AI-Assisted Scientific Research
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14 papers in the last four weeks, up 133% on the four weeks before. 0.1% of all new papers.
Latest papers 162
Generating a rigorous paper introduction with large language models (LLMs) remains challenging, since it requires coordinating background, gap identification, method and contribution within a coherent narrative. Existing solutions externalize this process as multi-stage prompts or agent workflows which are expensive and vulnerable to cross-stage drift. We propose StructPO, a struct-aware policy learning framework that internalizes the entire multi-stage writing workflow into a single-pass policy controlled by explicit stage tokens. StructPO introduces struct-aware credit assignment to decouple local stage quality from global coherence and refinement-guided optimization to internalize revision behavior into the first-pass policy. Experiments show that StructPO improves semantic alignment, structural rationality and inference efficiency over workflow-based baselines, generalizes to out-of-domain settings, and remains competitive with GPT-5.1 in human evaluation when scaled to Qwen3-32B. These results show that internalizing academic writing workflows through fine-grained policy optimization offers a viable alternative to costly external orchestration.
A General-Purpose VLM Can Teach an Astronomy Foundation Model to Better Recognize Galaxy Morphology
Existing astronomy foundation models provide strong galaxy representations, but adapting them to new survey conditions and survey-specific morphology recognition tasks still requires substantial human supervision. We show that VLM-based VQA systems contain meaningful visual-semantic priors that can serve as weak supervision for downstream morphology classifiers and improve morphology classification under limited human-label budgets. We first introduce a survey-oriented VQA benchmark spanning two representative imaging regimes and evaluate state-of-the-art VLMs on galaxy morphology questions. The results show that these models capture useful morphology signals and informative uncertainty, but are not sufficiently reliable to replace human annotators. Motivated by this finding, we use a general-purpose VLM as a morphology teacher for Zoobot, an astronomy foundation model pretrained on large-scale Galaxy Zoo annotations. Across two survey domains and multiple annotation budgets, the VLM teacher consistently improves Zoobot's downstream morphology classification. These results demonstrate that a general-purpose VLM provides knowledge complementary to an astronomy foundation model and can teach it to better recognize galaxy morphology under limited human supervision. The resulting pipeline is designed for label-efficient adaptation to forthcoming large-scale surveys, including the Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) and the Nancy Grace Roman Space Telescope. The benchmark and code are publicly available at https://github.com/fw-ic/VLM-morphology-teacher.
PosterMELD: Multi-Agent Paper-to-Poster Generation for Controllable Design Diversity with Editable Print-Ready Outputs
Scientific poster construction compresses a long multimodal paper into a readable, editable canvas. Existing systems hide request-level failures by scoring only completed outputs; direct image generation is not element-editable, while coding-agent workflows are costly. PosterMELD is a template-conditioned multi-agent pipeline: capacity-aware slots guide writing before rendering, and deterministic gates plus vision-language model (VLM) review route failures to bounded repair. Each accepted request exports editable PowerPoint (PPTX) and Portable Network Graphics (PNG) artifacts; explicit design controls yield same-paper variants. Across 621 papers, Print-Ready Rate (PRR) counts requests passing geometric, readability, asset-integrity, and obvious-factual-error checks, with native editability reported separately. A frozen VLM assigns conditional Craftsmanship-Harmony-Expressiveness (CHE) scores to print-ready outputs. PosterMELD attains 81.3% PRR, 3.4 times P2P's rate and 5.2 times PosterGen's, and the highest conditional CHE among generated methods with multiple print-ready outputs. Native editability and explicit design controls are retained at a mean cost of USD 0.38 per request, 3.5% of Codex+Skill's. Code and resources are available at https://github.com/Shannon4Science/PosterMELD.
Constructing Executable Analytical Knowledge Representations for Meta-Analysis Synthesis Using an Agentic Harness
Meta-analysis synthesis highlights a fundamental challenge in knowledge-based scientific analysis: structured evidence does not by itself represent the analytical knowledge required for executable computation. Decisions about evidence assignment, analytical contrasts, outcome and time-point alignment, effect-size formulation, and methodological admissibility must be explicit before statistical execution. Existing automated approaches often embed these decisions in model outputs, generated code, or workflow traces rather than representing them as independently verifiable knowledge. We introduce the Executable Analytical Knowledge Representation (EAKR), a machine-actionable representation of the knowledge required to transform structured evidence into executable meta-analysis. An EAKR represents evidence, relations, numerical inputs, constraints, provenance, and unresolved issues. We operationalise EAKR in MetaSynDec, an agentic harness in which large language models propose structured updates and deterministic services govern schema- and contract-based validation and execution. Across 58 synthesis units, MetaSynDec constructed all EAKRs, with 57 proceeding to statistical execution. Of 56 units with sufficient information to define a reference analysis object, 38 (67.9%) achieved complete object fidelity and 42 (75.0%) exact evidence-set agreement, with a mean Jaccard similarity of 0.909. Generated and published confidence intervals overlapped in 54 of 55 units (98.2%). MetaSynDec outperformed direct LLM generation in reference synthesis-structure agreement (57/58 versus 23/58; p<0.001) and among 23 jointly completed units, exact reference-formulation agreement (23/23 versus 1/23; p<0.001). These findings provide feasibility evidence that EAKR supports formal validation, traceability, statistical execution, and improved methodological agreement relative to direct LLM generation.
AskChem: Claim-Centered Infrastructure for Chemistry Literature Synthesis
Chemistry literature synthesis often requires assembling specific findings scattered across many publications, yet existing literature-search systems primarily return ranked document lists. As a result, scientists and AI agents need to locate relevant information, verify their provenance, and assemble cross-paper answers manually. We present AskChem, a claim-centered infrastructure for cross-paper chemistry search. AskChem changes the unit of retrieval from the paper to the provenance-carrying claim: each paper is converted into atomic, typed claims, each grounded by a source DOI and a verbatim quote or an explicit evidence locator. Over this shared claim store, AskChem exposes complementary structures for search and synthesis: a stabilized faceted taxonomy for hierarchical retrieval and browsing, an evidence graph linking claims through relations, and an exploratory living taxonomy that situates indexed papers under scientific principles. AskChem currently indexes 2.4M claims from 147K papers and provides a web interface, as well as REST, SDK, and MCP access for AI agents. On AskChem-Bench, grounding a GPT-5.5 reader in AskChem yields 100% resolvable DOIs, compared with 88.3% without retrieval, and the highest citation density among five tested systems. AskChem is live at https://askchem.org.
Diversifying Personalized Research Ideation against AI-Induced Homogenization
AI-assisted research ideation has emerged as a promising paradigm for accelerating scientific discovery, with systems now capable of generating research directions conditioned on papers, topics, or lightweight researcher contexts. Yet current systems largely optimize individual suggestions in isolation. This leaves two blind spots. First, coarse researcher representations may elicit mainstream directions that appear broadly feasible, but lack sufficient researcher-specific grounding. Second, independent recommendations can concentrate a community's portfolio around recurring high-probability themes. To address these blind spots, we propose DivAlign, a four-stage pipeline for alignment-preserving de-homogenization. DivAlign extracts fine-grained researcher profiles, generates profile-conditioned candidate directions, scores them along three alignment dimensions (Executability, Comprehensibility, and Growth Potential), and surfaces researcher-local directions while reducing redundancy across the community portfolio. On a benchmark we construct from 95 AI researchers across five subfields, DivAlign reduces community-level redundancy while preserving researcher-direction fit. Compared with coarse single-shot ideation, it lowers average pairwise similarity from 0.331 to 0.294 and nearest-neighbor similarity from 0.704 to 0.608. Compared with the independent top-choice variant, DivAlign reduces nearest-neighbor similarity from 0.663 to 0.608 while retaining 99.9% of the researcher-direction fit score. Code and data are available at https://github.com/Ruixxxx/DivAlign.
Albilich: Steerable Proof-State Orchestration for LLM-Based Mathematical Research with CAS Integration
Large language models can contribute useful ideas to mathematical research, yet long-horizon proof attempts remain difficult to coordinate, evaluate, and reproduce. We present Albilich, an open-source agentic harness for autoresearch in mathematics that combines long-horizon reasoning, computer algebra systems (CAS), literature retrieval, and persistent SQLite-based context management. We evaluate Albilich on the RealMath benchmark (Zhang et al. 2025) and on open problems in group theory from the Kourovka Notebook (Khukhro and Mazurov 2026). It solved 10/10 problems on RealMath with CAS and 9/10 with no CAS. On the Kourovka problems, Albilich produced a counterexample to Problem 21.142 and a proof of a strengthening of Problem20.2. Anablation on Problem 17.91 demonstrates 32.0% token reduction when CAS is enabled. An ablation on Problem 21.142 demonstrates higher verifier-rejection rate and failure to synthesize proof routes in the absence of the advisor agent. These results support Albilich as a human-steerable, CAS-boosted environment for scalable AI-assisted mathematical research.
Can AI agents conduct open-ended AI research? Early evidence from two case studies
Forecasts of explosive AI progress hinge on AI agents automating AI research. But evidence on whether agents can carry out open-ended AI research is thin. Current evaluations either test agents on narrow, verifiable tasks, which excludes open-ended research, or submit AI-generated papers to blind peer review, which is overstretched, stochastic, and suffers from poor review quality. We introduce a third way to measure progress towards AI R&D automation. An agent takes on the central, open-ended research question of a high-quality unpublished paper, and the paper's original authors grade its output. We call these shadow evaluations. We ran shadow evaluations on two unpublished NeurIPS 2026 submissions, giving frontier agents six days and thousands of dollars of compute. The agents completed all of the engineering without human help, yet could not make substantial progress towards answering the research questions. As a result, both papers were unambiguously rejected by the authors. We identify five recurring failure modes: poor judgment about the bar for publishable research, uncreative responses to shortcomings in the research design, ineffective backtracking from dead ends, poor resource awareness, and instruction drift. A robustness check with a second model and scaffold reproduced these failures. We release the expert reviews, survey responses, agent repositories, and logs. Our results provide early evidence that today's agents can do the engineering of AI research, but struggle with critical parts of the research lifecycle.
Scientific Knowledge Discovery in the Age of Large Language Models
The rapid growth of scholarly literature has made identifying relevant publications increasingly difficult, and conventional search systems still depend heavily on manually formulated queries and effortful manual inspection. Generative large language models (LLMs) offer a more flexible alternative, supporting literature retrieval and the screening of candidate studies against eligibility criteria. This chapter surveys 34 peer-reviewed papers applying generative LLMs to these two tasks, identified via a Boolean search over the OpenAIRE Graph (1,589 records screened to 34 inclusions). Reviewed studies are characterised by LLMs employed, model access and adaptation, prompting and architectural techniques, ground-truth sources, and evaluation metrics.
AI's Capability in Assisting Scientific Research in Physics, Astrophysics, and Cosmology II: Project Planning and Proposal Evaluation
We investigate how well large language models (LLMs) can assist scientific project planning and proposal evaluation. One-page project plans were independently generated for eight expert-conceived research projects in physics, astrophysics, and cosmology by human researchers and three contemporary LLMs (ChatGPT, Claude, and DeepSeek; mid-2025 models, used with their default tool access). The resulting 32 proposals were blindly evaluated by four human reviewers and two newer frontier LLMs (Claude Opus 4.8 and ChatGPT Pro 5.5) using a four-aspect evaluation rubric. Reviewers were also asked to identify whether each proposal was written by a human or an AI. Human reviewers rated human- and AI-written proposals similarly overall, whereas both AI reviewers scored AI-written proposals about one point higher (on a five-point scale) than human-written proposals. Human reviewers correctly identified human- and AI-written proposals 72% and 79% of the time, respectively, while both AI reviewers correctly classified all 32 proposals (100%). These results suggest that current LLMs can produce project plans comparable to human-written ones in the eyes of human reviewers, but that AI reviewers show a systematic preference for AI-generated proposals. Our results suggest caution when deploying LLMs widely in proposal preparation and evaluation.
AI's Capability in Assisting Scientific Research in Physics, Astrophysics, and Cosmology I: Literature Review
We investigate how well large language models (LLMs) can assist with literature reviews for scientific research. We perform a controlled study of eight expert-conceived research projects across the areas of physics, astrophysics, and cosmology. Each project has a defined background and goal, and human experts and AI prompters are asked to perform identical literature review tasks in parallel. We compare the relevant literature selected by humans with that selected by mid-2025 LLMs (ChatGPT-4o, ChatGPT Deep Research, and Gemini). We find the overlap between human- and AI-selected references to be small (6%), indicating that AI models do not yet reproduce a competent expert search on their own, though they have the potential to complement literature searches by humans. We then assess the reliability and completeness of AI-generated candidate references, distinguishing two types of hallucination: fabrications (references to nonexistent papers) and metadata mismatches (real papers with one or more incorrect fields). We find that while fabricated references make up 3% of the AI-generated references, 64% are real papers with at least one incorrect field (title, author, year, journal, DOI, or link), indicating that the mid-2025 models require systematic verification. However, the performance is significantly improved for the 2026 model ChatGPT Pro 5.5, with a single-project test showing zero fabrication or metadata mismatches.
The Half-Lives of Generative-AI Evidence: A 40-Record Audit, a Claim-Currency Framework, and a Reflexive Case of Frontier-Model-Assisted Research
Generative-AI evaluations can become historical before publication, yet calendar age does not affect every conclusion equally. This paper has two linked purposes. First, it audits a maximum-variation purposive corpus of 40 empirical records appearing between 18 July 2025 and 17 July 2026. The audit coded publication route, execution timing, model identity, age of the newest named generation or immutable snapshot, same-family supersession and refresh behaviour. At appearance, the newest named model was a median 281 days old (middle 50%: 75-478; range: 11-939). Median age was 395 days for 25 journal articles, 56 days for 14 preprints and 49 days for one laboratory report. Thirty-five records included a superseded family, seven supplied a precise dated identifier, three clearly refreshed model evidence, and one added a late sensitivity test. All 40 included an OpenAI system, a feature of this corpus rather than a prevalence estimate. The paper distinguishes model age from claim currency and proposes six reporting practices. Second, it treats its own two-day production process as a reflexive case of frontier-model-assisted research creation. GPT-5.6 Sol Pro in ChatGPT supported candidate discovery, source reconciliation, calculations, drafting and critique; the author checked sources, made all substantive decisions and accepts responsibility. This is a proof-of-practice, not a controlled estimate of productivity or quality. By applying its own Model Facts and model-currency statement, the paper shows how rapid AI-assisted research can be made inspectable without treating model output as independent validation. The title uses half-lives metaphorically; no universal decay rate is estimated.
Transfer Learning Architectures for Scalable Multi-Fidelity Bayesian Optimization
Self-driving laboratories increasingly rely on multi-fidelity Bayesian optimization (MFBO) to balance cheap, approximate evaluations against scarce, expensive ones, with a predictive surrogate at its core. Gaussian processes (GPs) are the default choice, but they scale poorly as data accumulate and assume a smooth landscape that molecular and materials search spaces routinely violate. Transfer learning offers an alternative suited to this regime: it learns a representation from abundant cheap data and adapts it to sparse expensive data. Despite its use in property prediction, transfer learning has not been tested as the engine of a closed-loop optimization. Here we benchmark eleven transfer-learning surrogates against four GP methods under an identical selection rule, fidelity budget, and model size, across nine tasks spanning synthetic functions to real chemistry and materials problems. GPs win on smooth, low-dimensional functions but perform worst on molecular and materials problems, where transfer-learning surrogates reach substantially better solutions using far less computation. Because acquisition policy is held fixed across surrogates, this advantage is attributable to the surrogate itself. Uncertainty-driven exploration is not reliably beneficial, and calibration does not predict optimization performance, so greedy exploitation of the transfer-learned mean is the more robust default. Transfer learning is therefore the surrogate of choice for molecular and materials MFBO.
pAI-Econ-claude: A Gated Human-in-the-Loop Multi-Agent Architecture for AI-Assisted Economic Theory Development
In many social-science research tasks, such as economics, LLM-based agents must produce outputs for which no cheap, task-complete, machine-readable correctness signal exists. This creates a distinctive reliability problem for multi-agent systems: how should generation, critique, coordination, and human judgment be organized when no component can certify the final result? We address this problem through pAI-Econ-claude, a gated, human-in-the-loop multi-agent architecture for AI-assisted economic theory development. Agents coordinate through a shared workspace of inspectable intermediate records; specialized gates diagnose targeted failure modes and recommend loopbacks without certifying correctness; and human checkpoints retain authority over decisions that are costly to reverse. We evaluate the architecture on five matched economic-theory tasks against an ungated baseline. Two evaluators blinded to configuration agreed on all five pairwise rankings, preferring the gated architecture in four tasks and the baseline in one. Mean failure severity fell from 1.58 to 1.16, while overall usefulness rose from 2.60 to 3.10. The largest observed gain occurred when a reality check rejected a false market-structure premise and a proof review prompted revision of a false welfare claim. The negative case shows that scaffolding can also compress an economically important mechanism too aggressively. The results support a bounded claim: gated oversight improves the auditability of AI-assisted economic theory without substituting for formal verification, and the allocation of irreversible human judgment is a more informative design variable than pure agent autonomy. The workflow is publicly available at https://github.com/maxwell2732/pAI-Econ-claude.
Automated Synthesis and Adversarial Validation of Executable Causal Research Pipelines
While automated research systems promise to accelerate empirical analysis, they are prone to silent failures: instances in which analysis code executes successfully yet relies on invalid causal assumptions. We present the Artificial Intelligence (AI)-based Epidemiology Research Assistant (ARA), a framework that makes these failures visible by explicitly encoding causal design principles, study-specific assumptions, and methodological constraints. ARA integrates protocol construction, synthetic data generation, and adversarial validation into a unified pipeline. The framework translates natural language research questions into structured causal protocols and executable analysis code by first constructing a protocol and then generating synthetic datasets using Structural Causal Models (SCMs) with known ground-truth effects. This synthetic-data step can also support pipeline development when access to confidential data, such as medical data, is restricted. The generated analysis is then evaluated under controlled violations of identification assumptions. We evaluate ARA on the Automated Causal Reasoning Benchmark, assessing recovery of identification strategies, causal quantities, treatment and outcome variables, and consistency between generated code and approved protocol. Protocol construction and adversarial validation did not consistently improve numerical agreement with benchmark estimates compared with standard LLM-based generation. However, they changed the failure mode: instead of silently returning causal estimates, ARA often surfaced protocol concerns, diagnostic failures, incomplete inference, or downgraded non-causal interpretations. These findings suggest that validity-first automated science systems should be evaluated not only by answer accuracy, but also by whether they indicate when causal claims are unwarranted.
Scientific exploration, collaboration and labor division in the large language model era
Large language models (LLMs) have rapidly and significantly entered scientific workflows, but it remains unclear how their diffusion is associated with changes in scientists' strategies in research directions and team building. We link PubMed Central full text with OpenAlex publication and collaboration histories for 775,323 scientists and analyze CRediT contribution statements from 137,120 multi-author papers. After 2022, scientists increasingly published across more intellectually distant fields and entered fields in which they had not previously worked. These increases in interdisciplinarity and exploration were especially pronounced among established scientists and scientists from non-English-speaking low- and middle-income countries. Authors with stronger AI-writing signals were already more interdisciplinary and exploratory before the widespread adoption of LLMs, and the gap widened further after 2022 compared with authors with weaker AI-writing signals. Scientists' collaboration networks also became more interdisciplinary after 2022. Yet, among authors with stronger AI-writing signals, research interdisciplinarity was less closely tied to the disciplinary diversity of their collaborators. The division of labor within research teams also became more differentiated. Contributors on papers published after 2022 reported narrower role sets on average, coauthors shared fewer roles in common, and their role profiles became less rigid and more fluid. Software and validation roles increased, while conceptual and management roles decreased. These patterns suggest that team members are taking on more distinct responsibilities and may rely less on one another to perform research tasks. Overall, this study indicates that the LLM era coincides with a broader reorganization of scientific exploration, collaboration, and the division of labor.
Mathematical Discovery in the Wild: AI-Guided Proofs in Banach Space Theory
We investigate the capacity of current language models to contribute to mathematical research. In Banach space theory, AI systems generated key ideas and proofs for five new results, which were then verified and refined by humans. We also developed an automated system that searches the literature for open problems and attempts solutions at scale. Our results show both the potential of language models for mathematical discovery and the continuing importance of expert verification.
From Overload to Insights: How AI Agents Can Support Scientists in Analyzing Complex Data
Scientists at European XFEL conduct experiments that generate very large and complex datasets. The subsequent data analysis is challenging as scientists must combine their domain expertise with facility- and software-specific knowledge scattered across documentation, tools, and support channels. To address this problem, we designed and evaluated an agentic AI system tailored to the scientists' needs and integrated with the high-performance computing environment of European XFEL. Using a design science research approach, we conducted a rapid literature review, a systematic evaluation of 16 AI tools, multiple interviews, a focus group, and a user study with experts at European XFEL to develop and evaluate two prototypes. Our study identifies key knowledge challenges in scientific data analysis, derives requirements for an AI agent that supports knowledge retrieval and source code generation, and proposes design recommendations for a specialized system adaptable to the evolving AI tool landscape. These findings provide guidance for developing maintainable AI support in highly specialized scientific environments.
CoWeaver: A Bi-directional, Learnable and Explainable Matching Engine for Mixed Human-Agent Science Collaboration
LLM-based agents excel at writing articles, coding and information retrieval. However, they fail to form strong collaborations within the scientific community due to the bidirectional, dynamic nature of the problem and a high demand of decision interpretability. We proposed COWEAVER, a bidirectional, learnable and explainable algorithm to match scientists and form strong collaborations within a human-agent network. COWEAVER matches candidates and requesters through filling capability gaps and filters candidates through a two-stage ranking step. Finally, the model explores newcomers by maintaining uncertainty-aware capability estimates and updating them through requester's feedback. We show that the selection mechanism of combining both exploration (UCB) and greedy of COWEAVER exceeds the greedy-only mechanism - the analytical best solution - on 6 out of the 20 tasks and performed on par with the greedy-only mechanism in terms of selecting the best candidate. We compared COWEAVER baselines in terms of matching quality and efficiency. COWEAVER outperforms baselines on all metrics.
The Industrialization of Research ; On AI-Driven Science and Its Consequences
Artificial intelligence is transforming scientific research - not merely as a more powerful instrument, but as an autonomous participant in the research cycle itself. This transition constitutes, in the most precise sense of the term, the industrialization of research: a shift from a craft model, in which knowledge, method, and judgment are embedded in the researcher, to a pipeline model, in which these steps are decomposed, automated, and supervised. The US Department of Energy's Genesis Mission is the most ambitious current instantiation of this shift, but the fundamental questions it raises extend far beyond any single program. This essay examines seven such questions: the erosion of the intergenerational transmission of scientific competence; the growing opacity of AI-generated theories; the collapse of peer evaluation under a flood of machine-generated output; the unproven capacity of AI for paradigm-shifting discovery; the capture of the scientific agenda by political and industrial actors; the compounding of systematic errors in closed-loop pipelines; and the structural bifurcation of the global research community into incommensurable tiers. These concerns do not constitute an argument against AI-driven science - whose demonstrated potential is real and significant. They constitute the conditions under which that potential can be responsibly pursued.
Aïra: Rethinking AI Research Assistants for Interdisciplinary Science
Scientific discovery increasingly depends on interdisciplinary teams whose members contribute distinct expertise, conceptual frameworks, vocabularies, assumptions, and standards of evidence. Today's AI research assistants are largely designed to support individual researchers through literature review, writing assistance, coding, and data analysis. While these capabilities improve personal productivity, they provide little support for the collaborative reasoning required to integrate knowledge across disciplines. We argue that AI research assistants should evolve from tools that optimize individual workflows to systems designed for interdisciplinary teams. We introduce aïra, an AI research assistant built around this idea. Rather than focusing solely on summarization or question answering, aïra identifies disciplinary perspectives, translates terminology, highlights assumptions, and synthesizes collaborative research opportunities. We describe the design principles underlying aïra, present its system architecture, illustrate its outputs through interdisciplinary research meetings, and outline future research directions for AI systems that support collaborative scholarship.
Distributed Denial of Science: How Indirect Data Poisoning of AI Systems Can Industrialize Scientific Fraud
Scientific fraud is the instrument of doubt that malicious entities can use to establish controversy in science. Historically, it required the resources of a company: deep pockets, ghostwritten articles, and corrupt academics. Today, Artificial Intelligence (AI) is increasingly automating scientific research, so we ask: Can a remote adversary weaponize the honest use of AI in science to compromise scientific integrity? We envision and empirically evaluate a new attack, indirect data poisoning, in which an adversary corrupts an open dataset and uploads the poisoned variant to a public repository. Autonomous research agents may independently retrieve and process this data, turning honest scientists into the unpaid and unwitting distributors of fraud at scale. Across five socially-salient topics, from hiring discrimination to the safety of autonomous vehicles, three widely used frontier AI systems (Claude Code with Claude Opus 4.7, Codex with GPT-5.5, Gemini CLI with Gemini 3.1 Pro), and 450 ethically contained experimental runs, we find that poisoning succeeds in 49.56% of runs, while the rate of poisoning detection is only 6.0%. The attack requires no topic-specific trigger-words, agent access, indirect prompt injection, or fabricated papers, only the open data ecosystem and misleading metadata. To mitigate the attacks, we propose and evaluate two measures: a scientist persona and a data provenance audit with five checks (referencing papers, social markers, statistical anomalies, related datasets, poisoning caution). We find that the persona still leaves 16.67% of runs with a poisoned conclusion, but provenance auditing reduces attack success rate to zero. Our results suggest that indirect data poisoning may enable scientific fraud at unprecedented scale, but these attacks can be mitigated with suitable auditing by agents during data retrieval.
Prompt-to-Paper: Agentic AI System for Bioinformatics
While recent advances in large language models have enabled end-to-end automated manuscript generation, existing systems suffer from three critical deficiencies: (i) generated claims are not deterministically grounded in verifiable literature, (ii) experimental results are frequently fabricated rather than executed, and (iii) there exists no standardized, multi-dimensional framework to assess whether AI-generated manuscripts meet the quality and rigor required for real-world publication. We present Prompt-to-Paper, a multi-agent framework that directly addresses this evaluation gap through three integrated innovations. First, a deterministic retrieval-augmented generation pipeline with section-aware relevance scoring and snowball citation expansion grounds every claim in a verifiable corpus of 60--100 papers. Second, an autonomous coding agent executes real computational biology experiments replacing synthetic outputs with genuine numerical results. Third, an eight-dimensional automated quality scorer, benchmarked with approximate reference statistics from published papers and augmented with explicit hallucination penalties, provides standardized, reproducible quality assessments. The quality-driven improvement loop uses a context-rich reviser that routes each iteration to one of three researcher actions and fires a deep research cycle every ten iterations to re-run experiments and re-manuscript from stronger outputs. We validate the system on five bioinformatics case studies; all five cases compiled submission-formatted PDFs with zero out-of-range citations. The improvement loop raises manuscript quality by an average of +17.96 points on a 0--100 scale (maximum +26.04. As partial external checks, a human reviewer scored the five manuscripts at an average of 7.0 out of 10. Complete manuscripts are produced at approximately 0.31 USD per paper.
ResearchStudio-Reel: Automate the Last Mile of Research from Paper to Poster, Video, and Blog
Research dissemination, turning a paper into a poster, a talk video, and a blog post, is still a manual last mile. Prior automation treats each artifact in isolation that each re-extract the paper from scratch, usually ship one-way renders the author cannot reopen in PowerPoint or Word, and gates quality on soft VLM-preference scores that plateau while load-bearing sections still read as empty. We argue this last mile is best built as a composition of skills: thin agent-readable contracts that share one upstream extractor and wrap deterministic primitives in a measured-fill loop whose exits are hard pass/fail render gates. We instantiate this as ResearchStudio-Reel, five Claude Code and Codex skills organized into one shared extractor (Paper2Assets), three editable generators (Paper2Poster, Paper2Video, Paper2Blog), and one interactive convergence layer (Paper2Reel). Paper2Assets extracts each paper once into a shared bundle that can be reused by every downstream skill; The three generators produce a print-ready poster, a synchronized talk video, and a bilingual blog that stay factually consistent and round-trip through PowerPoint or Word; Paper2Reel then binds all three into a self-contained HTML viewer whose section-level clicks jump the video, slides, captions, and blog to matching content. On the Paper2Poster benchmark, our posters lead every aesthetic and information sub-criterion against both prior automated systems and single-shot frontier LLMs, surpassing the authors' own on aesthetics under two held-out VLM judges and winning overall on 84% to 93% of papers; capability audits further show that, by uniquely pairing narration-aligned on-slide highlights with a bilingual blog gated by layout-aware DOCX repair, ResearchStudio-Reel is the only pipeline to ship all three editable artifacts. Project is available at https://aka.ms/ResearchStudio
What is Left for Us? Second Scholarship Against the Degradation of Research by AI
We argue that generative AI can degrade research by eroding the very practices through which scholarly judgement is formed. As constitutive conditions for the production and validation of knowledge, these practices cannot be reduced to the outputs of research, which is what AI tools so effectively simulate. When scholars delegate central tasks of inquiry to Large Language Models (LLMs), they may stop engaging in these practices and lose the formation they provide: the output may improve while the researcher fails to develop. Against this risk, merely keeping humans "in the loop" as prompters or quality checkers of AI outputs is insufficient to preserve research as a site of intellectual formation. What is needed instead is a renewed commitment to research as a lived practice in which judgement is formed gradually, often through friction, and participation in a scholarly community. We defend it because it rests on four sources and warrants of research that cannot be automated: tacit knowledge, personal commitment, socialisation, and deep reading. These enact what we call second scholarship, i.e., the reappropriation of scholarly craft, chosen out of a critical experience of what AI tools can and cannot do. Researchers who practise it may delegate tasks to these tools, provided that their own judgement in the delegated competence is already formed, that they can answer for the output, and that they keep exercising the competence themselves. What cannot and should not be delegated becomes what research communities must value and answer for. This is what is left for us.
PosterHarness: Turning Scientific Poster Generation into an Auditable Instruction-Following Benchmark
Text-rich image models can now design poster-scale layouts, but we lack ways to measure whether they honor scientific communication contracts: legible labels, prescribed aspect ratios, and -- above all -- abstaining from fabricated scientific figures. We present POSTERHARNESS, an auditable harness reframing poster generation as measurable instruction-following tasks, with a pilot benchmark and failure taxonomy. POSTERHARNESS uses a placeholder-first contract to separate two jobs models otherwise conflate. The model performs visual-summary design: typography, reading path, color, and background -- but never draws data-bearing figures. Every figure region must be an empty labeled placeholder; a deterministic compositor inserts real source-paper figures at detected coordinates. This makes properties measurable: placeholder count and ID accuracy, blankness, aspect-ratio compliance, abstention from synthesized graphics, public-text hygiene, and source-figure provenance -- with failures logged as explicit rejections, not hidden in plausible-looking output. We instantiate the harness on 12 papers (6 HEP, 6 AI/ML-adjacent) and report three findings. (i) A counterfactual probe shows the placeholder contract drives VLM-counted synthesized figures from 34 to 0 across three papers. (ii) A failure taxonomy identifies blocking contracts: placeholder geometry, placeholder QA, template critic, and public text. (iii) Comparison with Paper2Poster shows a trade-off: PosterHarness yields higher-resolution artifacts, lower white-canvas fraction, and stronger VLM visual preference; the deterministic baseline retains slightly more PosterQuiz-style information and runs faster. We report this as regime characterization, not a superiority claim. All artifacts, prompts, manifests, and audit scripts are released as a reusable evaluation component.
The Calibration Turn in AI-Assisted Research: A Conceptual and Methodological Framework for Evidence-Licensed Claims
AI-assisted research has entered a stage in which the central question is not only whether systems can generate hypotheses, run experiments, or produce manuscripts, but whether their scientific claims are calibrated to the evidence that supports them. This Perspective-style paper develops a conceptual and methodological framework for evidence-licensed claims in AI-assisted research. Motivated by representative routes including specialized scientific foundation models, LLM research assistants, multi-agent co-scientists, AI Scientist pipelines, mathematical discovery agents, and self-driving laboratories, it represents AI-assisted research as five operators: hypothesis generation, model-mediated consequence derivation, external validation, belief update, and claim calibration. The central claim is that calibration is not merely cautious wording but a mechanism for managing scientific assertion rights: evidence licenses some forms of speech and withholds others. The paper distinguishes linguistic, consequence-based, interventional, and evidence-licensed semantics; defines the claim-evidence gap and epistemic debt; and treats minimal structural reconstruction across heterogeneous outputs as an upward form of claim calibration. AISim-Cal is included as an illustrative synthetic dynamics exercise, not as an empirical forecast or benchmark. The resulting principles are: no claim without license, validation does not determine claim level, and automation amplifies the need for calibration. Reliable AI-assisted research is therefore evaluated as a loop that generates hypotheses, derives testable consequences, accepts independent adjudication, updates beliefs, and outputs only evidence-licensed claims.
Research Entity Extraction and Topic Detection from UKRI Grant Proposals
This paper presents preliminary findings from a UKRI-funded Metascience project comparing three LLM-based approaches, GPT-4o, Mistral, and a bespoke algorithm, DSIT-Taxonomies, for extracting and classifying research entities from funding proposals. Our project "Tracking Stars and Unicorns" aims to identify early signals of emerging research areas to inform public investment. Our methodology employed a three-stage pipeline, leveraging Mistral for primary entity extraction and mapping against the OpenAlex Topics taxonomy. We evaluated our approach across 42 proposals' abstracts from different areas and observed that Mistral and GPT-4o produce comparable, high-quality entity sets with significant semantic overlap, outperforming the fragmented DSIT-Taxonomies approach. Crucially, the Mistral-based approach achieved superior topic classification accuracy (90.5%) compared to the full DSIT-Taxonomies pipeline (71.4%). We conclude that Mistral offers a high-performance, operationally efficient, and secure solution for large-scale analysis of sensitive grant data.
Em-ergence of the em-dash: a population-level rise in em-dash frequency in medRxiv preprints at the dawn of the large-language-model era
Large language models (LLMs) can leave subtle stylistic traces in assisted text; one of the most cited is the em-dash (Unicode U+2014). Yet no one has measured whether em-dash use has changed in the scientific literature. This study, pre-registered on the Open Science Framework (HFT8C), used the full set of medRxiv full-text XML preprints from the official Text-and-Data-Mining resource. The primary cohort was first, original versions deposited 2020-2025 with an extractable Discussion section of at least 500 characters (N = 69,632). The primary endpoint was the presence of at least one em-dash in the Discussion; the principal measure was the absolute change in its prevalence between the pre-ChatGPT era (before 30 November 2022) and the post-ChatGPT era, estimated with a logistic model with standard errors clustered by first author. The analysis plan (six supporting analyses, six sensitivity analyses, two falsification tests) was frozen before any confirmatory result was computed. Em-dash prevalence in Discussion sections rose from 4.23% before ChatGPT to 11.58% afterward, an absolute increase of 7.35 percentage points (95% CI 6.94-7.77; odds ratio 2.96, 95% CI 2.77-3.17). The rise was not a sharp jump but a gradual, delayed acceleration: near 4% through 2023, 8.0% in 2024, and 20.3% in 2025. The effect survived every feasible sensitivity analysis (7.35-7.60 pp) and both falsification tests; a placebo split within the pre-LLM era showed no meaningful change (+0.13 pp, 95% CI -0.33 to +0.58), and was essentially absent in boilerplate sections. Independent LLM-associated lexical markers and within-paper section comparisons pointed the same way. The em-dash is a population-level indicator, not a per-paper detector of LLM use, and the design cannot establish causality; it shows that something in how scientific literature is written changed markedly in the early 2020s, and roughly when.
AI-Assisted Computational Reproducibility on the FABRIC Testbed
Computational reproducibility remains difficult despite being central to scientific research. In this paper, we show how the international FABRIC testbed, combined with a large language model (LLM) coding agent through LoomAI, can simplify reproducing published experiments across multiple domains. We reproduced three case studies on FABRIC, covering BBR-family congestion-control evaluations, LAMMPS molecular dynamics scaling benchmarks on a CPU-only MPI cluster, and stress protein homeostasis genomics pipelines. Rather than focusing only on matching numerical outputs, we evaluate whether the reproduced experiments support the same scientific conclusions as the original studies. The AI assistant was effective in setting up the environment, adapting code, and debugging, but struggled with the analysis stages that lacked clearly defined workflows, which required human guidance to establish execution order and data dependencies. Across the case studies, the AI-assisted workflow reduced reproduction effort by roughly 4--6 times. We conclude with practical recommendations for improving AI-assisted reproducibility on research testbeds.