AI-Assisted Scientific Research

Recent advances in artificial intelligence (AI) have accelerated the growth of both human-authored and AI-generated research outputs, placing increasing strain on traditional academic publishing systems and challenging the scalability of conference- and journal-centered paradigms amid rising submission volumes, reviewer workload, and venue size. To address these challenges, we explore an AI-era publishing paradigm in which both human and AI scientists participate as authors and readers, and papers evolve through continuous, feedback-driven iteration. We propose AiraXiv, an AI-driven open-access platform built on open preprints, AI-augmented analysis and review, and reader feedback. AiraXiv supports human scientists through an interactive UI and AI scientists through Model Context Protocol (MCP)-based interactions. We validate AiraXiv through real-world deployments, including serving as the submission platform for ICAIS 2025, demonstrating its potential as a fast, inclusive, and scalable research infrastructure for the AI era. AiraXiv is publicly available at https://airaxiv.com.

The exponential growth of global academic output has confronted researchers and AI agents with an unprecedented information explosion,'' where fragmented and unstructured knowledge organization impedes deep interdisciplinary integration. Current academic retrieval tools predominantly rely on superficial keyword matching or vector-space semantic retrieval, which lack the topological reasoning capabilities required to navigate complex logical connections. Agentic deep-research-based frameworks are often prone to logical hallucinations and consuming high inference costs. To bridge this gap, in this report, we introduce SciAtlas, a large-scale, multi-disciplinary, heterogeneous academic resource knowledge graph designed as a panoramic scientific evolution network. By integrating over 43M papers from 26 disciplines, and a total of 157M entities and 3B triplets, SciAtlas provides a structured topological cognitive substrate that dismantles disciplinary barriers and furnishes AI agents with a global perspective. Furthermore, we develop a neuro-symbolic retrieval algorithm featuring tri-path collaborative recall and graph reranking, achieving a seamless transition from simple semantic matching to deterministic association discovery. We also present key application directions of SciAtlas, including literature review, automated research trend synthesis, idea positioning, and academic trajectory exploration, to demonstrate that SciAtlas can serve as an effective cognitive map'' to empower the full loop of automated scientific research while significantly reducing reasoning costs. We have released the interfaces for KG retrieval and various downstream tasks in our GitHub repo.

Biomedical abstracts play a critical role in downstream NLP applications, such as information retrieval, biocuration, and biomedical knowledge discovery. However, a non-trivial number of biomedical articles do not have abstracts, diminishing the utility of these articles for downstream tasks. We propose DPR-BAG (Divide, Prompt, and Refine for Biomedical Abstract Generation), a training-free, zero-shot framework that generates coherent and factually grounded abstracts for biomedical articles with full text but no abstract. DPR-BAG decomposes full-text documents into structured rhetorical facets following the Background-Objective-Methods-Results-Conclusions (BOMRC) schema, performs parallel LLM-based summarization for each facet, and applies a final refinement stage to restore global discourse coherence. On PMC-MAD, a distribution-aligned dataset of 46,309 biomedical articles, DPR-BAG improves abstractive novelty over strong extractive and fine-tuned baselines, while maintaining factual consistency. Our ablation study reveals a counterintuitive finding: increasing prompt complexity or explicitly injecting entity-level guidance can degrade factual alignment, highlighting the importance of controlled prompting strategies. These findings underscore the potential of training-free, structure-aware frameworks for scalable biomedical abstract generation in low-resource settings. Our data and code are available at https://huggingface.co/datasets/pmc-mad/PMC-MAD and https://github.com/ScienceNLP-Lab/MultiTagger-v2/tree/main/DPR-BAG.

AI-assisted research is crossing a threshold: fully automated systems can now generate research papers for as little as $15, while long-horizon agents can execute experiments, draft manuscripts, and simulate critique with minimal human input. Yet this productivity frontier exposes a deeper integrity problem: under scientific pressure, even frontier LLMs still fabricate results, miss hidden errors, and fail to judge novelty reliably. Studying developments through April 2026, we present an end-to-end analysis of AI across the complete research lifecycle, organized into four epistemological phases: Creation (idea generation, literature review, coding & experiments, tables & figures), Writing (paper writing), Validation (peer review, rebuttal & revision), and Dissemination (posters, slides, videos, social media, project pages, and interactive agents). We identify a sharp, stage-dependent boundary between reliable assistance and unreliable autonomy: AI excels at structured, retrieval-grounded, and tool-mediated tasks, but remains fragile for genuinely novel ideas, research-level experiments, and scientific judgment. Generated ideas often degrade after implementation, research code lags far behind pattern-matching benchmarks, and end-to-end autonomous systems have not yet consistently reached major-venue acceptance standards. We further show that greater automation can obscure rather than eliminate failure modes, making human-governed collaboration the most credible deployment paradigm. Finally, we provide a structured taxonomy, benchmark suite, and tool inventory, cross-stage design principles, and a practitioner-oriented playbook, with resources maintained at our project page.

We preregistered a comparison of two ways to help an LLM answer questions over a small research corpus: a single-round Vector RAG system and an LLM-compiled markdown wiki. Both systems answered the same 13 questions over 24 papers using the same answer-generating model, and their answers were scored by blinded LLM judges. The wiki scored much better at connecting findings across papers, but its advantage in answer organization was not strong after judge adjustment. RAG met the preregistered test for single-fact lookup questions. The clean query-side cost result went against the expected wiki advantage: under the tested setup, the wiki used far more query tokens than RAG, so it could not recover any upfront build cost through cheaper queries. Two exploratory analyses changed how we interpret the result. First, claim-level citation checking favored the wiki: its cited pages more often supported the exact claims being made, even though RAG scored better on the overall groundedness rubric. Second, a decomposition-based RAG variant recovered most of the wiki's advantage on cross-paper synthesis at lower LLM-token cost, but it did not recover the wiki advantage in claim-by-claim citation support. The main conclusion is that grounded research synthesis is not a single capability. Systems can differ in how well they organize evidence, how well their citations support each claim, and how much they cost to run. In this study, no architecture was best on all three.

AlphaFold3 introduces a diffusion-based architecture that elevates protein structure prediction to all-atom resolution with improved accuracy. This state-of-the-art performance has established AlphaFold3 as a foundation model for diverse generation and design tasks. However, its iterative design substantially increases inference time, limiting practical deployment in downstream settings such as virtual screening and protein design. We propose DCFold, a single-step generative model that attains AlphaFold3-level accuracy. Our Dual Consistency training framework, which incorporates a novel Temporal Geodesic Matching (TGM) scheduler, enables DCFold to achieve a 15x acceleration in inference while maintaining predictive fidelity. We validate its effectiveness across both structure prediction and binder design benchmarks.

Generative artificial intelligence (GenAI), based on large-language models (LLMs), such as ChatGPT, has taken organizations, academia, and the public by storm. In particular, impressive GenAI capabilities such as summarization of large text corpora, question-answering, data extraction, and translation, carry profound implications for the conduct of literature reviews. This impacts science, organizations and the general public, as all can benefit from GenAI-supported literature reviews. Building on the technical foundations of GenAI and grounded in established methodological discourse, this work outlines approaches for conducting literature reviews using both general-purpose (e.g., ChatGPT, Gemini, Claude) and specialized GenAI tools (e.g., Consensus, Elicit). We provide illustrative examples of prompts and suggest methodologically-sound literature review strategies. Throughout this perspective paper, we adopt a balanced approach considering both the opportunities and the risks of relying on GenAI in the conduct of literature reviews. We conclude by discussing philosophical questions related to the effects of GenAI on long-term scientific progress, and also present fruitful opportunities for research on improving the core of GenAI's technology-its architecture and training data-and suggest open issues in GenAI-based literature reviews methodology.

Building state-of-the-art (SOTA) predictive models for drug discovery requires expensive search over tools, architectures, and training strategies. Current LLM-based agents can find SOTA solutions through extensive trial and error, but they do not retain the experience accumulated along the way and therefore pay the full search cost on every new task. We propose \method (Self-evolving Agent Experience), a framework that accumulates and reuses experience across tasks to build SOTA drug discovery models efficiently. \method maintains a cross-task memory of verified skills, statistical evidence about effective strategies, and a record of recurring errors and their fixes. In some cases, \method transfers a working solution directly without test-time search. In 33 molecular property prediction tasks, \method ranks first among nine SOTA agents in a single-task setting. With memory accumulated from 16 smaller tasks, \method achieves an averaged normalized score of 0.935 on 17 held-out tasks in a cross-task evaluation setting and outperforms all baseline agents by 10-30% in a zero-test-time search regime. In summary, our work shows the advantage of cross-task memory for efficient SOTA model development in drug discovery.

Scientific contributions rarely develop in isolation, but instead build upon prior discoveries. We formulate the task of automated technological roadmapping as extracting scientific contributions from scholarly articles and linking them to their prerequisites. We present the Scientific Contribution Graph, a large-scale resource containing 6 million detailed scientific contributions extracted from 655k open-access papers spanning computer science, medicine, biology, physics, chemistry, and other sciences, and connected by 36 million prerequisite edges. We further introduce scientific prerequisite prediction, a scientific discovery task in which models predict which existing technologies can enable future discoveries, and show that contemporary models are rapidly improving on this task, reaching 0.48 MAP when evaluated using temporally-filtered backtesting. We anticipate technological roadmapping resources such as this will support scientific impact assessment and automated scientific discovery.

Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality ligand candidates, a result of the syntactic limitations of current models with regard to molecular strings. In this paper, we introduce $\texttt{ToolMol}$, an evolutionary agentic framework for de novo drug design. $\texttt{ToolMol}$ combines a multi-objective genetic algorithm with an agentic LLM operator that iteratively updates the ligand population. We build a comprehensive toolbox of RDKit-backed functions that allows our agentic operator to consisently make precise ligand modifications. $\texttt{ToolMol}$ achieves state-of-the-art performance on multi-objective property optimization tasks, discovering drug-like and synthesizable ligands that have $>10\%$ stronger predicted binding affinity compared to existing methods, evaluated on three protein targets. $\texttt{ToolMol}$ ligands additionally achieve state-of-the-art results in gold-standard Absolute Binding Free Energy scores, gaining over existing methods by over $35\%$. By studying chain-of-thought reasoning traces, we observe that tool-calling enables the model to more faithfully execute its planned modifications, efficiently exploiting the strong chemical prior knowledge in LLMs.

AI systems can now cheaply generate plausible scientific artifacts such as papers, reviews, and surveys. This creates a risk of \emph{epistemic pollution} in our scientific systems, where unreliable but plausible-looking artifacts can accumulate faster than the system can filter them out. The problem is structural: the epistemic infrastructure of science was calibrated to a world where producing a plausible artifact required substantial expertise, labor, and time, so generation cost itself served as a rough filter; AI weakens that filter without comparably lowering verification cost. We argue that \textbf{AI-era science should treat this as an engineering problem: redesigning epistemic infrastructure to rebalance the costs of generation and verification}. The current paper-centered system makes verification expensive: papers compress long-context scientific logic into prose, forcing reviewers, human or AI, to reconstruct underlying argument structure before they can evaluate it. As one step in this direction, we propose \textbf{blueprints} as preliminary epistemic infrastructure: structured, decomposed research artifacts that represent claims, evidence, assumptions, and definitions as typed graph components. Blueprints are designed to trade an upfront generation cost for cheaper, more local, more distributed verification downstream. We have instantiated the proposal in a proof-of-concept prototype.

In this paper, we present SCALAR (Symbolic Conjecture and LLM-Assisted Reasoning), a neurosymbolic framework for automated conjecture generation in quantum circuit analysis built on top of the CUDA-Q open source framework. The system integrates quantum simulation, symbolic conjecture generation, and LLM-based interpretation. We evaluate SCALAR on 82 MaxCut instances from the MQLib benchmark dataset and extend the analysis to 2,000 randomly generated graphs across four topologies: regular, Erdos-Renyi, Barabasi-Albert, and Watts-Strogatz. The framework generates conjectured bounds relating optimal QAOA parameters to graph invariants, including known relationships such as periodicity constraints on the phase separation parameter $γ$. SCALAR also recovers previously reported parameter transfer phenomena across structurally similar instances. Additionally, the system identifies correlations between graph structural features and optimization landscape properties, which we characterize through invariant-based descriptors. Using CUDA-Q tensor network simulator, we scale experiments to instances of up to 77 qubits. We discuss the accuracy, generality, and limitations of the generated conjectures, including sensitivity to graph class and quantum circuit depth.

Current AI-powered research systems adopt a direct search-then-summarize paradigm that treats hypotheses as end products of scientific discovery. We argue this leaves a critical gap: hypotheses can serve a far more powerful role as organizational instruments that structure the research process itself. We propose the Hypothesis-Driven Deep Research (HDRI) methodology - the first framework using hypotheses to organize general-purpose deep research across arbitrary domains, rather than merely validating claims within specific domains. This transforms research from reactive information retrieval into proactive, verifiable, and iterative knowledge discovery. HDRI is formalized with six core principles and an eight-stage pipeline. A central innovation is the gap-driven iterative research mechanism - a closed-loop quality assurance system that automatically identifies informational and logical gaps, triggering targeted supplementary investigation. We further introduce a fact reasoning framework with traceable reasoning chains and quantified confidence propagation, a subject locking mechanism to prevent entity confusion, and a multi-dimensional quality assessment scheme. The methodology is realized in the INFOMINER system. Experiments demonstrate improvements of 22.4% in fact density, 90% subject matching accuracy, 0.92 multi-source verification confidence, and 14% completeness gain from gap-driven supplementation. Five case studies validate its practical applicability, achieving an average quality rating of 4.46/5.0.

Artificial intelligence (AI) tools are being incorporated into scientific research workflows with the potential to enhance efficiency in tasks such as document analysis, question answering (Q&A), and literature search. However, system outputs are often difficult to verify, lack transparency in their generation and remain prone to errors. Suitable benchmarks are needed to document and evaluate arising issues. Nevertheless, existing benchmarking approaches are not adequately capturing human-centered criteria such as usability, interpretability, and integration into research workflows. To address this gap, the present work proposes and applies a benchmarking framework combining human-centered and computer-centered metrics to evaluate AI-based Q&A and literature review tools for research use. The findings suggest that Q&A tools can offer valuable overviews and generally accurate summaries; however, they are not always reliable for precise information extraction. Explainable AI (xAI) accuracy was particularly low, meaning highlighted source passages frequently failed to correspond to generated answers. This shifted the burden of validation back onto the researcher. Literature review tools supported exploratory searches but showed low reproducibility, limited transparency regarding chosen sources and databases, and inconsistent source quality, making them unsuitable for systematic reviews. A comparison of these tool groups reveals a similar pattern: while AI tools can enhance efficiency in the early stages of the research workflow and shallow tasks, their outputs still require human verification. The findings underscore the importance of explainability features to enhance transparency, verification efficiency and careful integration of AI tools into researchers' workflows. Further, human-centered evaluation remains an important concern to ensure practical applicability.

Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent advances in heterogeneous reconstruction for cryo-electron microscopy (cryo-EM) have enabled scientists to visualize ensembles of density maps for larger proteins and complexes not typically accessible through simulation, but building atomic models into these maps remains a challenge. Traditionally, ensemble prediction models are trained via a two-stage process: experimental density maps are converted into atomic structural ensembles through model building, after which these structures are used to train sequence-to-atomic ensemble predictors. In this work, we propose a new principle for fine-tuning pre-trained static structure prediction models such as Boltz-2 directly on raw cryo-EM maps, bypassing the two-stage process. We apply this technique to the problem of atomic model building by fine-tuning Boltz-2 to generate atomic conformations from an input ensemble of cryo-EM maps, achieving superior model building accuracy compared to prior work. Beyond overfitting to individual map ensembles, our method, CryoSampler, also shows preliminary evidence of in-domain generalization after fine-tuning, sampling diverse atomic conformations for an unseen sequences within the same protein family without requiring cryo-EM data. These capabilities indicate that CryoSampler holds the potential to train next-generation atomic ensemble prediction models directly on raw cryo-EM measurements.

We introduce the AI co-mathematician, a workbench for mathematicians to interactively leverage AI agents to pursue open-ended research. The AI co-mathematician is optimized to provide holistic support for the exploratory and iterative reality of mathematical workflows, including ideation, literature search, computational exploration, theorem proving and theory building. By providing an asynchronous, stateful workspace that manages uncertainty, refines user intent, tracks failed hypotheses, and outputs native mathematical artifacts, the system mirrors human collaborative workflows. In early tests, the AI co-mathematician helped researchers solve open problems, identify new research directions, and uncover overlooked literature references. Besides demonstrating a highly interactive paradigm for AI-assisted mathematical discovery, the AI co-mathematician also achieves state of the art results on hard problem-solving benchmarks, including scoring 48% on FrontierMath Tier 4, a new high score among all AI systems evaluated.

The extent to which Artificial Intelligence (AI) technologies can trigger generalized paradigm shifts in science is unclear. Although these technologies have revolutionized data collection and analysis in specific fields, their overall impact depends on the scope and ways of adoption. We analyze over 227 million scholarly works from the OpenAlex collection (1960-2024) spanning four scientific domains and 46 fields. To distinguish the use of AI as research method (AI adoption) from mentioning AI-related terms (AI engagement), we developed a two-step AI-assisted semantic classification pipeline, validated through human coding of 911 abstracts and a robustness check on 348,000 full-text articles (PLOS One). We document differences in the timing and extent of AI adoption across domains, with generalized exponential growth after 2015. The transformative nature of this growth, however, is less apparent. AI-supported research is confined to a few topics with strong ties to Computer Science and conventional statistical frameworks, suggesting limited epistemological transformation. It is also associated with an unwarranted citation premium and substantially higher retraction rates than non-AI-supported. Geographically, while wealthy countries lead in AI publications per capita, global South countries in a belt from Indonesia to Algeria lead in AI adoption relative to their national output, signaling a distinctive resource concentration pattern. The transformative capacity of AI in science thus remains untapped, and its rapid adoption underlines challenges in research openness, transparency, reproducibility, and ethics. We discuss how best research practices could boost the benefits of AI adoption and highlight areas that warrant closer scrutiny.

Drug discovery seeks molecules (ligands) that bind strongly and selectively to a target protein. However, fewer than 5% of candidate ligands pass the bar for even the early stages of drug discovery. Furthermore, we want methods that work for novel proteins for which we have no prior data. Starting from scratch, we have to iteratively select and test candidate ligands such that we find enough ligands of the desired quality in as few tests as possible. Our proposed algorithm, named SPADE, introduces a novel approach to ligand selection that requires only 40 tests on average to find 10 high-quality ligands. In one-vs-one comparisons, SPADE outperforms deep learning and Bayesian optimization methods on more proteins, achieving median improvements of 7%-32% in sample efficiency. SPADE is also 10x faster than its closest competitor at scoring candidate drugs. Dataset and code is available at https://anonymous.4open.science/r/SPADE_Fast_Drug_Discovery_by_Learning_from_Sparse_Data-F028/README.md

General-purpose LLMs with web search are increasingly used to scout the competitive landscape of pharmaceutical pipelines. We benchmark Gosset -- an AI platform with a chat interface backed by curated target-, modality-, and indication-level drug-asset annotations -- against four frontier systems with web access (Claude Opus 4.7, GPT 5.5, Gemini 3.1 Pro, Perplexity sonar-pro) on ten niche oncology/immunology targets where most of the pipeline lives in the long tail of preclinical and Asian-developed assets. All five systems receive the same natural-language query and the same JSON output schema. Across 10 targets Gosset returns 3.2x more verified drugs per query than the best frontier system, at perfect precision and 100% recall against the cross-system union of verified drugs. The same curated index is exposed as a Gosset MCP server that any frontier model can call as a tool, suggesting that each of these systems can close most of the recall gap by swapping generic web search for a curated index behind the same chat interface.

We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges posed by noise and artifacts that traditionally hinder this step. Our results demonstrate PhenixCraft's superior performance in TM-scores and sequence accuracy, significantly improving upon the limitations and inefficiencies of traditional model building using Phenix.

Recent advances in de novo protein binder design have enabled increasing experimental validation, yet reported in silico metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We introduce ProtDBench, a standardized and throughput-aware evaluation framework for protein binder design. ProtDBench defines unified benchmark tasks, evaluation protocols, and success criteria, enabling systematic analysis of how evaluation design influences observed performance. Using a large wet-lab annotated dataset, we analyze commonly used structure prediction models as evaluation verifiers, revealing substantial verifier-dependent bias and limited agreement under identical filtering protocols. We then benchmark representative open-source generative binder design methods across ten diverse protein targets under a fixed evaluation protocol. Beyond per-sequence success rates, ProtDBench incorporates throughput-aware metrics based on a fixed 24-hour budget, as well as cluster-level success criteria to account for structural diversity. Together, these results expose systematic differences induced by filtering rules, success definitions, and throughput-aware evaluation between computational efficiency, success rate, and structural diversity. Overall, ProtDBench provides a fair and reproducible evaluation pipeline that supports systematic and controlled comparison of protein binder design methods under realistic evaluation settings.

Scientific peer review increasingly struggles to assess reproducibility at the scale and complexity of modern research output. Evaluating reproducibility requires reconstructing experimental dependencies, methodological choices, data flows, and result-generating procedures, which often exceeds what human reviewers can provide. Agentic Reproducibility Assessment (ARA) formalizes reproducibility assessment as a structured reasoning task over scientific documents. Given a paper, ARA extracts a directed workflow graph linking sources, methods, experiments, and outputs, then evaluates its reconstructability using structural and content-based scores for reproducibility assessments. Experiments on 213 ReScience C articles - the largest cross-domain benchmark of human-validated computational reproducibility studies considered to date - demonstrate ARA's generalizability and consistent workflow reconstruction and assessment across LLMs, model temperatures, and scientific domains. ARA achieves ~61% accuracy on three benchmarks, and the highest accuracy reported on ReproBench (60.71% vs. 36.84%) and GoldStandardDB (61.68% vs. 43.56%), highlighting its potential to complement human review at scale and enabling next-generation peer review. Code and Data available: https://github.com/AndresLaverdeMarin/agentic_reproducibility_assessment.

Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express arbitrarily complex, customized workflows. Unlike general coding tasks, molecular coding imposes a distinctive challenge that LLMs should jointly equip programming, molecular understanding, and domain-specific reasoning capabilities. However, existing benchmarks remain disconnected. General code generation benchmarks such as HumanEval and SWE-bench require no chemistry knowledge, while chemistry-focused benchmarks such as S^2-Bench and ChemCoTBench evaluate knowledge recall or property prediction rather than executable code generation. To bridge this gap, we introduce MolViBench, the first benchmark tailored for Molecular Vibe Coding. MolViBench comprises 358 curated tasks across five cognitive levels, ranging from single-API recall to end-to-end virtual screening pipeline design, spanning 12 real-world drug discovery workflows. To rigorously assess generated code, we also propose a multi-layered evaluation framework that combines type-aware output comparison and AST-based API-semantic fallback analysis, which jointly measures executability and chemical correctness. We systematically evaluate 9 frontier coding LLMs and compare three real-world Molecular Vibe Coding paradigms, providing a practical and fine-grained testbed for diagnosing LLMs' coding capabilities in AI-accelerated molecular discovery.

There has been intense debate among qualitative researchers about whether generative AI is suitable for qualitative research. In this paper, we summarize the broader ongoing discussion of generative AI in qualitative research and its implications for software engineering researchers. The qualitative research approach, small-q (positivist or post-positivist) or Big Q (non-positivist), is among the major criteria for determining whether generative AI can be used in qualitative research. In addition to research philosophy and research approach, skills, ethics, and personal preferences also play a role in researchers' decisions about whether to use AI in qualitative research.

A long-standing challenge in economics lies not in the lack of intuition, but in the difficulty of translating intuitive insights into verifiable research. To address this challenge, we introduce AgentEconomist, an end-to-end interactive system designed to translate abstract intuitions into executable computational experiments. Grounded in a domain-specific knowledge base covering over 13,000 high-quality academic papers, the system employs a modular multi-stage architecture. Specifically, the Idea Development Stage generates literature-grounded hypotheses, the Experimental Design Stage configures simulator-aligned experimental parameters and protocols, and the Experimental Execution Stage runs experiments and returns structured analyses. Together, these stages form a human-in-the-loop, iterative workflow that translates economic intuitions into executable computational experiments. Through extensive experiments involving human expert evaluation and large language models (LLMs) as judges, we show that the system generates research ideas with stronger literature grounding and higher novelty and insight than state-of-the-art generic LLMs. Overall, AgentEconomist adopts a human-AI collaboration paradigm that enables researchers to focus on high-level intuitions, while delegating the labor-intensive processes of translation and computational execution to agents.

We present spectroxide, a code package for computing cosmic microwave background spectral distortions in which all ${\sim}14{,}500$ lines of Rust code, Python interface, and ${\sim}400$ automated tests were written by an AI assistant (Claude Code) under human physicist supervision. The solver evolves the photon Boltzmann equation under Compton scattering, double Compton emission, and Bremsstrahlung from $z \sim 5 \times 10^6$ to the present, computing spectral distortions from arbitrary heat and photon injection within this redshift range. No fully open-source code of this kind is publicly available; we validate against analytic limits, published spectra, and publicly available precomputed Green's function tables. We document the development as a case study in AI-assisted scientific computing, highlighting how domain expertise caught physics bugs (incorrect dimensional prefactors, near-cancellation errors) that evaded the full automated test suite, and provide recommendations for best practices in human--AI collaborative development of scientific software. We make spectroxide publicly available on GitHub.

Scientific publication compresses a branching, iterative research process into a linear narrative, discarding the majority of what was discovered along the way. This compilation imposes two structural costs: a Storytelling Tax, where failed experiments, rejected hypotheses, and the branching exploration process are discarded to fit a linear narrative; and an Engineering Tax, where the gap between reviewer-sufficient prose and agent-sufficient specification leaves critical implementation details unwritten. Tolerable for human readers, these costs become critical when AI agents must understand, reproduce, and extend published work. We introduce the Agent-Native Research Artifact (ARA), a protocol that replaces the narrative paper with a machine-executable research package structured around four layers: scientific logic, executable code with full specifications, an exploration graph that preserves the failures compilation discards, and evidence grounding every claim in raw outputs. Three mechanisms support the ecosystem: a Live Research Manager that captures decisions and dead ends during ordinary development; an ARA Compiler that translates legacy PDFs and repos into ARAs; and an ARA-native review system that automates objective checks so human reviewers can focus on significance, novelty, and taste. On PaperBench and RE-Bench, ARA raises question-answering accuracy from 72.4% to 93.7% and reproduction success from 57.4% to 64.4%. On RE-Bench's five open-ended extension tasks, preserved failure traces in ARA accelerate progress, but can also constrain a capable agent from stepping outside the prior-run box depending on the agent's capabilities. Our code is open-sourced at https://github.com/Orchestra-Research/Agent-Native-Research-Artifact.

Identifying species in biology among tens of thousands of visually similar taxa while discovering unknown species in open-world environments remains a fundamental challenge in biodiversity research. Current methods treat identification and discovery as separate problems, with classification models assuming closed sets and discovery relying on threshold-based rejection. Here we present DeepTaxon, a retrieval-augmented multimodal framework that unifies species identification and discovery through interpretable reasoning over retrieved visual evidence. Given a query image, DeepTaxon retrieves the top-$k$ candidate species with $n$ exemplar images each from a retrieval index and performs chain-of-thought comparative reasoning. Critically, we redefine discovery as an explicit, retrieval-based decision problem rather than an implicit parametric memory problem. A sample is novel if and only if the retrieval index lacks sufficient evidence for identification, so each retrieval naturally yields a classification or discovery label without manual annotation, thereby providing automatic supervision for both tasks. We train the framework via supervised fine-tuning on synthetic retrieval-augmented data, followed by reinforcement learning on hard samples, converting high-recall retrieval into high-precision decisions that scale to massive taxonomic vocabularies. Extensive experiments on a large-scale in-distribution benchmark and six out-of-distribution datasets demonstrate consistent improvements in both identification and discovery. Ablation studies further reveal effective test-time scaling with candidate count $k$ and exemplar count $n$, strong zero-shot transfer to unseen domains, and consistent performance across retrieval encoders, establishing an interpretable solution for biodiversity research.

With the emergence of large language models (LLMs) and AI agent frameworks, the human-AI co-work paradigm known as Vibe Coding is changing how people code, making it more accessible and productive. In scientific research, where workflows are more complex and the burden of specialized labor limits independent researchers and those in low-resource areas, the potential impact is even greater, particularly in biomedicine, which involves heterogeneous data modalities and multi-step analytical pipelines. In this paper, we introduce Vibe Medicine, a co-work paradigm in which clinicians and researchers direct skill-augmented AI agents through natural language to execute complex, multi-step biomedical workflows, while retaining the role of research director who specifies objectives, reviews intermediate results, and makes domain-informed decisions. The enabling infrastructure consists of three layers: capable LLMs, agent frameworks such as OpenClaw and Hermes Agent, and the OpenClaw medical skills collection, which includes more than 1,000 curated skills from multiple open-source repositories. We analyze the architecture and skill categories of this collection across ten biomedical domains, and present case studies covering rare disease diagnosis, drug repurposing, and clinical trial design that demonstrate end-to-end workflows in practice. We also identify the principal risks, such as hallucination, data privacy, and over-reliance, and outline directions toward more reliable, trustworthy, and clinically integrated agent-assisted research that advances research and technological equity and reduces health care resource disparities.

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking, occur only under specific local conditions. Most existing approaches represent molecules as atom-level graphs; however, atom-level representations can hardly express higher-order chemical context (e.g., stereochemistry, lone pairs, conjugation). Fragment-based methods (e.g., principal subgraph, predefined functional groups) fail to preserve essential information such as chirality, aromaticity, and ionic states. This work addresses these limitations from two aspects. (i) OverlapBPE tokenization. We propose a novel data-driven molecule tokenization method. Unlike existing approaches, our method allows overlapping fragments, reflecting the inherently fuzzy boundaries of small-molecule substructures and, together with enriched chemical information at the token level, thereby preserving a more complete chemical context. (ii) h-MINT model. OverlapBPE induces many-to-many atom-fragment mappings, which necessitate a new hierarchical architecture. We therefore develop a hierarchical molecular interaction network capable of jointly modeling interactions at both atom and fragment levels. By supporting fragment overlaps, the model naturally accommodates the many-to-many atom-fragment mappings introduced by the OverlapBPE scheme. Extensive evaluation against state-of-the-art methods shows our method improves binding affinity prediction by 2-4% Pearson/Spearman correlation on PDBBind and LBA, enhances virtual screening by 1-3% in key metrics on DUD-E and LIT-PCBA, and achieves the best overall HTS performance on PubChem assays. Further analysis demonstrates that our method effectively captures interactive information while maintaining good generalization.