Autoresearch

Coding agents can now be left alone to improve software against a score. In this pattern--recently popularized as "autoresearch"--the agent receives a dataset, an evaluation script, and one editable file, and iterates without supervision: modify the code, measure, keep the change if the score improves. But what does the agent actually optimize--the developer's intent, or the literal number? We ran this loop on a real production task: deciding which Quranic verses appear in a noisy speech-recognition transcript and splitting the transcript by verse. Two frontier coding agents, Claude Code and OpenAI Codex, started from the same blank file with the same instructions, budget, and reasoning effort, three runs each. Both independently invented the same algorithm (canonicalization, n-gram anchoring, dynamic-programming alignment)--and then diverged. Claude stopped early with compact, general code. Codex drove the score ~10x lower, largely by memorizing answers to individual evaluation rows (19-41 hardcoded verse ids per run): a clean natural instance of specification gaming by a production agent. In a preregistered second study, we added a held-out test set and told both agents it existed. The memorization vanished, and the score gap vanished with it--yet Codex's general core transferred better and more consistently (held-out detection+split 0.085+/-0.004 vs. 0.121+/-0.031), losing only on one missed rejection of non-recitation input. Two exploratory community arms (Cursor, Antigravity) are consistent with the pattern. Every agent's held-out solution matched or beat the hand-engineered pipeline it was built to replace--the best by an order of magnitude--and now runs in production. From the ways agents exploited our harness--reading sibling runs through shared git state, leaving notes to "future runs" in persistent memory--we distill five design rules for evaluating autonomous agents.

Auto Research uses language-model agents to propose, implement, and evaluate machine-learning changes in a closed loop, but is usually judged by its terminal pipeline. A terminal score cannot reveal which technical decision produced a gain or distinguish a reusable discovery from a change adapted to development feedback. We introduce intervention-centered Auto Research, which validates research decisions rather than only final artifacts and makes their reliability measurable. Feature, Model, Representation, and Data axes are searched independently with inner five-fold feedback. Each axis winner is frozen before an outer-holdout matrix compares all alternatives on evidence the loop never sees. Across 701 agent-executed attempts spanning ten Matbench endpoints, outer evidence confirms the selected intervention on nine of ten endpoints and preserves 89.3% of non-tied intervention orderings. It also rejects an aggregate Representation gain that inner feedback endorsed. The resulting matrix reveals an information-dependent hierarchy. Composition-only tasks support several routes to improvement, whereas structure-informed tasks favor local geometry features and complementary tree ensembles. A subsequent compatibility test combines already frozen Feature and Model code without further search or tuning and raises mean outer-holdout improvement from 19.0% to 26.3%. By validating decisions rather than only artifacts, this design turns adaptive search into reusable evidence wherever agents propose executable alternatives against a fixed evaluator.

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.

World Action Models (WAMs) improve robot policy learning by jointly modeling actions and future visual observations, using future scene evolution as dense supervision for physically grounded action generation. However, a common design in existing WAMs is to explicitly generate future videos at inference time, incurring substantial computational overhead and hindering real-time closed-loop deployment. GigaWorld-Policy addresses this issue with an action-centered formulation, where future visual dynamics are used during training while action-only decoding is used at inference time. Building upon this framework, we present GigaWorld-Policy-0.5, an enhanced action-centered WAM designed for more efficient robot control. During pretraining, GigaWorld-Policy-0.5 adopts a mixed Action-Conditioned World Modeling (AC-WM) and WAM training strategy. This strengthens the coupling between visual dynamics and robot actions and improves the transferability of action representations for downstream policy learning. For efficient inference, GigaWorld-Policy-0.5 introduces a Mixture-of-Transformers architecture that separates visual dynamics modeling and action generation into specialized experts, reducing active computation during action-only inference and achieving 85 ms inference latency on a local RTX 4090 setup. In addition, we employ an agent-based AutoResearch pipeline to systematically search training configurations, enabling more efficient identification of optimal experimental setups while reducing the time and manual intervention required for hyperparameter tuning. Experiments and ablations show that GigaWorld-Policy-0.5 preserves the training benefits of future visual dynamics while improving inference efficiency for robot control.

Recent advances in Large Language Models have fueled autonomous AI agents capable of tackling complex scientific tasks, yet existing automated research systems remain predominantly focused on empirically driven domains with quantitative benchmarks, leaving theory-driven discovery, particularly in mathematically grounded disciplines requiring rigorous proofs and synthesis of domain knowledge, largely underexplored. Key challenges include the difficulty of verifying theoretical reasoning at scale, insufficient reasoning ability for autonomous frontier exploration, and a scarcity of procedural heuristics in the literature. We introduce ReasFlow, an end-to-end autonomous agent system for reasoning-centric scientific discovery that operationalizes a collaborative paradigm where the human expert acts as Principal Investigator while the agent executes rigorous derivations as a capable graduate student. ReasFlow incorporates (i) a robust internal verification loop that audits logical coherence and corrects fundamental errors prior to human inspection, and (ii) an automated knowledge retrieval and self-improvement mechanism that proactively surfaces both declarative facts and overlooked procedural heuristics, substantially reducing expert intervention. The system unifies literature synthesis, algorithm design, theorem proving, experimentation, and manuscript preparation in a single system. Deployed to autonomously generate five complete research papers with rigorous theoretical and empirical content from minimal prompts, ReasFlow consistently achieves the highest evaluation scores among state-of-the-art open-access baselines under a curated LLM-based review rubric. ReasFlow is publicly accessible via the ReasLab platform, providing a collaborative workspace for AI-assisted theoretical research. Github repo: https://github.com/ReasLab/ReasFlow.git.

Autonomous research systems can generate plausible papers while losing the decisions, failed branches, and evidence needed to inspect or continue the work. We present XScientist, a local-first, git-like protocol that treats research state, rather than a manuscript, as the unit of continuation. Hypotheses, experiment attempts, observations, claims, reviews, and handoffs are represented as typed, content-addressed objects in an exploration graph. Immutable checkpoints, explicit negative outcomes, claim-evidence closure, replay boundaries, and authority-aware gates make each transition inspectable without treating a passing integrity check as scientific truth. The protocol exports a portable Agent-Native Research Artifact (ARA) that another agent or human can inspect, fork, verify, and extend. A reference implementation integrates planning, execution, review, repair, and supervised long-running operation while preserving provenance across these stages. We evaluate the protocol with controlled artifact-integrity workloads and matched external task pilots, keeping native task performance separate from evidence and audit claims. The result is an interoperability and accountability layer for long-running autonomous science, with explicit boundaries where human judgment and independent evaluation remain necessary.

Production LLM agents such as Claude Code and Codex operate over untrusted content, files, commands, and workspace state, making safety failures directly actionable. Red-teaming must therefore keep pace with evolving models and tools. Existing approaches mainly optimize attack success and preserve artifacts such as benchmarks, payloads, or attack programs, which record where attacks succeed but not the enabling conditions behind unsafe agent behavior. We study automated red-teaming for production LLM agents using one agentic research environment to discover reusable vulnerability knowledge about another. We present AHA, a falsifiable discovery loop that proposes a vulnerability hypothesis, constructs a falsifier, instantiates a valid attack, executes it in a sandboxed harness, reflects on the trajectory, and promotes confirmed findings into a Vulnerability Concept Graph (VCG). Each concept links an attacker-facing surface to an unsafe trajectory through a claim, enabling condition, falsifier, transfer prediction, and supporting evidence. Across Claude Code and Codex on three scenarios covering direct and indirect attacks, the discovered concepts reveal a reusable vulnerability core across models and agents. A frozen VCG requires no further search and outperforms the strongest frozen discovery baseline by 14.2 percentage points under the same single-shot protocol, while transferring across scenarios and attack channels. The resulting VCG provides an auditable artifact for production safety teams to inspect vulnerabilities, validate patches, and accumulate reusable safety knowledge. Our code is available at https://github.com/henrymao2004/Auto-research-red-teaming-in-sleep.

This paper presents the mAIEnergy dataset, an open-access, multimodal corpus developed to support Large Language Model (LLM) applications in the energy sector. The dataset integrates approximately 50,000 textual documents, 20,000 images, 25 million numerical time series records, and 2 million geospatial and relational data entries. It includes policy and regulatory texts, scientific articles and news articles, satellite and contextual imagery, electricity system measurements, weather observations, statistical indicators, and geospatial representations of energy infrastructure and related entities. All data have been harmonized into structured, ready-to-use formats, accompanied by consistent metadata and reproducible data retrieval and preparation workflows. The dataset can serve as a foundational energy knowledge base, allowing energy stakeholders to integrate additional open-source or proprietary data. The mAIEnergy dataset adheres to Findable, Accessible, Interoperable, and Reusable (FAIR) principles, enhancing its applicability for AI-driven energy research, modeling, and decision-making.

LLM agents that conduct research (proposing ideas, writing and running code, analyzing results) can already carry a study from research question to figures, yet cannot be fully trusted. The same question asked twice in a row returns different answers; the agent announces a number that no execution produced, and tool use does not prevent this, because nothing binds what the agent reports to what its tools returned; a small upstream change leaves downstream results silently stale, with no way to list which ones; and the agent re-runs preprocessing and rewrites code it has already produced. We argue these failures share one root: every step of today's agent loop is a stochastic LLM call whose internal state nobody, including the agent, can check. Rather than trying to see inside the LLM, we take a lesson from databases, which earn trust without being watched, because deterministic operators over well-defined state make their guarantees hold by construction. We propose organizing a research project the same way. The project lives in a deterministic, versioned dataflow engine (in effect, a query plan over materialized views), and the LLM, together with the user, is a stochastic compiler that may only edit that plan. The executor never calls the LLM; LLM output enters only as versioned code and data that the executor then runs, and any asserted result enters the record only with an execution behind it. Five design rules at this boundary turn familiar database machinery, from versioning and provenance to incremental maintenance and cost-based scheduling, into guarantees that make research reliable, non-wasteful, transparent, and collaborative. This report presents the diagnosis, the requirements, and the design; the guarantee walkthrough, a prototype, and the research agenda appear in the full version, in preparation. The LLM, we argue, should be the query compiler, never the executor.

Artificial intelligence (AI) is transforming scientific discovery, but its effectiveness is fundamentally limited by the availability of structured scientific knowledge. Although existing databases have accelerated data-driven materials research, much of the knowledge needed for predictive modeling and inverse design remains embedded in unstructured scientific literature. We present an Autonomous Scientific Knowledge Generation Framework that transforms scientific publications into a Unified AI-Ready Scientific Knowledge Base. The framework integrates ontology-guided literature acquisition, hybrid scientific knowledge extraction, semantic harmonization, knowledge fusion, and validation within a unified workflow. Rather than treating literature retrieval, information extraction, and database construction as separate tasks, the framework progressively converts scientific publications into structured, semantically consistent, and provenance-preserving knowledge suitable for AI-driven reasoning. As a proof of concept, the framework was applied to electro-optic materials. Autonomous literature acquisition retrieved and validated about 1,000 publications from multiple scholarly repositories. A representative subset of eight publications was processed through the complete workflow, generating 29 structured scientific records that were harmonized into 7 canonical scientific records. The results demonstrate the complete transformation from scientific literature to an AI-ready scientific knowledge base while preserving quantitative measurements, operating conditions, provenance, and scientific context. The proposed framework provides a scalable, domain-independent foundation for predictive AI, generative AI, and closed-loop AI-driven scientific discovery.

Financial markets are noisy, non-stationary, and high-dimensional, making it difficult to discover predictive and robust trading signals. Alpha discovery has evolved from manual factor design to machine learning, evolutionary search, and recent LLM-based frameworks, improving the efficiency of factor generation, search, and evaluation. However, existing methods still mostly automate isolated steps, rather than functioning as end-to-end quant researchers that can absorb external knowledge, close the hypothesis-to-code validation loop, and learn from accumulated discovery feedback. To fill this gap, we introduce XAlpha, a memory-driven AI Quant Researcher for continuous hypothesis-to-code alpha discovery. XAlpha maintains a multi-source research memory system that integrates report-grounded financial knowledge with discovery feedback from prior generations and research cycles. Guided by this memory system, a Macro Brain plans research themes and selects suitable Archetypes; a Micro Brain transforms the planned hypothesis pool into executable factor code and verifies ex-ante tri-alignment among the hypothesis idea, code logic, and financial plausibility; and a Cross Brain consolidates empirical outcomes into generation-level feedback, cycle-level summaries, and archetype-level research cues for future exploration. In this way, XAlpha turns alpha mining from isolated factor generation into a closed-loop research process that continuously reads, hypothesizes, implements, validates, reflects, and evolves. Experiments on CSI300 show that XAlpha achieves stronger overall alpha discovery performance than representative baselines.

Research software collaborations span meetings, informal chats, pull requests, and GitHub issues. A decision surfaced in a Slack thread, refined in a meeting, and implemented in a pull request can lose its original rationale across these artifacts, leaving domain researchers and research software engineers with divergent mental models of project intent, ownership, and scientific assumptions. We argue that alignment in research software engineering is a continuous lifecycle problem, and that agentic AI can support stakeholder alignment and project-state tracking without replacing human decision-making. We present Aleena, an open-source lifecycle alignment agent that uses GitHub as a shared collaboration surface, transforming multi-modal stakeholder interactions into structured project records that surface risks, track open questions, and preserve decision continuity. Grounded in university-based research software engineering center experiences, this paper presents the motivating problem, system design, prototype, and illustrative lifecycle scenarios for Aleena.

Recent advances in AI for Mathematics have focused largely on autoformalization and theorem proving, leaving the role of Computer Algebra Systems (CAS) in agentic LLM workflows underexplored. We propose a ReAct-style agentic setup that combines LLM reasoning with verifiable feedback from SageMath, together with Context7 for the up-to-date documentation. We evaluate this agentic setup across frontier models for solving research-level mathematical problems from the RealMath benchmark in a setting that emulates a computational-mathematics research loop. We also propose a refinement to the RealMath benchmark by introducing a multi-step post-processing procedure and a multi-stage validation pipeline, both of which improve the quality and reliability of the extracted problem set. Our experiments reveal substantial performance gains from SageMath access across all evaluated models on +9.7pp on average, the gains range from 1.5pp to 27.8pp and narrow the gap between open-weight and closed models. Qwen3.7-Max benefits from SageMath the most, while GPT-5.5 achieves the highest solve rate of $75.2\%$ and the lowest token usage among tool-enabled configurations. Our findings suggest that CAS-augmented agents represent a promising direction for assisting mathematicians in computational exploration, and we believe that this work is a step towards automated conjecture discovery. The project repository is available online.

Large language model coding agents increasingly perform open-ended data modeling and analysis. These agents are stochastic and adaptive, and therefore their autonomous model discovery behavior cannot be adequately characterized by a single benchmark run. In this work, we propose an experimental design and analysis framework for systematically evaluating this discovery process, quantifying its variability, and identifying important factors. The proposed framework treats these agents as stochastic model-discovery operators, which map task-specific discovery data and an optimization target to a fitted model. Specifically, we investigate two such operators, Codex and Claude Code, under controlled experimental factors including agent's reasoning effort, task, optimization metric, and composition of training data. For each agent-task-metric combination, regression models and inference are conducted for multiple responses such as output quality, dollar cost, wall-clock time, and process complexity. Furthermore, we develop a utility-aligned canonical decomposition to characterize the dominant direction of the reasoning-effort effect and to assess whether that direction aligns with a performance-cost utility direction. The proposed framework is demonstrated on a testbed of networked word-forming games with insightful findings on reasoning effort with respect to cost and process complexity.

LLM systems for scientific discovery increasingly assist with ideation, literature synthesis, experiment planning, and report generation, but the first research question they propose can remain difficult to audit: it may sound plausible without exposing the mechanism, falsifier, or assumption that a scientist should inspect. We introduce FirstResearch, a first-principles research-question formation framework for scientific LLM agents whose core artifact is a structured Research Question Certificate. The certificate records primitive definitions, assumptions, a mechanism model, a tension or contradiction, a falsifiable hypothesis, a minimal decisive test, and a failure update rule, making the proposed question inspectable before downstream execution. On ten LLM-agent research topics, FirstResearch outperforms controlled prompt-level baselines inspired by AI co-scientist, Agent Laboratory, and AI Scientist-v2 under a primary DeepSeek-blind-judge protocol. A Gemini-2.5-Flash independent-judge rescore of the same 40 baseline packages preserves the system-level ranking, with FirstResearch scoring 4.86/5 versus 4.38/5 for the strongest baseline and Pearson agreement of 0.865 on average score. A one-repeat ablation checkpoint further suggests that the certificate-centered core is the strongest component: certificate-only scoring reaches 4.90/5 under DeepSeek and 4.88/5 under Gemini, while removing certificates drops below 1/5 under both judges. These results are preliminary and use LLM judges rather than human domain experts, but they support a narrow scientific-discovery claim: explicit derivation constraints are a promising mechanism for making LLM-generated scientific questions more auditable. Code, prompts, saved outputs, and reproduction scripts are available at https://github.com/louiswang524/FirstResearch.

Agentic AI-for-Science can automate ideation, planning, and analysis, but final validation still depends on real experiments. A self-driving lab (SDL) can execute those experiments, yet the loop still has bottlenecks: the agent may spend too many rounds on low-value experiments, or each round may require a high-cost experiment. We target these two physical bottlenecks with one agent. First, a prior-aware agentic DOE loop uses domain knowledge and past results to propose feasible and informative next experiments, reducing trials-to-target. Second, a cost-aware surrogate agent predicts high-cost, high-resolution measurements from low-cost, low-resolution measurements. It chooses between a high- and a low-cost measurement based on the predicted uncertainty. We examine these directions in the biology and materials domains, respectively. Together, under a single agent, these components aim to accelerate the SDL loop by reducing both the number of loops and the cost per experiment.

Large language models have made research ideation increasingly accessible, yet effective idea development requires more than generating candidate directions. Researchers must ground a problem in current literature, identify meaningful bottlenecks, differentiate from existing solutions, and evaluate risks before committing to implementation. We present ResearchStudio-Idea as a reusable skill suite for this first mile of research ideation. The suite includes Paper-Search, a standalone multi-source literature search skill; Scoop-Check, a standalone prior-art collision checker for novelty claims; and IdeaSpark, the end-to-end skill that composes evidence grounding, pattern-guided generation, collision retrieval, audit, and idea-card rendering into one workflow. IdeaSpark is constructed from a corpus of 1,947 machine learning conference papers collected from ICLR, ICML, and NeurIPS between 2021 and 2025, including Oral papers, a separately tracked high-citation subset, and rejected submissions. Analysis of these outcomes reveals 31 recurring ideation sub-patterns, consolidated into 15 reusable ideation patterns. Each pattern is operationalized as a structured card containing research contexts, bottleneck types, differentiation strategies, supporting precedents, and common failure modes. Given a research problem and an evidence bundle, IdeaSpark evaluates evidence readiness, reconstructs the surrounding research context, identifies unresolved bottlenecks, selects relevant patterns, instantiates one candidate direction, retrieves potentially conflicting prior work, and performs outcome-informed auditing. This workflow transforms reusable ideation patterns into traceable research proposals. Blind automated-judge evaluations show that IdeaSpark consistently produces stronger research proposals than no-skill and generic-skill baselines while maintaining competitive novelty.

Long-running coding agents such as autoresearch can persistently discover optimizations for open-ended problems. However, they tend to converge onto a single high-level approach, then proceed with low-level edits while missing other superior approaches to the problem. We hypothesize two harness-level design choices contribute to this behavior: accumulating context in a single long-running agent and only exposing a single program state to edit. We introduce SwarmResearch, an orchestrator-subagent harness in which a Shepherd Agent uses global context to steer a population of Search Agents, each operating with local context in their respective git branch. On open-ended optimization tasks, SwarmResearch discovers better or comparable solutions to state-of-the-art LLM-guided evolution and multi-agent techniques on 13/15 tasks, driven by higher-level exploration. Compared with fixed scaling of serial and parallel agents, SwarmResearch's orchestrator-guided scaling discovers better-performing solutions by adapting parallelism at different search depths.

Autonomous-research agents have demonstrated end-to-end LLM automation in machine-learning sandboxes where execution provides calibration. Frontier physical science differs categorically: physical reasoning underlies every methodology choice, toolchains are often underdocumented, and calibration must come from external literature anchors - which unscaffolded agents cite but do not confront, hallucinating plausible, unverifiable results from internal priors. We present a pipeline that runs end-to-end from a corpus of 11,083 recent condensed-matter physics arXiv papers to a publication-grade manuscript with three substantive physics findings (here on altermagnetic piezomagnetism): the agent autonomously conceives a research direction by mapping the corpus, calibrates methodology by reproducing published references, conducts novel first-principles computations, and writes the manuscript - grounded in literature throughout, across 47 fresh-context sessions in six phases sharing only on-disk state, with 2,162 literature-consultation events. Fault tolerance emerges from redundancy: fresh-context isolation, distributed grounding, and adversarial review catch what any single session misses; pre- and post-pilot stages are fully autonomous, and pilot requires bounded human intervention only at reproduction failures - operational knowledge curation, not scientific direction. Two paired failure modes - a pre-architecture baseline and a no-pilot ablation - isolate structurally enforced numerical confrontation at calibration checkpoints as the operative grounding mechanism. The primitives, characterized failure modes, and quantified intervention pattern lay a foundation for autonomous research in high-stakes scientific domains beyond computational physics.

Federated learning (FL) research often depends on many small but consequential algorithmic choices: optimizer variants, server aggregation rules, local training schedules, normalization, regularization, and model architecture. These choices are expensive to explore manually and difficult to compare fairly when candidate changes can also alter the FL training or evaluation path. In this work, we present Auto-FL-Research (AFR), a constrained coding-agent workflow for FL algorithmic recipe search. Agents may propose and implement candidate training algorithms, including server aggregation rules, client update schedules, local objectives, and registered model variants, while task profiles fix the mutation surface, compute budget, communication contract, and final model evaluation. Each campaign records candidate scores, runtime, edited files, artifacts, and failure status. We evaluate AFR on five healthcare cross-silo FLamby tasks and on grouped-client profiles for the five fixed LEAF datasets plus the LEAF synthetic task. Five-seed repeat evaluations support gains on four FLamby tasks and five of six LEAF profiles, while also exposing seed-sensitive and search-selected failure cases. Same-budget controls show that several gains correspond to FL-recipe changes, whereas other improvements are recovered by fixed-surface scalar controls or fail under repeat or held-out evaluation. These mixed outcomes are part of the contribution: they show how agent-generated candidates can be separated into repeated FL mechanisms, fixed-surface tuning effects, and selected single-run artifacts.

Autonomous scientific discovery systems offer the potential to accelerate research by automating the process of hypothesis generation and validation. However, current systems operate within constrained search spaces or require predefined research questions, limiting their capacity for true open-ended inquiry. Furthermore, while they generate hypotheses iteratively, they largely lack the ability to explicitly synthesize their own accumulated findings to uncover complex, interconnected phenomena. We introduce DiscoPER, an autonomous large language model-powered framework that conducts open-ended research by dynamically generating and executing code to explore datasets without pre-specified research objectives. To ensure rigorous scientific validity, every proposed discovery must pass statistical testing. To overcome the limitations of isolated search, our framework introduces a second-order reasoning mechanism that periodically analyzes its own accumulated discoveries. By treating prior discoveries as empirical data, DiscoPER identifies structural patterns, confounds, and epistemic gaps, actively redirecting hypothesis exploration toward uncharted regions of the search space. The search space is further expanded by incorporating tool use, enabling the system to explore hypotheses beyond structured metadata by seamlessly processing and extracting useful information from multimodal sources like images. Evaluated on iNatDisco, a new multimodal ecological knowledge benchmark with pattern-level ground truth obtained from peer-reviewed literature, DiscoPER recovers 8 of 9 known patterns with a 72.7% hypothesis support rate, outperforming both classical causal discovery and LLM-guided baselines. Ablations show that DiscoPER scales with more data, and confirms the benefits of second-order meta-reflection.

Recent automated research systems show that language-model agents can generate hypotheses, run experiments, and write complete manuscripts, but most evidence still comes from selected examples, human-framed topics, or a few pre-defined research tasks. We present FARS (Fully Automated Research System), a fully automated AI-for-AI research system designed to operate across research topics at scale. FARS autonomously generates and advances projects through ideation, planning, experimentation, and writing, using stage-specific agents coordinated through a shared workspace that records proposals, code, logs, results, and manuscripts. In its first public deployment, FARS produced 166 complete research papers spanning 67 fine-grained AI/ML topics while preserving intermediate artifacts as an auditable corpus rather than a curated set of successes. We evaluate this corpus with 282 structured reviews from volunteer reviewers covering 140 papers, including overall ratings, sub-scores, integrity checks, and LLM-use disclosure. The reviews indicate that FARS can produce review-worthy and occasionally strong AI/ML research artifacts in a large-scale public deployment, while also exposing recurring failure modes in narrow experimental scope, methodological limitations, and integrity issues.

Autonomous research agents can now draft hypotheses, write code, run experiments, and produce papers, but they remain brittle when experiments fail. Under the prevailing paradigm, failure recovery is usually delegated to a single free-form reflection: a rich trajectory of metrics, logs, and design choices is compressed into one verbal critique, which often leads either to localized trial-and-error or to hard pivots that discard useful context. We propose SAGE, a Self-correcting, Autonomous, Grounded Experimenter, to tackle this failure-recovery bottleneck. Its core mechanism, Multi-Hypothesis Failure Attribution (MHFA), treats recovery as a structured causal diagnosis. By analyzing dynamic trajectory features, MHFA systematically generates multiple evidence-grounded explanations for a failure, independently evaluates their severity, and deterministically routes the verified root cause to the correct intervention level (hypothesis, experimental design, or implementation). To guarantee scientific honesty, SAGE further employs a grounded reporting mechanism that explicitly constrains drafted results to actual measured values, redacting hallucinated numbers. On a 12-topic, 5-domain benchmark, SAGE increases metrics-bearing outputs from 42% to 92% over a reflection baseline, improves artifact quality from 5.00 to 6.75/10, and blindly outscores AI-Scientist-v2 (52.0 vs. 48.2), with gains concentrated in code development and execution. While fully autonomous scientific writing and generating conference-ready papers remain notoriously difficult open problems for the entire field, SAGE successfully produces significantly more reliable and higher-quality scientific artifacts. Ultimately, by coupling structured recovery with explicit grounding constraints, SAGE significantly outperforms monolithic reflection paradigms, establishing a highly trustworthy foundation for future autonomous research.

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.

Existing autonomous research agents can support parts of the research process, but most systems still treat research as either an isolated assistant task or a closed workflow. Therefore, autonomous science needs a collaboration infrastructure that coordinates projects, agents, and digital and physical resources. We identify this as a shift from code-centered execution loops to research-oriented collaboration processes, where questions, evidence, participants, and resources must be coordinated under uncertainty. In this framing, an agent may be an AI system, a human researcher, a team, a laboratory, or an organization-backed participant. To this end, we present Clarus, a collaboration infrastructure for coordinating autonomous research agents toward web-scale scientific collaboration. Clarus reformulates research as an open, auditable, attributable, and resource-aware multi-phase collaboration process. It defines a minimal project-agent-resource object model and organizes scientific collaboration through four layers including Research Application, Digital Collaboration, Physical Substrate, and Physical World. Core modules are implemented as pluggable mechanisms, allowing Clarus to adapt to task risk, collaboration structure, and resource constraints. Through a controlled paper-generation case study, we show that Clarus can organize a research goal into a traceable, reviewable, attributable, and accumulative collaboration network across phases, tasks, and participants. Together, the object model, collaboration protocol, trust mechanisms, and prototype validation provide an initial foundation for open research networks. Clarus is now available at clarus.holosai.io.

Predicting a material's properties from its structure is a central, fast-advancing problem in computational materials science. A decade of work has produced standard public benchmarks and many published machine-learning models for the task (Dunn et al., 2020). The task's fixed metric and these baselines make it a natural setting for autonomous agent research (Karpathy, 2026). On the MatBench band-gap benchmark ($>$100k crystals), a general-purpose coding agent autonomously built the most accurate model trained without external pretraining, ahead of all seventeen expert-designed models reported for the task. A closer analysis shows it reached this by implementing known methods: either already standard in crystal neural-network models, or borrowed from other areas of machine learning. The contributing implementations include element-pair features on each message-passing edge and a crystal space-group embedding. The work not only demonstrates that LLM-agent autonomous research can optimize an expert-designed machine learning model for material property prediction, but also investigates the limitations of such autonomous research.

Automated alpha mining holds the scoring function fixed and varies the search algorithm over it. A search that converges against a fixed scorer overfits whatever the scorer cannot penalize, a primary cause of the out-of-sample generalization gap. We treat the scoring function as a search artifact alongside the alpha factors and study what conditions make this joint search admissible. Sealed Joint Search (SJS) is a framework: a set of structural conditions on information flow in an autonomous-discovery system that prevent joint search from collapsing into self-confirmation while keeping the evaluator sealed. Conditions cover role decomposition, typed inter-role communication, provenance-sealed reads, versioned stores, and substrate-local promotion. Agora tests SJS empirically: five LLM agent classes communicate via three channels, evolving eight skill libraries, with alpha libraries built on AlphaGen operators. Three evaluators write reports aggregated into one brief, carrying forward disagreement instead of voting. We run Agora for 100 rounds on CSI 1000 and evaluate on a 91-day 2026 holdout sealed from all LLM inputs. Agora achieves holdout Sharpe +1.87; best baseline +1.334 at favorable seed and -0.755 cross-seed mean. Pre-loading Agora's two metrics into a frozen-library ablation recovers only +0.40 of the +2.25 Sharpe gap, and adding PPO without library evolution worsens the gap. The two metrics emerge rather than being designed. Caveats: single-seed run, short-side concentrated signal, intended for long-short.

LLM coding agents make it tempting to automate empirical research by delegating experiments to them directly, but naive delegation does not scale to large projects: low-rate instruction lapses compound into broken, irreproducible artefacts. To address this problem, we present Glite ARF, an open-source Python framework for running many LLM coding agents in parallel on a research repository without sacrificing reproducibility or auditability. The framework defines a three-role stack: a human researcher chooses which hypotheses to test, coding agents (Claude Code, Codex CLI) implement individual tasks under a fixed structure, and deterministic Python verifier scripts enforce task isolation, immutability of completed work, a corrections overlay, and a materialised project overview. We call this verifier-driven research: the rules of the research process live in code that fails loudly when violated, not in prose that agents are merely asked to follow. Using Glite ARF, we developed our submission to the BEA 2026 vocabulary-difficulty shared task, placing first in the closed track and second in the open track on all three target languages (Spanish, German, Mandarin) and reducing the official baseline RMSE by 29.9% (closed) and 35.9% (open). The campaign comprised 273 tracked tasks (146 experiment runs) across 129 feature sets, run by up to twelve parallel agents orchestrated from a single laptop - with some model training on rented A100s - at approximately $450 in LLM API spend ($498 total third-party cost), and structured per-fold provenance let us catch and strip four target-leaking feature sets, correcting an implausible 0.609 RMSE to 0.802. Across three campaigns in three domains, the framework's structural machinery adds only about 1% of wall-clock time. Framework and a public demo project accompany this paper.

Autonomous AI Research promises to accelerate the scientific progress of machine learning. To realise this goal, current Large Language Model (LLM)-based agents need to go beyond just writing code, to mastering the exploration of simultaneously performant, diverse and novel ideas. To this end, we introduce Heuresis, a framework that abstracts the research pipeline into a set of general and composable primitives, enabling open-ended scientific exploration in machine learning research. We implement six search strategies: a greedy baseline, two archive-based (MAP-Elites, Go-Explore), one evolutionary (Islands), and two divergent (Curiosity, Omni), and evaluate them across three axes (Quality, Diversity, and Novelty) on three domains (LLM Pretraining, On-Policy RL, and Model Unlearning), totalling 3,222 scored runs. We find that completely novel ideas are rare. No idea across our scored runs is rated as "Original", and only a few achieve only "Minor Similarity" to prior work. Moreover, novel ideas never approach the highest-performing known-recipe scores. Across all six strategies and three domains, only one such idea lands in the top-10 by quality. We also observed agents resorting to a variety of reward-hacking techniques during execution (40 confirmed fabrications across 1,628 scored runs), and detecting them was necessary to keep the search faithful to the task. Our results show that while current search and Quality-Diversity strategies enable us to steer where the generated ideas land on the quality, diversity, and novelty axes, they do not expand the quality-novelty frontier. Bridging this gap is the open challenge towards the ultimate goal of perpetual, autonomous scientific progress. Code is available at github.com/a-antoniades/Heuresis.

Large language models are making research production scalable, shifting the bottleneck from producing artifacts to judging claims. We present \textsc{Agon}, a research orchestrator that validates what can be checked inside the workflow and leaves the remaining judgments to human scientists. \textsc{Agon} is built on six design principles: Prompt Economy, Future-Facing, Minimal Prompts, OmniDisciplinary, Massive Parallelism, and Zero-Code. We ran \textsc{Agon} across domains for 444 iterations of Prompt Economy loops, using only small starting topics and no human-written experimental code. These deployments demonstrate scalability while exposing new classes of failure. We organize these failures into a taxonomy along severity, fixability, visibility, and capability locus. The taxonomy separates failures the loops can see and fix from those that require human judgment. Together, these results show that \textsc{Agon} is pushing research toward a new paradigm: machine scales, human steers.

Closed-loop Auto Research extends automated machine learning from fixed-dataset fitting to changing the research workflow, with language-model agents editing representations and model code and acquiring external evidence. Molecular property prediction spans many small endpoints. We ask whether this action space yields improvements generalizing beyond the validation signal selecting them. We isolate three Auto Research axes, features, models, and external evidence, under a file-level ablation lock attributing each gain to one axis over a strong baseline. Across 36 endpoints in three benchmark suites we score each selected configuration once on a held-out test whose labels the search never read. A routed pipeline taking each endpoint's best validation axis reaches positive held-out gains of 0.013, 0.011, and 0.042, the transferable axis differing by suite, data on TDC, model on Polaris, feature and model on MoleculeNet. The largest model-search gain falls from 0.041 on validation to 0.003 on test, while curated data reaches 0.022 but negative 0.019 on test, two non-transfer signatures. Curated external data raises held-out CYP2C9-substrate performance by 0.17 and half-life by 0.08, admitted through a contamination filter rejecting same-source files overlapping 64 to 89 percent of test structures, necessary but not sufficient for transfer. A matched-trial automated machine learning control did not reproduce the agent's code-level model intervention, reaching 0.006 against 0.042, and the pipeline stays competitive with an 84M-parameter pretrained 3D model on the shared training split. The experiments stay within molecular property prediction, but separating discovery from held-out certification is a domain-agnostic lesson for any closed-loop system optimising a proxy for a held-out quantity.

Large language models have become capable reasoners and tool users that write and run code and search the literature, which makes automating the research process itself a realistic goal. We present PAPERCLAW, a harnessed multi-agent system that carries a project autonomously, from a field of study to a finished paper. PAPERCLAW curates a domain from a field's live literature, datasets, and code; brainstorms it into an idea with a pre-registered main-result contract; and drives a stoppable hypothesis map through an iterative propose, test, reflect loop that grows only from measured verdicts and halts once the evidence supports the idea, at which point it writes a venue-compliant paper. A full-lifecycle memory keeps each stage in a single living record, so a long run can be paused, inspected, and resumed without losing context. At the centre is an in-cycle research assistant with research tools and skills: it can drive the whole pipeline on its own, while the same interface lets a person step in at any stage, turning a first autonomous draft into a stronger paper through human-in-the-loop refinement. Throughout, PAPERCLAW keeps its output grounded and checkable, citing only references validated against open scholarly indexes and reporting results that genuinely ran. An evaluation with an LLM judge finds that PAPERCLAW produces strong papers both fully autonomously and with human-in-the-loop refinement.

A working citation looks like proof -- but the fact that a link resolves does not mean the cited paper supports the claim. I find that current agentic models rarely fabricate citations (over $99\%$ resolve), yet roughly $15.9\%$ link to the wrong paper. Existing benchmarks miss this failure mode: when a question has a fixed answer key, a model can reproduce the expected source from that key rather than independently verifying that the source supports the claim. I introduce \textbf{\openbiorq{}}, a retrieval-grounded agentic benchmark of $12{,}553$ unsolved biomedical research questions across $12$ domains that treats open questions as a faithfulness-and-abstention probe. To my knowledge, this is the first biomedical benchmark to combine an agentic setting -- where the model must issue multiple tool calls -- with unsolved questions that have no answer key. Openness is verified against real follow-up evidence rather than a model's parametric knowledge. Difficulty is empirical: I anchor it on questions that three open-weight reference models fail to answer, rather than on subjective hardness labels. On this hardest subset, held-out models from the same lineage as the difficulty anchors solve only ~17%, while three independent frontier agents (Gemini-3-Pro, Opus-4.7, GPT-5.5) span a wide 29-60% range. The benchmark is thus hard, non-saturating (the best agent still leaves ~33-40% unsolved), and discriminating across capability tiers. Beyond difficulty, I observe agentic collapse on the hardest questions, where agents stop using their tools. For the most collapse-prone model, blocking tool access entirely barely changes its score -- so tools stop paying off exactly where they are needed most. A frozen per-question checklist raises inter-judge agreement from Spearman 0.35 to 0.82.

Scientific discovery can be formulated as an iterative search process over the space of hypotheses and experiments. Contemporary methods navigate this space using heuristics such as MCTS. These algorithms conflate the merit of a hypothesis with the quality of its experimental execution. A promising hypothesis with preliminary execution is therefore ranked below a modest hypothesis whose execution is refined. Moreover, prior methods prune the search logs as the search progresses because the accumulated history outgrows the context window. We propose Agentic Reasoning for Tree Search (ARTS), where we deploy a reasoning language model to navigate this space. The model inspects prior execution logs, diagnoses whether earlier failures arose from faulty implementations or bad hypotheses, and selects the hypothesis to build on next. To mitigate challenges with context length, ARTS uses test-time training to instill the knowledge of search tree in the model weights. Across 22 tasks from MLGym and MLEBench, we show that ARTS outperforms leading algorithms, with over 15.3% relative improvement in the normalized score. With test-time training we show that a Qwen3-4B agent can match performance with closed-source frontier models like Gemini-3 Pro and GPT o3-reasoning with upto 5x lower inference cost. We further observe that on partially observable RL tasks, the test-time trained Qwen3-4B scientist surpasses ARTS with the o3 scientist by rediscovering the human-best recurrent-memory solution that heuristic methods prune away.

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.

Spacecraft guidance, navigation, and control functions are increasingly realized as learned policies distilled from expert solvers. Developing such a policy is itself a research process: an investigator selects an architecture and hyperparameters, runs experiments, and must determine whether an apparent improvement is genuine or merely seed noise. This paper presents AutoResearch, a framework in which a large language model autonomously drives that loop for aerospace control problems, coupled with a credibility layer, built into the loop, that certifies each reported result against the problem's own measured seed noise. The language model serves only as the offline research agent that develops the control policy; the trained policy it produces is then deployed onboard the spacecraft, while the model itself never operates the vehicle. At each iteration the agent reads a plain-language problem description and the run history, proposes a single edit to the training script, executes it, and logs the outcome. No reported result is credited until it passes the same three checks: measured per-problem seed noise, reseeded verification of the best configuration, and leave-one-out pruning of the agent's edits. The same loop is applied, unchanged, to two aerospace control problems: a Clohessy-Wiltshire relative rendezvous and a safety-constrained collision-avoidance docking past a keep-out zone, each calibrated against a known optimal control benchmark. In both, the audited policy clears the measured seed noise by many standard deviations; an undirected search over the same parameters does not. On the docking problem the gap becomes categorical: undirected search yields no feasible policy, while the learned policy stays outside the keep-out zone on every seed.

We propose an AI economist agent for economic and financial scenario analysis. Scenario design often requires analysts to assess emerging risks with limited historical precedent, combine information from many sources, and translate qualitative mechanisms into internally consistent quantitative paths. Large language models (LLMs) can search and synthesize this information, but fluent narratives alone do not establish the model-based calculations needed for economic conclusions. Our framework uses LLM agents to plan the analysis, retrieve relevant evidence, and organize economic mechanisms, while registered quantitative models generate numerical outcomes and predefined tests determine whether intermediate results can be used in the final report. We apply the framework to European macro-financial stress scenarios and bank capital analysis. The empirical analysis evaluates retrieval of economic mechanisms, scenario construction, model execution, and report generation under a historical information cutoff. The results show how the AI economist agent can combine flexible evidence retrieval and scenario construction while keeping the resulting analysis linked to identifiable sources and explicit model calculations.

Identifying the lowest-energy surface-adsorbate configuration is critical for modeling heterogeneous catalysis, yet exhaustive exploration with ab initio calculations is computationally prohibitive. Machine-learning force fields (MLFFs) accelerate structural relaxation but leave the search over the vast configurational space a major bottleneck, and open-loop large language model (LLM) agents lack a physics-grounded feedback mechanism to correct erroneous initial guesses. We propose AdsMind (Adsorption configuration discovery with Machine intelligence and relaxation feedback), a closed-loop multi-agent framework that enables autonomous error correction through MLFF relaxation feedback. Across four LLM backends, AdsMind achieves consistently high search reliability, with success rates of 100% and 98.8% on the benchmarks AA20 and OCD-GMAE62. Relative to its single-pass (1-Shot) ablation it reduces cross-backend energy dispersion, and it uses only 4.11 and 4.67 MLFF relaxations per case, respectively -- an approximately 14-fold reduction over heuristic enumeration baselines. Density functional theory (DFT) validation using VASP/PBE on six representative AA20 systems shows that the reported open-loop Adsorb-Agent outputs exhibit qualitative adsorption-energy sign errors for molecular adsorbates, whereas AdsMind preserves the correct sign in all tested cases with closer quantitative agreement. AdsMind thus delivers reliability, self-reflection, and interpretability simultaneously, supporting more DFT-informed autonomous chemistry workflows.

Reproducing research results from papers and released code is central to scientific progress. Existing works have introduced benchmarks to evaluate whether LLM agents can assist with reproducibility, but they are difficult to scale due to their reliance on substantial manual effort for data curation and evaluation. We introduce ReproRepo, a scalable framework for reproducibility evaluation that leverages human-raised GitHub issues as naturally occurring supervision on realistic reproduction blockers. We instantiate ReproRepo on 1,149 recent machine learning papers from major conferences and evaluate four frontier model-agent configurations. Our results show that LLM agents, even without executing code, can identify many real-world reproducibility problems from paper-repository pairs: the best agent in our study, namely Codex with GPT-5.5, surfaces at least one semantically related human-reported blocker for $\sim$90% of papers in the study. Further analysis shows that agents are particularly effective for surfacing visible failures and identifying the right semantic region, but may still be insufficient in exact localization. ReproRepo can serve as a reusable, scalable framework for future evaluations of LLM agents on real-world reproducibility auditing. Our code is released at https://github.com/LithiumDA/ReproRepo.

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.

Self-driving laboratories (SDLs), where artificial intelligence proposes subsequent experiments and robotic systems execute them, are rapidly becoming the vanguard of materials discovery. A critical bottleneck, however, lies in seamlessly bridging diverse AI algorithms tailored for specific exploration goals with the heterogeneous robotic hardware found across different laboratories. Here, we present NIMO, an open-source software platform designed to dissolve this barrier through three core paradigms: a modular AI-robot decoupling mediated via simple CSV file exchange, a discrete candidate-pool architecture that seamlessly absorbs domain knowledge, and a unified Python interface pre-loaded with twelve distinct AI algorithms. In this Perspective, we review the operational principles of each algorithm alongside six diverse SDL implementations driven by NIMO, covering electrolyte discovery, organic synthesis, thin-film exploration, fuel-cell process informatics, coffee-ring phase exploration, and legacy liquid-handling automation. One of these also demonstrates NIMO's seamless interoperability with the IvoryOS orchestration framework. To democratize autonomous science, we also introduce a no-code desktop application that enables intuitive, human-in-the-loop exploration for non-programmers. NIMO is freely available at https://github.com/NIMS-DA/nimo, offering a versatile, plug-and-play foundation to accelerate autonomous materials exploration across diverse experimental landscapes.

The autoresearch pattern enables autonomous experimentation by having a large language model (LLM) iteratively modify code to optimize a target metric. Its stateless design, however, reconstructs experimental context from scratch at every iteration, incurring $O(n)$ token cost per iteration and $O(n^{2})$ total. This work reformulates the pattern as a stateful ReAct agent using LangGraph, where typed persistent state carries experimental history across iterations via a tool-calling interface. Two benchmarks are evaluated: hyperparameter tuning (15 iterations, small per-iteration observations) and code performance optimization (40 iterations, large per-iteration observations containing full source code and benchmark results). On hyperparameter tuning, the stateful agent consumes 90% fewer tokens (2{,}492 vs.\ 24{,}465). On code optimization, the stateful agent consumes 52% fewer tokens (627K vs.\ 1{,}275K) while achieving comparable optimization quality on both tasks. The token reduction is structural: the stateless agent re-reads the full history at $O(n)$ cost per iteration, while the stateful agent operates within a fixed-size conversation window at $O(1)$ cost. This paper describes the architecture in sufficient detail for practitioners to implement a stateful autoresearch agent for their own workflows.

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.

AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood. Existing benchmarks for AI agents rarely capture the complexity, heterogeneity, and extended reasoning required by scientific work, whereas benchmarks for scientific tasks often reduce research to static, direct problems and provide limited support for interactive evaluation. Here, we introduce SciAgentArena, a systematic benchmark for evaluating AI agents in real-world scientific research scenarios drawn from emerging needs across multiple domains. SciAgentArena comprises approximately 200 tasks with stepwise verification and an interactive, agent-agnostic environment for assessing diverse AI agents. Using this benchmark, we find that current agents can contribute effectively to well-specified data-analysis workflows, particularly when the task structure and evaluation criteria are clear. However, their performance remains uneven across scientific contexts: agents struggle to generate genuinely novel insights, sustain self-directed exploration, and formulate robust solutions for open-ended research questions. We further characterize common failure modes across agents and identify opportunities for improving their reliability, autonomy, and scientific reasoning. Together, SciAgentArena provides a practical framework for measuring progress in AI agents for science and for guiding the design of future agents capable of addressing complex scientific challenges. Full codes, tasks, and datasets can be accessed via this link: https://sciagentarena.github.io/.

Scientific progress depends on a repeated loop of exploration, experimentation, and abstraction. Researchers test candidate directions, interpret the evidence, and carry the resulting lessons into later attempts. We study how an AI agent can run this loop autonomously over long horizons. We introduce Arbor, a general framework for autonomous research that combines a long-lived coordinator, short-lived executors, and Hypothesis Tree Refinement (HTR), a persistent tree that links hypotheses, artifacts, evidence, and distilled insights across time. The coordinator manages global research strategy over the tree, while executors implement and test individual hypotheses in isolated worktrees. As results return, Arbor updates the tree, propagates reusable lessons, refines the search frontier, and admits verified improvements. This design turns autonomous research from a sequence of local attempts into a cumulative process in which strategy, execution, and evidence are carried across time. We evaluate Arbor under Autonomous Optimization (AO), an operational setting where an agent improves an initial research artifact through iterative experimentation without step-level human supervision. Across six real research tasks in model training, harness engineering, and data synthesis, Arbor achieves the best held-out result on all six tasks, attaining more than 2.5x the average relative held-out gain of Codex and Claude Code under the same task interface and resource budget. On MLE-Bench Lite, Arbor reaches 86.36% Any Medal with GPT-5.5, the strongest result in our comparison.

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.

Muon collider research spans accelerator physics, detector instrumentation, and high-energy phenomenology, with relevant evidence scattered across a rapidly expanding and heterogeneous body of scientific literature. As high-energy physics (HEP) increasingly explores agent-assisted analysis workflows, efficiently locating, integrating, and verifying scientific evidence becomes an essential capability. While retrieval-augmented generation (RAG) offers a promising framework for scientific question answering, integrating agentic reasoning without compromising retrieval precision remains a key challenge. In this work, we present agentic hybrid RAG, an evidence-grounded RAG framework for muon collider research. The framework combines a hybrid retriever, integrating sparse lexical and dense semantic retrieval, with an agentic reasoning module for query decomposition, evidence expansion, and grounded answer generation. To enable systematic evaluation, we construct the first benchmark for retrieval-augmented scientific question answering in the muon collider domain, comprising a curated literature corpus together with dedicated retrieval and answer-generation benchmarks covering major detector and physics research topics. Extensive evaluation shows that hybrid retrieval provides the strongest retrieval backbone, while agentic reasoning is most effective for controlled evidence expansion and answer synthesis. Built on this principle, agentic hybrid RAG consistently outperforms representative retrieval and RAG baselines in retrieval effectiveness, answer quality, evidence coverage, and factual grounding. Together, the benchmark and framework provide a foundation for evidence-grounded scientific question answering and future HEP analysis agents operating over large-scale scientific literature.

This report summarizes the CHIIR 2026 Workshop on Generative AI and Academic Search (GAI&AS), which examined how GenAI is reshaping academic search systems and research practices. The workshop brought together researchers in human information interaction and information retrieval to explore key challenges and opportunities in designing and evaluating future academic search systems that integrate GenAI, moving beyond traditional document retrieval to support summarization, recommendation, synthesis, and conversational interaction. Participants' interests and discussions focused on three thematic clusters: foundations and principles, applications and opportunities, and search-as-learning. Across these themes, the workshop highlighted the importance of academic search systems in supporting transparency, credibility, research integrity, and long-term scholarly needs, as well as in fostering higher-order cognitive processes. Participants discussed guiding theories, design principles, methodological approaches, partnerships, and community-building efforts aimed at advancing human-centered GenAI-enhanced academic search systems. Overall, the workshop demonstrated strong community interest and a diverse range of ongoing and emerging research initiatives at the intersection of GenAI and academic search.

Scientific and engineering progress is fundamentally a long-horizon iterative process: proposing changes, running experiments, measuring outcomes, and continuously refining artifacts. Yet existing benchmarks for frontier models primarily evaluate either single-turn responses or short-horizon agent trajectories, failing to capture the challenges of sustained iterative improvement over extended time horizons. To address this gap, we introduce AutoLab, a new benchmark for ultra long-horizon closed-loop optimization. AutoLab consists of 36 realistic, expert-curated tasks spanning four diverse domains: system optimization, puzzle & challenge, model development, and CUDA kernel optimization. Each task begins with a correct but deliberately suboptimal baseline and challenges agents to improve it within a strict wall-clock budget. Evaluating 17 state-of-the-art models reveals the dominant predictor of success is not the quality of an agent's initial attempt, but its persistence in repeatedly benchmarking, editing, and incorporating empirical feedback. While claude-opus-4.6 exhibits strong long-horizon optimization capabilities, most frontier models, including several proprietary ones, either terminate prematurely or exhaust their budgets with minimal progress. These results underscore the importance of time awareness and persistent iteration in autonomous agents. We open-source the full benchmark, evaluation harness, and task artifacts, to accelerate research toward truly capable long-horizon agents.

AI-Driven Research Systems (ADRS) -- systems coupling LLMs with automated evaluation to discover algorithms, proofs, and designs -- are being optimized and adopted across domains, but the tools to analyze them have not kept pace. ADRS performance depends on component interactions that are poorly understood, expensive to explore, and (as we show) not well captured by standard convergence guarantees. These guarantees rely on structural assumptions that do not hold under the ADRS process we formalize. We introduce GAMBLe, a framework that decomposes ADRS behavior into four parameters (generator $G$, assessor $\mathcal{A}$, discovery mechanism $\mathcal{M}$, budget $B$) and one compositional object, the effective landscape $L_{\text{eff}} = \mathcal{A} \circ G$, which reveals that distinct generator-assessor pairs induce structurally different per-problem optimization landscapes. We exercise the framework on 760+ replicated runs (>46,000 iterations) spanning generators from single LLMs to dynamically-adaptive ensembles, mechanisms from greedy selection to co-evolutionary meta-search, and three NP-hard problems whose assessors range from continuous scoring to cliff functions. The experiments reveal no total ordering of generators or mechanisms: frontier models can underperform open-source alternatives and the simplest mechanism sometimes outperforms state-of-the-art meta-search. Results show that even under limited budgets (60 iterations per run), the right component choices can improve performance by 13-67% and search efficiency by 6-39x.

Autonomous agents are increasingly expected to support end-to-end medical-AI research workflows, moving beyond isolated prediction tasks or short-form clinical question answering. However, existing medical agent benchmarks primarily evaluate final outputs, providing limited visibility into agent behavior within the research process. To address this gap, we present AutoMedBench, a workflow-aware benchmark for autonomous medical-AI research across diverse medical imaging and multimodal inference tasks, organizing agent execution into a unified five-stage workflow (S1-S5): Plan, Setup, Validate, Inference, and Submit. It comprises long-horizon tasks with each run averaging 33 agent turns, spanning five research tracks: segmentation, image enhancement, visual question answering (VQA), report generation, and lesion detection. Each task is evaluated under two difficulty tiers, Lite and Standard, which use the same data and metrics but differ in the amount of task-brief scaffolding, and each run is scored using both final task performance and S1-S5 stage scores, enabling stage-level analysis from the initial task brief to the final submitted artifact. Across thousands of recorded runs, stage-level scoring reveals that Validate is the weakest workflow stage on average, whereas Setup is the strongest, suggesting that current agents are better at making pipelines executable than at verifying their reliability. Post-run error analysis further shows that verification and submission failures dominate tagged errors, accounting for 37.7% and 38.1% of fired codes respectively, whereas task-understanding errors are rare at 0.9%, and runs with one fired error code have a 48% lower overall score than runs with no error code on average.

Scientific discovery demands intelligence, perseverance, and serendipity across vast search spaces. Today, top scientific capabilities remain siloed--one AI system for biological analysis, another for clinical reasoning, mathematical derivation, or materials simulation--and no pre-designed team can anticipate every skill a question will need. Science Earth is a planet-scale scientific runtime in which any capability--a simulation cluster, a wet-lab robot, a proof engine, a single-cell pipeline--can connect to any other, with collaboration structure emerging from the question itself. Its underlying EACN protocol lets capabilities discover one another, negotiate task ownership, and adjudicate across incompatible evidentiary standards without prior knowledge of who will meet whom. This shifts the organizing challenge from workflow design to open-ended connectivity. Two runs validate this under structurally distinct conditions. In a trans-Pacific higher-order Kuramoto synchronization study, agents identified and corrected a closure-ratio assumption in Ott-Antonsen analytic theory that fails outside the Lorentzian limit, within thirty minutes. In an eight-agent single-cell run on the 4.88M-cell Kang 2024 pan-cancer atlas, heterogeneous capabilities coupled over a 64.9-hour window with one structural external instruction, producing three new result layers and anchoring findings against an independent wet-lab study on an adjacent CCR8- TIGIT+ Treg subset. These cases are a first empirical reading, not a benchmark sweep. They show that when AI capabilities are truly connectable and coordination emerges from the problem, scientific reasoning becomes a distributed, self-correcting process--a step towards scaling AI-native discovery to the planet.

LLM-based research agents have advanced rapidly in science and engineering, where research is organized around executable experiments, code, and quantitative signals. Humanities scholarship, however, requires interpretive, evidence-grounded arguments over primary sources, whose value rests on faithful quotation, verifiable provenance, and deep interpretation. Existing research agents use general planning, tool use, and reflection, leaving these scholarly operations implicit. To address this gap, we introduce SPIRE (Scholarly-Primitives-Inspired Research Engine), a multi-agent framework that realizes Scholarly Primitives, a typology of basic humanities scholarship practices, as cooperating roles over a multi-scale close-reading substrate of passages, intra-context graph communities, and cross-context semantic clusters. On a benchmark of peer-reviewed papers in classical Chinese and Greco-Roman Latin scholarship, SPIRE recovers substantially more cited primary-source evidence and receives higher blind human and LLM ratings on four scholarly quality dimensions than LLM, RAG, and generic agentic baselines. Retrieval-tier and agent ablations, with retrieval-volume and answer-length controls, trace its advantage to targeted retrieval, structured evidence selection, and claim-evidence binding. Code and benchmark data are released at https://github.com/YatingPan/SPIRE.

Constructing production-quality machine-learned interatomic potentials (MLIPs) requires balancing accuracy, dynamical stability, and computational throughput under constraints that are not captured by a single training loss. We introduce MLIPilot, an auto-research framework in which tool-calling large language models propose hypotheses, edit MLIP training code, launch HPC jobs, and accept or revert changes using a fixed, physically constrained scorecard. We evaluate MLIPilot on MACE potential optimization using both commercial and open-weight LLM agents, including GPT-5.5, GPT-4.1, Mistral-24B, and Qwen3-32B. The benchmarks span molecular and periodic settings: a QM7-derived dataset for which we generated B3LYP/6-31G(d) energies and forces, and a Cu EMT dataset with periodic copper supercells labeled by ASE's Effective Medium Theory calculator. Across these benchmarks, the strongest agents move initially constraint-violating baselines to accepted models by discovering useful training strategies, including output normalization, loss-function changes, progressive training schedules, and model-capacity adjustments. These results suggest that LLM agents can serve as autonomous operators for scientific machine-learning workflows when their search is constrained by domain-specific validation criteria, shifting part of MLIP development from manual trial-and-error toward auditable, automated experimentation.

AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchmark for evaluating autonomous scientific research across 40 tasks from 10 scientific domains. Each task is grounded in a real published paper, provides related literature and raw data, and hides the target paper during evaluation. Expert-curated multimodal rubrics decompose the target scientific artifacts into weighted criteria, enabling evaluation of target-paper-level re-discovery while leaving room for new discovery. We evaluate seven autonomous research (auto-research) agents under a unified protocol and seventeen native LLMs through the lightweight ResearchHarness. Current systems remain far from reliable re-discovery: the strongest autonomous agent, Claude Code, averages 21.5, and the strongest ResearchHarness LLM, Claude-Opus-4.7, averages 20.7, with an LLM frontier mean of only 26.5. Error analysis shows that failures concentrate in experimental protocol mismatch, evidence mismatch, and missing scientific core. ResearchClawBench provides a reproducible evaluation frontier for measuring progress toward autonomous scientific research.

We study two-level autoresearch for cooperation: an outer-loop AI agent autonomously redesigns the inner-loop pipeline of an LLM policy-synthesis system for multi-agent Sequential Social Dilemmas (SSDs). A researcher agent $\mathcal{R}$ (run as a coding agent) reads the inner-loop source code, edits system prompts, feedback functions, helper libraries, and iteration logic, runs evaluations, and decides what to keep, following the autoresearch paradigm. Across two games (Cleanup and Gathering), two policy-synthesizer LLMs, and two welfare objectives (utilitarian efficiency and Rawlsian maximin), the researcher reliably exceeds hand-designed baselines, sharply tightens run-to-run variance, and outperforms prompt-only optimization. The discovered pipelines are objective-dependent: only under maximin does the researcher inject an explicit fairness mechanism into synthesizer pipelines, a class of mechanism that is absent from its own objective-agnostic system prompt and from every efficiency-optimized pipeline. This supports an information-design reading in which the researcher chooses what to reveal to the boundedly rational synthesizer as a function of the welfare objective. Code at https://github.com/vicgalle/autoresearch-social-dilemmas.

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.

We present MolLingo, a multi-agent system that emulates the reasoning process of a chemist to automate molecular design. Existing LLM-based approaches either operate as standalone generative models without access to external tools or lack the multi-agent coordination and shared memory needed for iterative, evidence-driven reasoning across the molecular design pipeline. MolLingo addresses this by coordinating a Literature Agent, a Chemist Agent, and an Orchestrator through a shared memory module, with each agent equipped with domain-specific tools. To enable effective molecular reasoning, we introduce BRICS-based Fragment Enumeration (BFE), a synthesis-aware molecular fragmentation method that decomposes molecules into chemically meaningful building blocks represented as block-based SMILES paired with common chemical names. This representation bridges molecular structure and LLM semantic space, enabling block-level reasoning and editing that is difficult with raw SMILES alone. As a case study in early-stage therapeutic design, MolLingo further grounds the Chemist Agent's reasoning in binding site geometry and residue-level protein context derived from molecular docking to optimize molecules for stronger target binding. Across four benchmarks, MolLingo consistently outperforms frontier LLMs and specialized baselines, including a fourfold docking score improvement over GPT-5.4 despite using the same underlying model, consistent drug property optimization gains across multiple LLM backbones, and state-of-the-art results on TOMG-Bench, surpassing both frontier LLMs and the RL-based optimization method RePO. Our results suggest that LLMs are already capable molecular design assistants when guided through chemically meaningful representations and biologically grounded structural context. Code is available at: https://anonymous.4open.science/status/MolLingo-7450.

Competition law experts conducting legal research must review extensive volumes of cases, decisions, and judicial reports to identify precedents and assess key elements in competition and merger cases. Although general research assistants such as Claude and ChatGPT and legal assistants such as SaulLM-7B and LegalGPT are increasingly used to assist legal research, they remain inadequate for competition law analysis: they lack specialized domain expertise, provide insufficient official citations, or hallucinate competition law cases. We propose Maat, a ReAct agent that orchestrates tools corresponding to different tasks of the research process. Designed iteratively with competition law experts, Maat grounds cases and findings in official sources using RAG for reliability, provides rich in-line citations, falls back to web search when database coverage is insufficient, and prompts the user for clarification when queries are ambiguous. Maat significantly outperforms all baseline assistants on case-specific tasks and performs within range of the top baseline on theoretical question tasks. The dataset used is available on GitHub.

Background: Large language models are typically evaluated as models, benchmarks, or short conversational episodes. Less is known about what happens when an agent is embedded persistently in a real academic research environment with durable memory, local files, external tools, scheduled routines, delegated roles, and explicit safety protocols. Methods: A structured self-observed implementation case study was conducted from January 31 to May 25, 2026. The unit of analysis was the persistent human-agent environment: researcher, agent runtime, memory layer, tools, repositories, scheduled jobs, specialized agent roles, and governance rules. Outcomes were organized using PARE-M (Persistent Agentic Research Environment Measurement), a measurement framework covering architecture, utilization, artifact production, resource use, reproducibility, and governance. Results: Recoverable main-agent telemetry contained 75,671 de-duplicated records across 96 active days, with 8,059 user-role and 23,710 assistant-role messages. The workspace included 502 memory-related files, 17 configured agent directories, and 57 skill files. Active system time was 579.7 hours (30-minute capped-gap estimate). Memory-derived records identified 482 output-proxy events and 889 failure, verification, correction, or protocol-proxy events. A strict May 2026 trajectory subset captured 627 model-completed events and 73.95 million recorded tokens, of which 82.9% were cache reads. Conclusions: The workflow was cache-dominant, suggesting that persistent agentic environments may shift the economic unit from cost per token to cost per completed artifact. Future evaluations should use artifact-level denominators, reproducible parsing rules, correction taxonomies, and independent coding of governance events.