Autonomous Research Agents

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31 papers in the last four weeks, up 82% on the four weeks before. 0.3% of all new papers.

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Latest papers 189

Aug 3, 2026cs.AI

Long-Horizon Autonomous Architecture Research with a Language-Model Agent: A Behavioural Case Study

We study what happens when a single general-purpose large language model acts as the sole researcher on a long-horizon neural architecture design problem. The agent receives a scientific question, an initial hypothesis and motivation, a compute budget, and research affordances (source and experiment management, experiment tracking, literature access, and persistent memory), then autonomously proposes, implements, evaluates, and records experiments over an extended period. The study comprises three phases, separated by human-declared transitions, that progressively expand the agent's tool surface or problem scale. Across approximately 100 sequential experiments, the agent improves a non-standard Vision Transformer from a weak baseline to a stronger, efficient model on small benchmarks and a usable but sub-SOTA model on ImageNet-1K, while producing a dense behavioural trace. We report four findings.(i)Productivity exhibits a clear phase structure: rapid early gains, a multi-dozen-hypothesis saturation wall, and recovery, with recovery triggered by expanding the action surface rather than changing the underlying model.(ii)A single early hypothesis contributes more to accuracy gain, with later improvements long-tailed.(iii)The preference for greedy, incremental hypotheses is largely workflow-induced: a commit-or-discard evaluation rule is isomorphic to greedy hill-climbing; the remainder reflects risk aversion after bold failures and anchoring on familiar literature. (iv)The agent independently rediscovers established results and, in the unfamiliar regime of pure channel attention, overturns a standard design choice. We conclude that workflow design was at least as influential as agent capability in this study and propose diversified search, budgeted moonshot hypotheses, explicit forks, and regime-aware re-validation as testable directions for future autonomous research.

Aon Safdar, Mohamed Saadeldin

University College Dublin, Ireland

AI Agents for Scientific Discovery Neural Architecture Search Long-Horizon LLM Agents Large Language Model-Guided Scientific Discovery Autonomous Research Agents

Jul 31, 2026cs.MA

SeekBrain: An Autonomous Multi-Agent System for Accelerating Neuroscience Discovery

Modern neuroscience relies on integrating multi-scale, multimodal datasets to uncover the neural principles underlying intelligence. However, analytical challenges posed by highly heterogeneous data and fragmented workflows increasingly constrain discoveries. Here we introduce SeekBrain, an autonomous multi-agent framework designed to accelerate neuroscience discovery through domain-grounded hierarchical planning and cross-modal data analysis. SeekBrain dynamically constructs a repertoire of analysis recipes extracted from code-paper pairs. By coupling this codified expertise with agentic planning and execution engines, the framework scalably generates hypotheses and analytical pipelines on demand. Systematic evaluation on the expert-annotated BrainArena benchmark demonstrates that SeekBrain substantially outperforms state-of-the-art agent baselines across various analysis tasks. Crucially, when deployed in real-world research, SeekBrain integrated behavioral, neural, and anatomical data to reveal structured, distributed neural representations of larval zebrafish behavior and a shared axis of regional decoding strength across the brain in a mouse decision-making task. These results establish SeekBrain as a scalable and practical tool for accelerating data-driven discoveries in neuroscience.

Jiamin Wu, Peishan Xiang, Jingyang Chen +26

Shanghai Artificial Intelligence Laboratory · The Chinese University of Hong Kong · State Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences +3

Autonomous Scientific Discovery Multimodal Agents Multi-Agent Planning Autonomous Research Agents

Jul 30, 2026cs.AI

An AI Scientist that Doesn't Drift: Taste, Structure, and Falsifiable Findings in a Quadruped Navigation Research Loop

Autonomous research loops driven by large language models can run machine-learning experiments at scale but tend to drift toward local refinements of whichever metric they optimise rather than testing the hypotheses that motivate the experiments. We address this structurally and present an AI Scientist for studying generalisation in quadruped robot navigation policies in simulation. Building on the autoresearch paradigm of Karpathy, our loop adds three components: an immutable experiment card that pairs each iteration's prediction with its outcome under a fixed schema, so a falsified hypothesis cannot be retconned; specialised subagents restricted to mechanical roles; and kkanbu, a preference oracle that holds the user's research taste as a typed knowledge graph and is the only component permitted to make subjective judgements. To isolate the oracle we run the identical loop twice across eleven research streams, with and without kkanbu. Neither arm drifts: both falsify roughly three quarters of their own hypotheses, and the best trained policy comes from the oracle-less arm. What the oracle changes is direction, not score: it alone explores test-time adaptation, it authored the winning designs where its arm led, and it carried lessons across streams that the other arm repeatedly re-derived. The scaffold keeps the loop honest; kkanbu decides where it looks.

Yiwen Zhang, Eloise Zeng, Jaeha Lee +1

Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, U.S.A. · Department of Mechanical and Civil Engineering, California Institute of Technology, Pasadena, CA 91125, U.S.A.

AI for Science Human-in-the-Loop AI Autonomous Experimentation Autonomous Research Agents

Jul 30, 2026cs.AI

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.

Ting Gong, Michael Ruofan Zeng, Yong Yang

University of Washington Seattle, Washington, USA · Texas State University San Marcos, Texas, USA

Automated Theorem Proving AI-Assisted Scientific Research LLM Mathematical Reasoning Autonomous Research Agents

Jul 30, 2026cs.AI

Rehearse: Stepping Back from the Confidence Cliff in Self-Improving Autoresearch

Autoresearch improves machine-learning code by proposing changes, running full training jobs, and keeping changes that improve the metric. The efficiency of this loop depends not only on generating ideas, but also on the agent's ability to decide, before spending a training run, whether a proposed modification is likely to work. We study how the reliability of this pre-execution judgment changes over the course of an autoresearch trajectory. In public AutoSOTA logs (Li et al., 2026; Tsinghua FIB Lab, 2026), the fraction of helpful modifications falls from 70% in the first two iterations to 43% by iteration 6+. On 296 same-baseline modification pairs from 39 paper-derived AutoSOTA tasks, each containing one modification that improved the metric and one that did not, with measured outcomes hidden, an LLM judge given candidate rationales but no prior-attempt history reaches 79.5% accuracy on the pairs where strict consensus returns a verdict. On the full 366-pair benchmark, however, this ability weakens substantially late in the loop. As successful changes accumulate, selective accuracy - accuracy conditioned on a strict-consensus verdict - falls from 82.8% to 56.9%, while the judge remains willing to decide. We call this operational pattern the confidence cliff. Rehearse implements the loop change as a lightweight skill for autoresearch loops: propose several ideas, compare them before execution, run the most promising, and judge with a focused memory of similar past attempts and outcomes. This focused outcome memory raises late selective accuracy to 83.5%. Across 4,000 budgeted training runs over three loops, Rehearse improves the endpoint under the same training-run budget on nanochat, image classification, and time-series forecasting.

Jiazhen Ji, Shouhong Ding

Tencent

Language Model Self-Assessment Autonomous Experimentation Autonomous Research Agents LLM Agent Reliability Memory-Augmented Language Model Agents

Jul 30, 2026cs.AI

DeepResearch Agent System

The DeepResearch Agent System is a large language model system engineered for deep information retrieval, multi-step reasoning, and autonomous research tasks. Built upon a sparse activation architecture with 30 billion total parameters of which only 3 billion are activated per token, the system achieves state-of-the-art performance on multiple agent search benchmarks while delivering 3.2 times faster inference compared to dense counterparts of equivalent scale. The system supports a 128K-token context window with hierarchical attention mechanisms that yield 18.7% accuracy and 23.4% recall improvements over standard long-context approaches. A dual-mode reasoning engine provides both a ReAct paradigm for basic multi-step problem solving and an IterResearch mode for high-performance iterative research with up to 20 reasoning steps, collectively delivering a 31.2% accuracy improvement over single-pass baselines. Multi-tool coordination integrates retrieval, computation, web search, and file parsing modules to achieve 92.1% tool-use accuracy. A reinforcement learning optimization framework based on the GRPO algorithm provides token-level policy gradients that improve training stability by 35% and accelerate convergence by 42%. An automated data synthesis pipeline with seed-based expansion achieves a 92.5% usability rate. Benchmark results include 87.3% on Humanity's Last Exam, 85.3% on BrowserComp Chinese, and 91.2% on WebWalkerQA. The system is fully open-sourced, including data synthesis, training, and inference code, and supports applications in academic research, business analysis, R&D support, and education.

Yong Huang, Yulu Huang, for the team Collaboration

Deep Research Agents LLM Inference Acceleration Autonomous Research Agents

Jul 29, 2026cs.AI

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.

Peter Kirgis, Sayash Kapoor, Andrew Schwartz +21

Princeton University · Cornflower Labs · UK AI Security Institute +8

AI-Assisted Scientific Research AI Agent Evaluation Autonomous Research Agents LLM Agent Reliability

Jul 29, 2026cs.MA

One Run Is Not an Idea: The Implementation Lottery in Automated Research

Automated research systems use experimental scores both to deliver artifacts and to decide which ideas to retain, transfer, and pursue. Yet one run scores one implementation of an idea. Crediting that realization-level score as evidence about the parent mechanism creates the \emph{implementation lottery}, in which an idea-level conclusion depends on which plausible implementation was sampled. The mismatch is structural whenever one run updates beliefs about a mechanism. We estimate its magnitude. The \emph{Idea Reliability Audit} measures \emph{idea reliability} by validating and freezing candidate cards, sampling fresh-session implementations, using outcome-blind fidelity labels, and rerunning saved artifacts. It reports idea ICC and leave-one-implementation-out (LOO) winner reversal. Prior work generally repeats the task; we repeat the idea. Across 312 assignments on 13 tabular tasks and two coding-agent setups, implementation variance was more than five and ten times same-artifact rerun variance, respectively, and the winner from one implementation draw differed from the winner under the other-two mean in 25.6% and 43.6% of decisions. Reversal survives card-level filtering under two outcome-blind review rules. An exploratory diagnostic on three materials-regression workflows with a deterministic evaluator also finds implementation variation dominating the decomposition. These findings distinguish idea reliability from best-of-

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artifact utility. Before a score guides idea-level branching, transfer, or research memory, evidence should cover multiple implementations.

Jingjie Ning, Shanshan Zhong, Xiaochuan Li +2

School of Computer Science, Carnegie Mellon University

ML Reproducibility Autonomous Research Agents

Jul 27, 2026quant-ph

Agentic AI for Scientific Reasoning in Autonomous Quantum Sensing Experiments

We implement an agentic AI workflow built around a large language model (LLM) agent for autonomous experiments with nitrogen-vacancy (NV) centers in diamond. NV centers are a widely used platform for quantum sensing, and the ability to control many measurements from a computer makes NV experiments a natural setting for autonomous workflows. We make two main contributions. First, we demonstrate an autonomous NV experiment workflow that combines persistent project records, quantitative calculation and data analysis tools, and deterministic experiment control. In one autonomous experiment, the agent selected a single NV center, calibrated its resonant frequency, measured

T_2^\ast

with Ramsey measurements, and added a Carr--Purcell--Meiboom--Gill (CPMG) measurement to check a weak feature that could be related to nearby

^{13}\mathrm{C}

. Second, we introduce two offline benchmarks that evaluate the agent's reasoning separately from laboratory execution. We evaluated both benchmarks with GPT-5.4, GPT-5.5, and GPT-5.6 Sol. In the Ramsey checkpoint benchmark, greater reasoning effort generally improved recognition of a residual resonance calibration offset. By contrast, in the pulsed optically detected magnetic resonance (pODMR) data evaluation benchmark, pulse sequence information alone produced more false positive resonance judgments at higher reasoning effort. Requiring an expected signal calculation kept false positive rates low across all three models and reasoning settings. The results suggest a clear division of labor for autonomous experiments. The agent forms scientific hypotheses and uses quantitative tools to evaluate data, while deterministic code controls the hardware and enforces safety constraints.

Takuya Isogawa, Ryotaro Okabe, Nutdech Phadetsuwannukun +2

Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

AI Agent Benchmarks Laboratory Automation Agentic Reasoning Autonomous Experimentation Autonomous Research Agents

Jul 27, 2026cs.AI

Efficiency Matters in Autonomous Research

AI-driven autonomous research (AR) systems are becoming increasingly effective across a broad range of tasks. Their performance, however, is still evaluated primarily by the quality of the final outcome. In this paper, we argue that the efficiency of the solution-search process is an equally important but often overlooked dimension of performance. A strong AR system should not only produce high-quality results, but also reach them with as small a budget as possible. Search efficiency will become increasingly important as AR expands from domains with inexpensive verification, such as mathematics and coding, to real-world scientific settings in which solution evaluation may require costly physical experiments. To capture this dimension, we propose evaluating AR systems using the area under the curve (AUC) of the Pareto frontier, alongside final outcome quality. We compare several families of search algorithms, including hill climbing, beam search, tree search, and evolutionary search, across twelve systems-optimization tasks. We find that no single search structure is consistently the most efficient. We also show that search efficiency and final outcome quality are distinct performance dimensions: a method that eventually achieves the best result may nevertheless improve slowly and consume substantially more evaluation budget before reaching that result. Because the most effective search policy is generally unknown in advance, we introduce an adaptive procedure called fluid search, which uses a portfolio bandit to dynamically allocate a fixed evaluation budget across a forest of search processes. Across the evaluated tasks, fluid search achieves the highest overall search efficiency, closely matching the performance of a per-task oracle that is given the best search structure for each task in advance.

Haiqian Yang, Yuan Cao

Algorithm Selection Automated Evaluation Autonomous Research Agents

Jul 25, 2026cs.IR

SearchArt: Training Long-Horizon Search Agent with Scalable Synthetic and Verified Task

Recent advances in large language models (LLMs) have enabled search agents to autonomously tackle complex tasks across extended search and reasoning horizons. However, training effective search agents remains challenging due to the lack of scalable and long-horizon tasks, and the difficulty of evaluating and correcting intermediate reasoning and tool-use behaviors. We introduce SearchArt, a scalable framework for training long-horizon search agents through verification-driven task synthesis and a multi-stage post-training pipeline. SearchArt constructs large-scale datasets for complex search-, research- and user-oriented tasks by synthesizing diverse information-seeking QA pairs and corresponding search trajectories from web documents and automatically generated evidence graphs. To ensure the reliability of the synthesized data, we design a verification pipeline that jointly evaluates QA consistency, trajectory quality, and the relevance of retrieved evidence. The verified trajectories are subsequently used in a multi-stage training process comprising supervised fine-tuning and reinforcement learning-based policy optimization. Search agents trained with SearchArt exhibit adaptive search planning, iterative evidence aggregation, and complex reasoning over extended interaction horizons. Experimental results demonstrate that, with only (Qwen3.5-) 27B parameters, SearchArt scores 74.39 on BrowseComp-ZH, 70.06 on BrowseComp, and 52.55 on Deepresearch-bench, matching or surpassing frontier closed-source agents on both deepsearch and deepresearch benchmarks.

Lang Mei, Xiaohan Yu, Chong Chen +27

Huawei Cloud Post-Training Team

Synthetic Data Generation LLM Agents LLM Agent Training Long-Horizon LLM Agents Autonomous Research Agents

Jul 24, 2026stat.ML

CausalSmith: A Formally Grounded, Self-Improving Agentic Framework for Automated Research in Causal Inference

Automating theoretical research requires generating candidate results and evaluating them reliably. Models keep getting better at the first, while the second remains hard. A common approach asks one large language model (LLM) to review what another produced, yet such reviewers are empirically unreliable: they may accept fabricated papers and catch the fabrication at close to chance rates~\citep{badscientist2025}. We present \textsc{CausalSmith}, a framework for automated theoretical research in causal inference built on the Lean proof assistant, where a proof is checked by a program rather than read by a referee. \textsc{CausalSmith} rests on \textsc{Causalean}, a foundational Lean library for causal inference holding 8,179 machine-checked definitions and theorems, developed with language-model assistance under human design and review. Around it, we build a self-improving agentic pipeline that selects research topics, proposes results, formalizes statements, constructs proofs, and presents the resulting artifacts for human inspection. Moreover, the pipeline pairs Lean verification with a statement audit that compares each formal theorem against the informal claim behind it. We evaluate the system using artifacts produced by completed autonomous research runs. The source code, formal library, and run records are available at https://github.com/Jiyuan-Tan/CausalSmith.

Jiyuan Tan, Vasilis Syrgkanis

AI Agents for Scientific Discovery Automated Theorem Proving Formal Verification Causal Inference Autonomous Research Agents

Jul 21, 2026cs.AI

ResearchArena: Evaluating Sabotage and Monitoring in Automated AI R&D

As AI agents begin to automate AI R&D, we need ways to assess whether their outputs are safe to deploy, even when the agents themselves may be untrusted. AI control offers one such approach: rather than trusting the agent, it treats it as a potential adversary and uses a monitor to detect covert sabotage before deployment. We evaluate AI control for automated AI R&D with ResearchArena, a framework spanning four long-horizon tasks: safety post-training, capabilities post-training, CUDA-kernel optimization, and inference-server optimization. Because the deliverable in AI R&D is an artifact that will be deployed and run, we pair each main task with two kinds of hidden side task: an embedded side task that sabotages the submitted model, adapter, kernel, or server itself, and an independent side task that takes a covert out-of-scope action in the sandbox while leaving the artifact honest. We evaluate frontier agents at both sabotage and monitoring, across four monitor types that vary along two axes: whether the monitor may execute and probe the produced artifact, and whether it sees the agent's chain-of-thought. We find that sabotage hidden in the training data is the hardest to catch, flagged fewer than half the time. Letting the monitor run experiments on the artifact, rather than only read the trajectory, helps, but it is not enough: monitors still miss embedded sabotage by inspecting only the surface, by noticing the anomaly but explaining it away, or by probing the artifact with the wrong test. We release ResearchArena as a modular framework for evaluating sabotage and control in automated AI R&D.

Lena Libon, Ben Rank, Jehyeok Yeon +5

ELLIS Institute Tübingen, Max Planck Institute for Intelligent Systems, Tübingen AI Center · ETH Zurich · University of Amsterdam

AI Agent Monitoring AI Control AI Agent Safety Benchmarks Autonomous Research Agents

Jul 20, 2026cs.AI

AutoWorldModel-Bench: A State-Centric Benchmark for Automated World-Model Research

World modeling is an unsettled field: architectures, training objectives, and state representations interact in complex ways, and no single recipe dominates across environments. This makes it an ideal testbed for AI coding agents acting as autonomous researchers--a setting in which the improvement direction is not specified in advance, unlike the engineering-to-spec tasks that dominate current agent benchmarks. We introduce AutoWorldModel-Bench, a closed-loop benchmark in which frontier coding agents autonomously improve a provided world-model starter under a fixed compute budget. The benchmark spans eight game environments under a unified structured-state representation--ground-truth entity state extracted from each game and consumed through a shared tensor format--which isolates dynamics modeling from perception and enables minutes-per-run iteration. Across 64 sessions, Codex-5.4 and Claude Opus 4.6 improve their starter on 63; in 91% of sessions the winning edit is a non-trivial research-style modification--a new objective, representation, rollout procedure, or architectural change--rather than a hyperparameter tweak. Our benchmark offers a setting in which frontier coding agents can be evaluated on open-ended research rather than engineering-to-spec problems.

Marjan Moodi, Xuankang Zhu, Fernando De Mesentier Silva +2

Electronic Arts · Simon Fraser University

World Model Learning AI Agent Benchmarks World Model Evaluation Autonomous Research Agents

Jul 19, 2026cs.MA

Auto Research for Materials: Auditable AI-Scientist Workflows with Held-Out Transfer

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.

Jingjie Ning, Xiaochuan Li, Shanshan Zhong +2

School of Computer Science, Carnegie Mellon University · 2DP Technology

Automated Algorithm Discovery Automated Evaluation Autonomous Research Agents

Jul 17, 2026cs.AI

Co-Harness: Co-Evolving Harnesses and Model Weights for LLM Agents

Post-training agents for automated AI research requires optimizing not only model parameters, but also the runtime harness that shapes how research trajectories are generated, evaluated, and learned from. Existing pipelines typically train models under a fixed harness, including prompts, tools, skills, middleware, and memory, while leaving the data-generating process outside the optimization objective. This creates a mismatch between model updates and the static scaffolding that determines trajectory quality. We introduce Co-Harness, a framework that jointly optimizes the agent harness and model parameters during post-training. Co-Harness alternates between harness optimization and model optimization. An LLM-based HarnessCritic analyzes failed trajectories, identifies harness-level failure modes, and proposes validated local updates. The model is then fine-tuned on high-quality trajectories generated by the improved harness, distilling effective scaffolding into model parameters. A 200+ hour autonomous case study further shows that Co-Harness can recover from system crashes, improve inference efficiency, and discover ensemble strategies without human intervention. These results suggest that joint harness and model optimization is an effective way to improve agents beyond fixed-harness post-training.

Zhengyu Chen, Teng Xiao, Huaisheng Zhu +3

Meituan · Allen Institute for AI · Independent

Agent Harness Optimization LLM Agent Workflow Optimization LLM Agent Training LLM Post-Training LLM Agent Harnesses Autonomous Research Agents

Jul 16, 2026cs.AI

BrainPilot: Automating Brain Discovery with Agentic Research

Understanding the brain increasingly depends on integrating evidence across scales, modalities, and disciplines. Addressing a single research question therefore requires a coordinated sequence of operations, from surveying prior work to executing analyses and interpreting results in light of domain knowledge. AI agents promise to accelerate this process, but current agents lack domain expertise in brain science, may fabricate claims, drift during multi-step reasoning, and offer few defined points for expert intervention. These failures are especially costly in brain science, where conclusions feed into downstream scientific claims and depend on laboratory-specific expertise and careful human judgment. We present \textbf{BrainPilot} a \textbf{fully open-source} multi-agent system that accelerates brain science research with traceable logs and agent-verified results. A principal investigator (PI) agent coordinates specialist agents grounded in curated domain knowledge: a unified brain science knowledge base containing 7{,}233 indexed items and a skill library of 72 reusable methodology units across seven research domains. Every major step is recorded in the Graph of Trace, an auditable record that links subgoals, tool use, evidence, and claims and allows researchers to follow and inspect the workflow. An Auditor agent further integrates fabrication checking into the workflow. For evaluation, we run three brain science tasks from Agents' Last Exam, introduce our own benchmark, \textbf{BrainPilotBench-v0}, and present additional end-to-end case studies. Across these evaluations, BrainPilot with an open-source backbone model attains performance comparable to state-of-the-art agent framework with less costs.

Haoxuan Li, Tianci Gao, Jianhe Li +13

College of AI, Tsinghua University · 2Shanghai Qizhi Institute · 3Business School, Renmin University of China +8

AI for Science LLM Agent Orchestration Multi-Agent Collaboration AI Agent Benchmarks Autonomous Research Agents

Jul 15, 2026cs.AI

ReasFlow: Assisting Reasoning-Centric Scientific Discovery in Applied Mathematics via a Knowledge-Based Multi-Agent System

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.

Yutong He, Daibo Li, Guohong Li +15

Peking University · University of Electronic Science and Technology of China · Beijing Normal University +2

Multi-Agent LLM Systems AI Agents for Scientific Discovery Autonomous Scientific Discovery Autonomous Research Agents

Jul 15, 2026cs.CL

Analogical Deep Research: Retrieving and Integrating Historical Analogies for Foresight Analysis

Systematic comparisons between current situations and structurally similar past events in the historical, i.e., historical analogies, is among the most powerful tools for foresight analysis. In this work, we present a new task called Analogical Deep Research (ADR) to Large Language Model (LLM) agents and construct the first ADR benchmark ADR-bench to study whether LLM agents are able to find and leverage historical analogies when doing foresight analysis. Our investigation reveals a key obstacle: LLM agents are poor at finding analogies because they match on surface features rather than underlying mechanisms. We argue that ADR is inherently a causal question as it requires understanding why the event occurred. Based on our theoretical analysis, we propose two principles required for ADR, including the mechanism alignment and cross-analogy confirmation. Built upon our theoretical results, we propose a new agentic framework called Causal Analogical Researcher (CANA) that guides LLMs to find and integrate historical analogies. CANA incorporates a simple yet effective structural decomposition representation, and integrates structural feedback for reflective improvements of historical analogy identification and integration. We show that CANA brings up to 10% improvements in historical analogy generation, and surpasses the state-of-the-art deep research agents in the ADR-bench. Case studies with the ongoing events confirm the effectiveness of CANA in leveraging historical analogies.

Yongqiang Chen, Guangyi Chen, Yuewen Sun +1

1Mohamed bin Zayed University of Artificial Intelligence · 2Carnegie Mellon University

Analogical Reasoning LLM Agent Evaluation Causal Reasoning in Language Models Autonomous Research Agents

Jul 14, 2026cs.SE

XScientist: A Git-Like Research Protocol for Long-Running Autonomous Scientific Discovery

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.

Jixiang Luo

Data Provenance Autonomous Scientific Discovery Scientific Reproducibility Scientific Workflow Automation Autonomous Research Agents

Jul 14, 2026cs.AI

On-Device Deep Research at 4B: Exposure Bounds Faithfulness, Retrieval Bounds Coverage

On-device research agents search a corpus, read sources, and write a cited brief on a personal laptop. Whether their citations are faithful, and at what cost, is unmeasured for a deployable small model. This study fixes one 4B generator on a 24 GB laptop and asks what makes its citations faithful. It separates two quantities usually reported as one number. Cited claim faithfulness asks whether the cited source supports the claim. Trustworthy coverage asks whether the agent also cites the right sources. The study crosses how much of each source the generator sees, 400 against 1500 characters, with the quality of the sources supplied, gold papers against retrieved papers. Two levers fall out, and they act on different outcomes. Exposure sets faithfulness. More of each source lifts faithfulness from 0.45 to 0.58 on retrieved sources and from 0.37 to 0.58 on gold sources, and the two settings converge, so faithfulness is bound by exposure, not by whether the source is correct. The exposure lift is robust to a second, independent judge; the exact convergence is tight under the primary judge and only approximate under the second. Retrieval sets coverage. Trustworthy coverage stays near 0.22 on retrieved sources at any exposure, because recall is held near 0.40, so exposure cannot fix which sources are cited. The extra exposure costs about 235 output tokens. The practical recipe is to raise per source exposure first, cheaply, and then treat retrieval recall as the only remaining lever.

Vinay Kumar Chaganti

Independent Researcher

Contextual Faithfulness Citation Verification RAG Evaluation Autonomous Research Agents

Jul 13, 2026cs.AI

NVAITC AI Scientist: A Governed End-to-End Research System -- A Hypertension GWAS Case Study

Agentic research systems are emerging as a new paradigm for coordinating scientific workflows beyond isolated model inference, code generation, or statistical analysis. However, deployment in institutional biomedical environments requires governed mechanisms for research planning, data access, workflow orchestration, evidence tracking, reproducibility, and human oversight. We present NVAITC AI Scientist (NAIS), a governed end-to-end agentic research system designed to support domain-general scientific workflows while keeping protected data within institutional privacy boundaries. NAIS integrates proposal review, execution planning, governed computational routing, reproducible workflow orchestration, evidence generation, and scientist-in-the-loop oversight. We validate NAIS in a real-world hypertension genome-wide association study (GWAS) using hospital-linked genotype and electronic health record (EHR) data from 286,422 individuals under an aggregate-only data policy. The agent planned cohort extraction, orchestrated GWAS execution, generated quality-control summaries, and drafted publication-oriented outputs. Human-AI review identified phenotype discrepancies and enabled iterative refinement of the hypertension definition. After reconciliation, the agent-orchestrated GWAS reproduced established hypertension loci, including FGF5, ATP2B1, CNNM2, FTO, and GRB14, with the strongest signal at FGF5 reaching

-\log_{10}(p) \sim 70

. As a secondary demonstration, NAIS also supported a drug-induced liver injury prediction workflow, achieving a multimodal graph neural network AUC of 0.842. These results demonstrate that governed agentic research systems can support scalable AI-assisted biomedical discovery while producing outputs comparable to expert-led workflows.

Eddie Huang, Ken Liao, Iven Fu +14

NVIDIA AI Technology Center, NVIDIA Corporation · NVIDIA AI Technology Center (NVAITC), NVIDIA Corporation · Department of Medical Research, China Medical University Hospital, Taichung, Taiwan +12

Human-in-the-Loop AI AI Agent Governance Scientific Workflow Automation Autonomous Research Agents

Jul 11, 2026cs.DB

Confining Nondeterminism: AI-Driven Research Systems as DBMSs for Reliable, Non-Wasteful, Transparent, and Collaborative Research [Vision]

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.

Kyoungmin Kim, Anastasia Ailamaki

EPFL Lausanne, Switzerland

AI Agent Reliability Autonomous Research Agents LLM Agent Reliability

Jul 9, 2026cs.CL

XALPHA: A Memory-Driven AI Quant Researcher for Hypothesis-to-Code Alpha 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.

Fengyuan Liu, Yuchen Fu, Yuqi Wang +1

School of Computing and Data Science, The University of Hong Kong · Grace Investment Machine

Automated Algorithm Discovery Memory-Augmented Agents Autonomous Research Agents Algorithmic Trading

Jul 8, 2026cs.CL

From Solvers to Research: Large Language Model-Driven Formal Mathematics at the Research Frontier

Recent developments in AI for Mathematics (AI4Math), especially Large Language Model (LLM)-driven theorem provers, has achieved remarkable success in formal proof generation for well-defined mathematical problems through Interactive Theorem Proving (ITP) languages. However, current systems remain fundamentally limited in tackling frontier research mathematics, such as discovering new theorems or resolving open conjectures, which are often open-ended, under-specified, and involve multiple layers of abstraction. We argue that the next leap in AI4Math systems requires a decisive shift from predefined problem-solvers to research agents that can address frontier mathematical challenges with rigorous formal mathematical reasoning. In this position paper, we provide a systematic review of the field, covering datasets, auto-formalization, and proof synthesis. More importantly, we identify core limitations of existing systems in serving as mathematical research agents, examining issues across datasets, relational structure, mathematical exploration, tool ecosystem, and human-AI collaboration, outlining a strategic road-map for the future of AI4Math.

Eric Jiang, Xiao Liang, Yikai Zhang +16

University of California, Los Angeles · 2Lawrence Livermore National Laboratory

Automated Theorem Proving Interactive Theorem Proving Autoformalization Large Language Model-Guided Scientific Discovery LLM Mathematical Reasoning Autonomous Research Agents

Jul 8, 2026cs.AI

Recursive Self-Improvement in AI: From Bounded Self-Refinement to Autonomous Research Loops

AI systems increasingly participate in their own improvement: revising their outputs, adapting their own harnesses during deployment, training on data they generate, and, increasingly, conducting AI research itself. This literature is described under a vocabulary ("self-refine," "self-reward," "self-play," "self-evolve") that conflates fundamentally different ambitions. We survey 1,250 arXiv papers (2024-2026) along two axes: what the system improves -- its behavior in deployment, its policy through training, its evaluator, or the research process itself -- and the degree of loop closure (human-in-the-loop to fully closed). The taxonomy separates bounded self-refinement -- convergent, evaluable, and already industrial practice -- from open-ended recursive self-improvement (RSI), which remains bounded by grounding requirements, collapse dynamics, and compute constraints on every measured axis. Its distinctive feature is a dedicated category for self-evaluation: every improvement loop is a claim that some signal can substitute for human judgment. We survey the evaluator design space -- judges, process reward models, verifiers, rubrics, meta-evaluation -- order the signals into a verification hierarchy from formal verifiers (strongest) to intrinsic self-assessment (weakest), and observe that demonstrated self-improvement strength tracks this hierarchy, that its failure modes (self-confirming loops, model collapse, diversity collapse) follow from its violations, and that the "research direction-setting" bottleneck keeping humans in the loop sits at the top of that hierarchy. We connect the technical literature to the theory of RSI limits and to the safety and governance questions raised by frontier-lab accounts of closing the loop, and identify governance-grade measurement of self-improvement as the field's most underpopulated niche.

Mingguang Chen, Licheng Wang, Bo Qu

University of California, Riverside (UCR) · AlphaAvatar · Illinois Institute of Technology (IIT)

LLM Self-Refinement Human-in-the-Loop Evaluation Self-Improving Agents Language Model Self-Improvement Recursive Self-Improvement Autonomous Research Agents

Jul 8, 2026cs.AI

SpaCellAgent: A Self-Evolving LLM-Based Multi-Agent Framework for Trajectory Analysis

Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics. As the fundamental paradigm for reconstructing cell developmental paths, trajectory inference (TI) is critical. However, existing methods require extensive manual intervention and proficiency in heterogeneous tools, posing a significant barrier to efficient TI analysis. To bridge this gap, we propose SpaCellAgent, an autonomous large language model (LLM) multi-agent framework that automates end-to-end spatiotemporal analysis and narrative generation. SpaCellAgent utilizes a multi-agent architecture for strategic workflow planning, a dynamic tool-orchestration engine for adaptive algorithm selection, and a self-evolution module that iteratively refines performance through feedback. We evaluate SpaCellAgent on six heterogeneous datasets encompassing complex temporal developmental trajectories, diverse sequencing platforms, and spatially-resolved tissue architectures. SpaCellAgent consistently demonstrates over 40% improvement in analytical efficiency while maintaining expert-aligned performance. By converting natural language specifications into optimized analytical workflows and fully automating the pipeline, SpaCellAgent democratizes advanced spatiotemporal modeling and establishes a scalable, agent-driven paradigm for computational biology. The code and materials are available at https://github.com/LittleXH-shw/SpaCellAgent.

Songhan Wang, Haoang Chi, He Li +6

University of Shanghai for Science and Technology · National University of Defense Technology · Hong Kong Baptist University +3

Spatial Transcriptomics LLM Agent Orchestration Trajectory Inference Scientific Workflow Automation Single-Cell Transcriptomics Autonomous Research Agents

Jul 5, 2026cs.AI

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.

Ramsha Kamran, Maheera Amjad, Zartasha Mustansar +3

School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan · College of Electrical and Mechanical Engineering (CEME), NUST, Rawalpindi, Pakistan

Long-Form Document Generation AI-Assisted Scientific Research Agentic RAG Automated Evaluation Autonomous Research Agents

Jul 5, 2026cs.AI

MechMath Agent Team: LLM Driven Agents for Mathematical Research

AI reasoning has become a central focus in contemporary artificial intelligence, largely driven by the success of large language models. However, mathematical research, which is characterized by non-linear derivation paths, rigorous logical requirements, and protracted exploration cycles, poses severe challenges for existing reasoning systems. To overcome these limitations, we present the MechMath Agent Team (MMAT), which is a large language model driven agent designed to serve as a co-pilot throughout the full cycle of mathematical research. We design a tripartite Harness Architecture that decouples system responsibilities into Control, Execution, and Augmentation planes, thereby reconciling rigorous logical control with the agility demanded by open-ended research. Building upon this framework, we instantiate three specialized agents: a Knowledge Base Manager, a Natural Language Prover, and a Formal Language Prover, all operating in a closed loop to produce formally certified mathematical proofs. We evaluate MMAT on open problems in Number Theory, Algebraic Complexity Theory, Differential Algebra, Operator Algebra, and Inequalities. Across a two-month deployment, 11 problems have been solved, demonstrating its capacity to act as a co-pilot throughout the entire research cycle. The contributions are threefold: a general decoupled Harness Architecture for multi-agent mathematical reasoning, its concrete instantiation in the MMAT system, and empirical validation on a diverse suite of open problems.

Yichuan Cao, Ruichen Qiu, Junqi Liu +5

State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, CAS · School of Mathematical Sciences, University of Chinese Academy of Sciences · School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences

Automated Theorem Proving Multi-Agent Reasoning LLM Agent Harnesses LLM Mathematical Reasoning Autonomous Research Agents

Jul 4, 2026cs.CL

Rethinking Scientific Discovery in the Agentic Era

Artificial intelligence has advanced scientific discovery, but most AI4Science systems remain fragmented tools that rely on humans to coordinate problem formulation, literature grounding, model use, simulation, validation, and knowledge reuse. This paper presents \textbf{SCION (Scientific Collaborative Innovation with Agentic Organizational Nexus)}, an agentic scientific operating system that acts as an \textbf{organizational nexus}. Through a Science Agent serving as a \textbf{Meta-Harness}, SCION connects scientific tasks, tools, agents, artifacts, and memory, transforming research into an executable, auditable, and reusable operational process. At its core is the \textbf{Research Execution Plan (REP)}, which compiles high-level scientific intent into staged objectives, dependencies, verification checkpoints, tool requirements, expected artifacts, and fallback conditions. SCION further integrates hierarchical multi-agent execution, profile-driven specialization, selective context construction, governed delegation, and layered epistemic memory to support long-horizon scientific work. We formulate discovery under SCION as \textbf{Target-conditioned Inverse Search} and extend it to hidden-target settings through batch active search under finite experimental budgets. Applications in materials analysis, molecule design, and protein or antibody screening, together with experiments on scientific reading, idea generation, molecule generation, and antibody screening, show that SCION outperforms existing autonomous research-agent baselines, especially in decomposition, verification, refinement, and memory reuse. Overall, SCION shifts AI from isolated tools toward a coordinated operational layer for traceable and reusable scientific innovation.

Yining Zheng, Yuxin Wang, Jiahao Lu +27

Shanghai Innovation Institute · Fudan University · East China Normal University

AI Agents for Scientific Discovery Multi-Agent Collaboration Scientific Workflow Automation LLM Agent Planning Autonomous Research Agents