformal approaches, Conformalized Quantile Regression (CQR) delivers the best coverage in the bin with the poorest model predictions. More importantly, only the Locally Valid and Discriminative (LVD) framework -- particularly when operating on AION-1 embeddings -- also provides finite-sample \emph{local validity}, producing intervals that adapt to each galaxy's local prediction difficulty rather than relying on marginal guarantees alone. These results establish conformal prediction, and LVD in particular, as the preferred UQ framework for uncertainty-aware inference on foundation-model embeddings in astrophysics.

As foundation models advance and agent scaffolding becomes increasingly sophisticated, agents have demonstrated remarkable proficiency in complex, long-horizon coding tasks and even autonomous experiment execution. Despite their evolution from research assistants into autonomous research agents, these systems still exhibit significant limitations in field sensitivity, research ethics, and nuanced scientific judgment. Consequently, frontier agents remain unable to fully replace human researchers. To bridge this gap, we conceptualize the AARR (Act As a Real Researcher) benchmark series. Unlike existing benchmarks that primarily assess macro-level execution capabilities, AARR focuses on whether agents can emulate the professionalism, thoroughness, and nuanced reasoning that characterize human researchers in granular research scenarios. In this work, we propose AARRI-Bench (Act As a Real Research Intern), the first benchmark in this series. We conduct extensive experiments across frontier models and agentic systems, revealing that even the best-performing configuration (Mini-SWE-Agent with Claude Opus 4.7) achieves only 68.3% success rate, frequently overlooking subtle yet critical details that are obvious to real human researchers. Our results indicate that developing researcher-like AI requires further exploration of research behavior, rather than merely complex scaffolding. Our data is released at https://github.com/AARR-bench/AARRI-bench.

The rapid pace of scientific publishing has made the identification and synthesis of high-impact work an increasingly urgent challenge. We introduce MIRAI (Multi-year Inference of Research trends and Academic Impact), a deep learning framework that predicts paper impact using only it's title, abstract, and publication date. We train MIRAI on the arXiv academic graph to predict 5-year PageRank and citation counts, achieving Spearman's $ρ$ of 0.4686 on PageRank prediction and 0.6192 on citation prediction for papers published in 2021. We propose a research ideation pipeline built on top of MIRAI that produces research ideas oriented towards high impact. These ideas were judged as more impactful than a baseline without MIRAI by an unbiased LLM judge at a 4:3 ratio. We make the 5-year citation prediction model publicly available at https://predict-paper-impact.vercel.app.

Systematic reviews rely on forest plots to synthesise quantitative evidence across biomedical studies, but generating them remains a fragmented and labour-intensive process. Researchers must interpret complex clinical texts, manually extract outcome data from trials, define appropriate interventions and comparators, harmonise inconsistent study designs, and carry out meta-analytic computations-typically using specialised software that demands structured inputs and domain expertise. While recent work has demonstrated that large language models can extract study-level data from unstructured text, no existing system automates the complete pipeline from raw documents to synthesised forest plots. To address this gap, we introduce AutoForest, the first end-to-end system that generates publication-ready forest plots directly from biomedical papers. Given one or more study papers, AutoForest automatically suggests ICO (Intervention, Comparator, Outcome) elements, extracts outcome data, performs statistical synthesis, and renders the final forest plot. We describe the system architecture, user interface and demonstrate its effectiveness on real-world examples through a user study involving clinicians, showing how AutoForest can accelerate evidence synthesis and substantially lower the barrier to conducting meta-analyses.

Methodology Inspiration Retrieval (MIR) asks a system to retrieve prior papers whose methods can inspire a new research proposal. Unlike general scientific retrieval, the central challenge is not topical similarity but whether a candidate paper provides concrete mechanisms that can instantiate an abstract methodological need. Existing MIR dense retrievers provide strong paper-level rankings, but the returned lists do not expose how proposal needs are bridged by retrieved methods, where evidence is weak, or which complementary snippets may help. We propose HyBIRD, a frozen-anchor framework that treats MIR as hyperbolic bridge retrieval and post-hoc method diagnosis. HyBIRD keeps a strong MIR dense retriever fixed, learns lightweight point, cone, and factorized hyperbolic bridge variants, and uses LLM-assisted method blocks for post-hoc explanation and evidence selection. On the MIR benchmark, the factorized bridge reaches 59.034 mAP while preserving the dense anchor's strong retrieval behavior. More importantly, HyBIRD converts ranked papers into inspectable query need profiles, factor coverage, maturity views, and complementary evidence bundles. The results suggest that hyperbolic geometry is most useful as calibrated structure over a dense anchor, rather than as a standalone replacement for dense retrieval.

This paper examines records retrieved from the ClinicalTrials.gov registry to characterize temporal trends in AI terminology and the geographical distribution of AI trials. The work also reports on an exploratory hybrid human-AI approach to analyzing human-AI interaction trends in registered clinical trials. The hybrid workflow comprised a frontier generative AI model (GPT-5.5) and human review to screen and categorize records returned by an AI-focused search. The findings indicate a marked increase in AI-related trials over time, with recent growth in references to machine learning, deep learning, chatbots, GPTs, and large language models. Geographically, China and the United States accounted for the largest numbers of AI-related trials, with notable recent increases in several other countries including Italy, France, Spain, the UK and Turkey (Türkiye). In a random sample of 100 records, human and AI classifiers showed good agreement in identifying studies not substantively using AI, but lower agreement in classifying human-AI interaction, particularly where health professional interaction was ambiguous or insufficiently described. Overall, the results suggest that hybrid human-AI screening of clinical trial records is potentially viable, but clearer trial reporting and more precise interaction definitions will benefit the process.

AI-assisted research compresses ideation, implementation, evaluation, and manuscript writing into a single interactive loop. This compression is useful, but it also creates a publication risk: paper claims can become easier to state than to audit. We present ResearchLoop, an evidence-gated control plane for AI-assisted computational research. ResearchLoop treats research questions, task contracts, evidence objects, claim ledgers, closeouts, and paper bindings as durable project state, realized here as a repository-backed runtime. This technical report provides the complete protocol specification, state model, transition rules, claim-admission algorithm, and insight-compounding mechanism. It also reports the full experimental record spanning nine versions (V0--V9), including a self-hosting case study, a controlled task-suite study with component ablations, a mathematical olympiad evaluation, and a supplementary SciCode boundary experiment evaluated with the official generated-code harness. All artifacts, manifests, and verification reports are preserved in the project repository.

Antibodies play a central role in the immune response by specifically recognizing and neutralizing antigens, and therapeutic antibodies have become major drugs for cancer and autoimmune diseases. However, their discovery still relies on extensive in vitro screening, and accurate computational modeling of antibody structures and antibody-antigen interactions can prioritize candidates, reduce experimental burden, and accelerate rational design. Despite recent advances in high-accuracy protein and complex prediction, a persistent performance gap remains for antibody-related tasks compared with general protein-protein interactions, limiting downstream design. This thesis investigates why antibody-related tasks are harder and proposes improvements along two complementary directions. First, we investigate protein language model (PLM)-based methods for antibody and antibody-antigen structure prediction. Using embeddings from multiple PLMs, our approach achieves the best CDR-H3 accuracy among compared PLM-based methods on antibody monomer prediction. Extending it to complex prediction does not generalize: without co-evolutionary signals between antibody and antigen, single-sequence PLM representations do not reliably identify binding interfaces. Second, we develop two MSA-based interventions for antibody-antigen complex prediction: MSA refinement, which combines CDR-focused filtering with depth recovery from a larger sequence database, and convergence-aware recycling, which selects a stable intermediate recycle state for final diffusion sampling. Together, these interventions provide consistent gains over the AlphaFold3 baseline on a held-out antibody-antigen test set. Because the methods modify MSA construction and recycling behavior rather than model parameters, they apply without retraining or weight access.

This report explores detector design considerations for the Future Circular Collider in its electron-positron mode (FCC-ee) through an extended dialogue between a physicist and an AI assistant. Starting from initial "prejudice" detector concepts proposed by the AI assistant without explicit physicist input, each subsystem is examined in detail, with the AI's assumptions challenged and revised through the exchange. The discussion covers the full detector from beam pipe to luminosity monitor, with particular attention to the interplay between subsystem choices and the practical considerations - calibration, stability, and operational simplicity - that are essential for a fifteen-year precision physics program. The narrative documents how the integrated detector design evolved substantially from the starting point to revised "prejudice" detector concepts of the AI assistant. The focus of this report is on the process to illustrate both the potential and the limitations of human-AI collaboration in experimental physics design, and the physics capabilities of any of the "prejudice" detector concepts remain to be explored.

AI Scientists have shown promising progress across multiple stages of the research pipeline, among which automatic scientific paper writing remains a formidable challenge. The Introduction writing is especially challenging, which demands not only linguistic fluency, but logical soundness and verifiable faithfulness. Most AI-assisted methods treat the task as text generation instead of reasoning and structuring, leading to severe drawbacks, e.g., hallucinating citations. To address this, we first formulate the Content-Conditional Introduction Generation (CCIG) task, which requires grounding the Introduction in the paper's core evidence. We then propose LECTOR, a novel Logic-Expression Co-Reinforcement Learning framework that can strictly follow the scientist's logic, add high-quality citations and keep structured expressions. LECTOR first constructs a logic-reasoning graph from the paper's main body to serve as a verifiable logical blueprint. Subsequently, it employs a Logic-Expression Co-Rewarding mechanism to jointly optimize for both the graph's structural fidelity and the final narrative's quality. We conduct a dataset from Nature Communications papers to assess our method. Extensive experiments show consistent improvements in both logic fidelity and Introduction generation quality metrics, e.g., Graph Quality (+26.7%), Citation Quality (+8.6%), and Paper Consistency (+3.3%). Code and data are available at https://github.com/Xiao-Youth/LECTOR.

Large language models (LLMs) can support scientific literature synthesis, but remain prone to hallucinated references, uneven coverage, and weakly grounded thematic organization. We evaluate whether bibliometric structure improves LLM-assisted synthesis by comparing six pipelines for generating cluster descriptions under different levels of evidence and structure. Using 100 published bibliometric analyses, we reconstruct Scopus corpora, extract human-written cluster descriptions, and assess outputs by human alignment, semantic coverage, clustering quality, graph quality, and reference grounding. Results show that LLMs produce descriptions semantically close to human-written ones, but are unreliable when asked to infer bibliometric structure from scratch. Performance improves when bibliometric algorithms define the clusters and the LLM interprets them. Overall, LLM-assisted bibliometric synthesis is most promising as a hybrid workflow in which algorithms provide auditable structure and LLMs generate readable descriptions.

Collaboration is the defining mode of modern science, yet its core mechanism -- feedback -- remains hard to observe, difficult to scale, and unequally distributed. Here we test whether large language models (LLMs) can contribute to this hidden but vital practice and reallocate scientific feedback, an essential yet scarce resource for knowledge production. In a global large-scale randomized field experiment, we delivered customized LLM-generated feedback for over 31,000 arXiv preprints across 150 fields and more than 45,000 researchers from 133 geographic regions. Relative to controls, authors who received feedback had a significantly higher likelihood of revising their manuscripts, corresponding to a 12.55% relative increase over the baseline revision rate. Exposure to AI feedback also increased authors' subsequent use of LLM tools in their future papers, suggesting longer-run shifts in scientific practice. These effects were strongest among authors from non-English-dominant research regions, manuscripts less embedded in the scholarly literature, and teams with lower h-indexes and earlier career stages, consistent with the idea that AI feedback may provide the greatest benefit where access to timely critique is otherwise limited. Together, these findings provide causal evidence that structured AI-based interventions can transform access to scientific feedback from a largely private advantage into a more widely distributed resource, with broader implications for productivity, equity, and capacity across the global research system.

Large Language Models (LLMs) are central to the one-for-all intelligent paradigm, but they face a fundamental challenge when dealing with heterogeneous scientific data such as molecules: the inherent gap between discrete linguistic symbols and topological molecular or continuous reaction data leads to significant information loss and semantic noise in text-based reasoning. We propose SciCore-Mol, a modular framework that bridges this gap through three deeply integrated pluggable cognitive modules: a topology-aware perception module, a latent diffusion-based molecular generation module, and a reaction-aware reasoning module. Each module is coupled to the LLM backbone through learned representation interfaces, enabling richer information exchange than is possible with text-only tool feedback. Our experiments on diverse chemical tasks demonstrate that SciCore-Mol achieves strong comprehensive performance across molecular understanding, generation, reaction prediction, and general chemistry knowledge, with an 8B-parameter open-source system that is competitive with and in several dimensions surpasses proprietary large models. This work provides a systematic blueprint for equipping LLMs with scientific expertise through decoupled, pluggable, and flexibly orchestrated modules, with direct implications for drug design, chemical synthesis, and broader scientific discovery.

Stellar spectra encode key information on the physical properties and chemical compositions of stars. Accurate stellar parameter determination is essential for addressing major questions such as galaxy and stellar evolution. Large-scale spectroscopic surveys have accumulated unprecedented spectral data. Traditional feature extraction or model-fitting approaches struggle with high-dimensional, massive datasets, limited generalization, and computational inefficiency. Recent advances in large language models demonstrate strong generalization and feature-learning in tasks like natural language processing, DNA/RNA sequence analysis, and protein/chemical parsing. Stellar spectra are continuous sequential signals, enabling the transfer of language models to stellar spectroscopy. Here, we propose a two-stage large language model framework for stellar parameter inference, achieving accurate estimation of effective temperature, surface gravity, metallicity, and abundances of ~20 chemical elements. Scaling-law analyses show systematic performance improvements with increasing data, providing a scalable framework for forthcoming large-scale surveys.

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond conventional function annotation. We propose TriProRep, a structure-aware pretraining method that jointly models three aligned residue-level views: amino-acid identity, backbone geometry, and local full-atom geometry, discretely encoded via VQ-VAE tokenizers. By pretraining to recover original tokens from generator-corrupted views, TriProRep learns to distinguish plausible but incorrect cross-view augmentations from the original protein. We further introduce RepSP, a benchmark for evaluating protein representations in structure-predictive settings. RepSP tests three uses of representations: homodimer co-folding from apo-chain representations, residue-level prediction of homodimer-derived interaction properties, and representation-aligned monomer structure prediction. Across these tasks, TriProRep improves over sequence-only and prior structure-aware representation models, while maintaining competitive performance on conventional benchmarks.