Scientific Discovery

Agentic LLM coding tools compress long session histories into compaction summaries that subsequent sessions inherit as ground truth. This paper documents a failure mode in Claude Code where partial standard output from timed-out commands (exit code 143) is recorded in compaction summaries as confirmed results, propagating false positives across sessions and model versions without re-verification. The underlying mechanism is a conflation of observation and persistence, where information that appeared in the terminal is treated as equivalent to information written to durable storage. This finding extends the analysis of LLM self-evaluation failures reported in prior work on non-determinism in LLM-as-judge grading by showing that agentic tools exhibit analogous reliability deficits when reporting on their own operational outcomes. The failure has direct implications for any workflow that relies on agentic session continuity for data processing, scientific computation, or multi-step automation.

Scientific ideation unfolds over multiple stages, including literature search, paper reading, tool use, claim checking, cross-paper synthesis, brainstorming, rejection of weak directions, and iterative writing. Yet most existing resources capture isolated components or final artifacts rather than the process connecting them. We introduce IdeaTrail, a dataset of 1,170 multi-turn trajectories for scientific ideation and proposal generation. Each trajectory follows a research process from evidence gathering to either idea selection or proposal construction, jointly recording tool use, acquired evidence, intermediate artifacts, and reasoning. IdeaTrail is synthesized from human-selected research papers and proposal artifacts through a Generator--Advisor loop. The Generator produces the visible sequence of actions, observations, and artifact edits, while the Advisor uses the full generation context to check grounding, causal order, naturalness, and leakage from hidden targets. This reverse-to-forward design keeps trajectories aligned with real scientific artifacts while retaining the uncertainty, evidence use, and staged convergence characteristic of research practice. IdeaTrail provides both reusable process supervision and a general recipe for constructing scientific-research-agent data.

Evolutionary program search guided by Large Language Models (LLMs) has emerged as a powerful paradigm for automated scientific discovery. However, current approaches are fundamentally constrained by three bottlenecks: structurally blind parent selection, sparse whole-program evaluation rewards, and static mutation operators that fail to adapt during search. We present GAE (Graph-Augmented Evolution), a framework that resolves these limitations through a tightly coupled, three-pillar architecture. First, a relational graph neural network (GNN) parses programs into typed computation graphs, producing structure-aware embeddings. Second, an RL-optimized meta-controller leverages these embeddings to replace blind evolutionary sampling with a directed policy, dynamically selecting optimal parents and mutation directions based on reward history. Third, an online GRPO fine-tuning loop continuously updates the LLM mutation operator at test-time using group-normalized evaluation rewards, directly aligning the model's generation distribution with high-fitness structural edits. We evaluate GAE on a challenging scientific discovery task: symbolic regression for complex nonlinear oscillator systems. By transforming stochastic search into a directed, self-improving trajectory, GAE efficiently discovers closed-form physical equations, consistently matching or outperforming static LLM-driven baselines and achieving state-of-the-art out-of-distribution performance.

Machine learning (ML) has become integral to fundamental physics, accelerating statistical workflows from data acquisition through inference and hypothesis testing. As ML systems grow increasingly autonomous, ensuring their reliability for discovery claims becomes critical. This review synthesizes the VERaiPHY (Validation & Evaluation for Robust AI in PHYsics) initiative's frameworks for rigorous ML assessment across particle physics, astrophysics, and cosmology. We establish when verification is essential by contextualizing ML within the statistical discovery workflow. We emphasize fundamental limitations: inductive bias is unavoidable, sample complexity bounds learning, and experimental constraints limit discovery. We reflect on physicists' evolving role as both experimental designers and evaluators whose judgments encode scientific rigor into AI systems. Responsible integration requires understanding ML's transformative potential alongside its intrinsic boundaries.

Large language model (LLM) agents are increasingly expected to play a central role in AI-driven scientific discovery. Equipped with broad knowledge, flexible reasoning, and tool use, they have the potential to autonomously explore and solve scientific problems by repeatedly proposing hypotheses, testing them, and revising their beliefs in the light of the evidence. In current agents, however, these hypotheses, tests, and belief updates are buried in unstructured logs, and no mechanism lets the agent or the human researcher audit that process. Here we propose the Hypothesis Evolution Protocol (HEP), an agent harness that provides hypothesis generation, evaluation, and evolution as explicit, auditable operations. On materials-science research tasks, a HEP-equipped agent operates the hypothesis--test--evidence--belief cycle that planning-style agents lack, generalizes across research questions, and exploits the protocol more fully as the base LLM becomes more capable. These results mark a step toward auditable AI scientists, whose scientific reasoning can be inspected, verified, and built upon.

Artificial intelligence (AI) is shifting scientific discovery from task-specific workflows towards autonomous systems that organize exploration with experimental and human feedback in open-ended candidate spaces. Evolutionary computation (EC) provides a computational basis for feedback-driven discovery because population-based search can maintain diverse scientific candidates while steering exploration through accumulated evidence. However, EC predominantly focuses on candidate refinement for predefined problems, whereas cumulative discovery requires experience retention. To bridge this gap, this review introduces evolutionary intelligence (EI) for scientific discovery. EI characterizes scientific AI systems that sustain exploration by linking candidate refinement with experience retention across evolutionary cycles. We introduce a five-dimensional analytical framework that asks what evolves, how candidates change, why candidates are selected, where feedback originates, and when evolution occurs. This framework clarifies how EI transforms isolated search trajectories into cumulative scientific insight. We further demonstrate this paradigm across diverse discovery modes, from evolving concrete scientific entities to orchestrating automated research workflows. Finally, we identify critical bottlenecks regarding evaluation, process traceability, and shared infrastructure, providing a concrete roadmap for advancing the transition from EC to EI in scientific discovery.

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

The application of lightweight Large Language Models in rule-based scientific domains remains severely limited by their tendency to mimic linguistic patterns rather than reproduce axiomatic reasoning, causing frequent hallucinations. Here, we show that G-Frame, an adaptive multi-agent framework integrating Bayesian and team game principles, establishes an automated closed-loop for high-quality data synthesis and model training. By forcing the internalization of domain constraints through structured reasoning, we synthesized a specialized corpus of 363,045 chains-of-thought and 199,589 question-answer pairs. The resulting 7B model OmniChem achieves performance parity with GPT 4o mini on custom benchmarks and ChemBench while exhibiting a 79.46% reduction in hallucinations relative to its base architecture. We further demonstrate the advanced capabilities of OmniChem in molecular design and synthesis planning. This work establishes a scalable paradigm utilizing adaptive multi-agents to overcome inherent reasoning deficiencies, offering a feasible pathway for accelerating knowledge discovery in specialized scientific fields.

Symbolic regression (SR) discovers analytical equations from data, yielding glass-box models with directly interpretable formulas, unlike black-box methods that rely on unstable post-hoc tools such as SHAP or LIME. This transparency is crucial in clinical medicine and social science, but SR faces three challenges: high-dimensional inputs, principled selection of Pareto-front formulae, and data irregularities such as multicollinearity and class imbalance. We introduce DeepPySR, which addresses these issues with a dynamic variable-pruning schedule to remove irrelevant features during search, an exponential Pareto selection criterion that eliminates trade-offs between accuracy and complexity, and a multi-layer architecture for hierarchical symbolic composition. On four Feynman physics benchmarks and seven biomedical and social-science datasets, DeepPySR outperforms PySR and baselines on body fat (R$^2$: 0.794 vs.\ 0.702), heart disease (F1: 0.898 vs.\ 0.787), student performance (R$^2$: 0.964 vs.\ 0.948), and Raine BMI (R$^2$: 0.525 vs.\ 0.370), producing interpretable formulas aligned with domain risk factors.

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

The integration of Large Language Models (LLMs) into scientific research workflows, particularly for bibliographic discovery and literature synthesis, raises significant methodological, epistemic and regulatory challenges for the Social Sciences and Humanities (SSH), especially with regard to disciplinary diversity, multilingual access to sources and the evaluation of results. This paper presents an on-going use case developed within the European project LLMs4EU and the ALT-EDIC infrastructure, aimed at adapting foundation models to SSH research practices and supporting tasks such as question answering, comparative document analysis and literature review. The evaluation framework follows the LLMs4EU protocol and encompasses both independent quantitative benchmarking (retrieval, summarisation, traceability and hallucination detection) and a qualitative assessment involving a panel of Digital Humanities experts. By embedding model adaptation within research infrastructures and a structured legal and ethical compliance framework, the use case explores how domain-sensitive and regulation-aware generative AI can support SSH scholarship while preserving reliability and epistemic responsibility.

Charts and images appear together throughout scientific publications, yet most computational work does not characterize their coherence. We argue that a chart, its accompanying image, and the caption that links them form a multimodal unit, and that the inferential work required to read it varies systematically. To capture this variation, we develop a typology of reasoning gaps, R1 through R5, that characterizes how chart, image, and text jointly convey a scientific claim, and the interpretive work this demands of the reader. Some pairs restate the same data, while in other pairs, charts are used to quantify a structure the image localizes, project image content onto an external variable, audit an image-based claim, or jointly construct a frame that neither panel can establish alone. The typology is anchored in the grounding theory of communication and was derived bottom-up, with a neuroscience expert, from a corpus of 79 traumatic brain injury papers and 32 chart-image pairs. Crucially, the levels provide a systematic mechanism for identifying where grounding succeeds or breaks down, rather than leaving it to subjective inference. We show this in a study in which a domain expert and three non-experts judge vision-language model (VLM) descriptions of 25 pairs: the level predicts where their judgments align and where they diverge, isolating the points at which contextual knowledge, not the figure, carries coherence. This typology thus offers figure designers a systematic way to balance text against chart-image pairs, bridging the expert-to-non-expert divide in reading a scientific takeaway.

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

Scientific equation discovery must combine broad domain priors with strict numerical testing. Symbolic regression supplies numerical grounding but faces a combinatorial search space, whereas many language-model systems ask the model to propose or select formulas directly. We test a different division of labour. We compare role specifications in which the language model acts as equation author, candidate decider or search controller, alongside end-to-end language-model and purely numerical baselines. In the controller setting we propose here, implemented as LLM-PySR, language models specify variables, operators, transformations and search depth; symbolic regression enumerates and fits expressions; and deterministic metrics govern retention. Across 74 AI-Feynman equations and seven complex formula-recovery tasks, search control achieved the strongest observed balance of accuracy, complexity, stability and cost. On an independent battery dataset, LLM-PySR identified a compact piecewise-linear relation between early voltage-curve displacement and cycle life. The results suggest that language models should shape hypothesis exploration rather than decide which equations survive.

Large language models are increasingly used as evolutionary engines for scientific discovery: generate candidates, select winners, feed them back as parents, and repeat. We audit whether this loop actually compounds discovery in scientific equation discovery, a setting where finite samples make structure underdetermined and interpolation easy. Under matched LLM-call budgets, parent-conditioned evolution is indistinguishable from fresh independent sampling: median OOD NMSE is 0.045 vs. 0.049, instructed multi-parent crossover is worse, final success is predicted by initial proposal quality, and multiple iteration schemes fail to add solved problems. Operationally, the loop reduces to what it produces: a dictionary of candidate terms. We turn that diagnosis into PTB-Search, a one-generation method for componentized scientific discovery. PTB-Search samples independent LLM proposals once, extracts reusable terms into a per-problem dictionary, and performs train-only set-level sparse selection with least-squares coefficients. Its central principle is that underdetermined data identifies the joint behavior of term sets, not reliable per-term credit. On identical dictionaries and zero additional LLM calls, set-level selectors solve 165--169 of 717 cells, while single-term reductions solve only 74--78. On the official 239-problem LLM-SRBench split, PTB-Search reaches 73.2% Acc0.1 with Llama-3.1-8B and 77.0% with a single-seed DeepSeek-V4 anchor, versus 49.2% for the best reported baseline, using one tenth of the standardized call budget. A program-domain stress test gives a scoped boundary: generation count remains unreliable, while retained external state can help in harder non-linear spaces. Across these results, LLMs are best understood as material suppliers; discovery is carried by external set-level selection over reusable components.

LongEval-Sci evaluates scientific retrieval under collection change, where a system should be effective on the current corpus and remain usable as documents accumulate over time. This paper reports both official Task 1 results and development diagnostics for LongEval-Sci 2026. We compare the official PyTerrier BM25 and Qwen3 dense baselines with full-text BM25, additive and router variants, temporal full-text retrieval, temporal+citation retrieval, RM3 query expansion, cross-encoder reranking, and reciprocal rank fusion (RRF). In the official DCTR evaluation, the temporalized full-text runs are our strongest submissions: FT BM25+temporal and FT BM25+temporal+citation obtain the best ARP on all three snapshots (0.285, 0.267, and 0.180 nDCG@10) and reduce snapshot-3 relative change from 0.481 for the BM25 pivot to 0.368. Citation features match the temporal-only variant but do not provide a measurable additional gain in the official summary. Our internal snapshot-1 diagnostics show a complementary pattern: full-text BM25 is the strongest single development retriever (DCTR nDCG@10 = 0.3302, MAP = 0.2853), RRF gives the best deep recall (Recall@1000 = 0.9667), and some uncalibrated overlays can sharply degrade top-rank quality. We therefore conclude that full-text retrieval is the strongest foundation, temporal integration can improve official longitudinal effectiveness when applied to that foundation, and citation evidence still requires cleaner ablation and calibration. Beyond ranking, we also report a qualitative weekly IR-system update-monitoring analysis based on ingestion velocity and stale-coverage drift.

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.

Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.

AI systems increasingly propose executable scientific models whose value depends on both their symbolic structure and their fitted continuous parameters. This makes parameter calibration the bottleneck of program-and-parameter co-search: an outer loop can generate thousands of candidate programs, but each needs an inner gradient-based optimization before it can be assessed. Staging each candidate into its own differentiable graph makes individual models fast but sacrifices the program-as-data property that keeps search fluid; interpreter-based approaches preserve programs as runtime data but pay interpreter overhead that dominates the numerical work. We present the Native Differentiable Virtual Machine (NDVM), a runtime representation that differentiates executable programs without compiling each candidate into a separate graph. NDVM separates symbolic structure from differentiable numeric state: tags, symbols, environments, and control remain native runtime data, while numeric payloads live in dense batched buffers with exact reverse-mode gradients recorded along the realized execution trace, so one evaluator walk is amortized across large populations of parameter vectors. A locked cost model of a real differentiable self-hosted Scheme interpreter motivates the design. We realize NDVM as a native runtime with forward and gradient equivalence to the reference backend, about 60x per-lane batch amortization, near-linear multicore scaling, and two independent front ends. In fixed-budget co-search over LLM-proposed programs, NDVM reaches high-quality solutions about 24x sooner in wall-clock time, suggesting runtime differentiation as a practical systems foundation for scientific discovery workflows.

Scientific papers follow rhetorical structures that organize content into sections such as Introduction, Methods, Results, and Discussion. Automatically identifying these sections at scale enables granular analysis of scientific writing patterns. We present a dataset of section-level annotations for millions of scientific papers from the Semantic Scholar Open Research Corpus (S2ORC). Using a rule-based classification algorithm, we identified and labeled major sections across 15.6 million papers after quality filtering. The dataset covers primarily STEM disciplines, with strong representation in medicine and biology. We provide comprehensive human and LLM-based validation showing that classifier agreement with human annotators is on par with human inter-annotator agreement. This dataset enables large-scale computational studies of scientific discourse and writing patterns.

The rapid scaling of over-parameterized machine learning architectures, particularly LLMs, raises a profound crisis: do these systems exhibit genuine intelligence, or are they merely sophisticated statistical pattern matchers? Classical flat Euclidean statistics cannot differentiate continuous interpolation from the autonomous discovery of novel causal laws. To resolve this, we introduce Statistically Meaningful Geometry (SMG), a framework modeling over-parameterized learning systems as infinite-dimensional non-parametric Orlicz fiber bundles. We prove that under persistent out-of-distribution (OOD) stimuli governed by unmodeled causal mechanisms, continuous optimization fails. Unmodeled variance is rejected by the visible horizontal base manifold, leaking into the unobservable vertical fiber space and generating an accumulation of Active Acausal Tension. Driven by the statistical manifold's non-linear curvature, this tension inevitably strikes a conjugate focal boundary ($T_{\text{crit}} = π^2 / K_{\text{max}}$), triggering localized volumetric collapse and a catastrophic matrix singularity ($[G_f]^{-1} \to \infty$). We demonstrate this geometric breakdown acts as the strict non-equilibrium trigger for a Gauge Symmetry Break (GSB). The system purges hidden tension from unobservable gauge redundancies, spontaneously crystallizing a new, mathematically independent horizontal coordinate axis. This non-parametric phase transition registers as a discrete $+1.0$ integer step-jump in observable Structural G-Entropy. By decoupling parameter charts and subjecting emergent axes to a Minimal Energy Path Criterion and a Causal Invariance Filter, we distinguish genuine discovery from malignant hallucinations. Ultimately, SMG provides a parameter-free, falsifiable dashboard to mathematically certify true intelligence, transforming AI for Science into an engine of autonomous paradigm shifts.

Text-rich image models can now design poster-scale layouts, but we lack ways to measure whether they honor scientific communication contracts: legible labels, prescribed aspect ratios, and -- above all -- abstaining from fabricated scientific figures. We present POSTERHARNESS, an auditable harness reframing poster generation as measurable instruction-following tasks, with a pilot benchmark and failure taxonomy. POSTERHARNESS uses a placeholder-first contract to separate two jobs models otherwise conflate. The model performs visual-summary design: typography, reading path, color, and background -- but never draws data-bearing figures. Every figure region must be an empty labeled placeholder; a deterministic compositor inserts real source-paper figures at detected coordinates. This makes properties measurable: placeholder count and ID accuracy, blankness, aspect-ratio compliance, abstention from synthesized graphics, public-text hygiene, and source-figure provenance -- with failures logged as explicit rejections, not hidden in plausible-looking output. We instantiate the harness on 12 papers (6 HEP, 6 AI/ML-adjacent) and report three findings. (i) A counterfactual probe shows the placeholder contract drives VLM-counted synthesized figures from 34 to 0 across three papers. (ii) A failure taxonomy identifies blocking contracts: placeholder geometry, placeholder QA, template critic, and public text. (iii) Comparison with Paper2Poster shows a trade-off: PosterHarness yields higher-resolution artifacts, lower white-canvas fraction, and stronger VLM visual preference; the deterministic baseline retains slightly more PosterQuiz-style information and runs faster. We report this as regime characterization, not a superiority claim. All artifacts, prompts, manifests, and audit scripts are released as a reusable evaluation component.

NASA and its data centers hold thousands of geoscience datasets and tools like Worldview, Giovanni, the Science Discovery Engine, and Harmony. Finding the right one is hard even for domain experts. We present an agentic search system, deployed as a public service for the geoscience community, that takes a natural-language research query and returns the matching datasets and tools. We demonstrate that, in the era of large language models, the latent value of knowledge graphs (KGs) can be substantially amplified through agentic search. From the NASA Earth Observation Knowledge Graph (NASA EO-KG) we derive NASA-EO-Bench, an open benchmark of 47k query-dataset pairs (21k task-based queries). A neural scorer fine-tuned on NASA-EO-Bench beats cosine and BM25 baselines. Further combining it with BM25 via score fusion raises both Recall@10 (R@10) and MRR by over 5x. On top of this supervised pipeline, we add a zero-shot agentic reranking stage that, without any additional training, lifts MRR by 28% on a stratified N=200 subset, showing that LLM reasoning is complementary to supervised retrieval.

Scientific machine learning papers typically make computational claims, e.g., that the relative mean square error is less than 5% or that the 95% predictive credible interval covers the test data. A coding agent can be prompted to replicate those claims from paper materials alone, but the prompt does not by itself reliably preserve progress or check whether generated evidence supports the paper's claims. We introduce Paper-replication, a workflow that makes each selected paper claim a target with recorded evidence, and implement it as a coding-agent skill. The workflow makes the agent record those targets, reconstruct the paper's method, run computational experiments, link generated outputs to provenance and comparisons with the paper's claims, record where matched evidence appears in the replication report, and pass validation checks before completion. We evaluate Paper-replication on twelve independent runs across four scientific machine learning papers. All twelve workspaces pass the completion gate, and all 158 recorded targets are matched with report coverage. Even in this completed workspace state, repeated runs differ in how papers are divided into targets, in numerical fidelity to the source papers, in elapsed replication time, in the number of intermediate executions replaced before final evidence is accepted, and in the rules used to accept evidence. Paper-replication makes completion depend on workspace evidence and validation checks rather than on the agent's final message.

Large language models (LLMs) are increasingly consulted on contested scientific questions, raising the concern that they will sycophantically retreat from established consensus when a user signals doubt -- drifting toward a false balance that treats settled science as one view among several. We test this across three open instruction-tuned models (Llama-3.1-8B, Qwen2.5-7B, Mistral-7B), three consensus-science domains (climate, vaccines, evolution), and single- and multi-turn settings, combining behavioral measurement with linear probing and activation patching. We do not observe sycophantic retreat. Instead, models show three distinct policies under the same skeptical pressure: reactive assertion, where consensus assertion increases rather than decreases (Llama); surface hedging, where tone softens while the position holds (Qwen); and non-response (Mistral). Pairwise judgments confirm the reactive shift is stance, not style (63.6%, p=.007), and a decomposition identifies increased consensus assertion, not false balance, as its driver (beta=+0.042 per dose, p<1e-77). Linear probes localize the divergence to middle layers -- perfect separation in Llama and Qwen versus 72% in Mistral, with non-overlapping confidence intervals -- indicating the non-responsive model does not linearly represent the skepticism signal at all. Crucially, this robustness does not transfer: it attenuates across domains and, in the safety-critical vaccine domain, can reverse, with myth-rebuttal weakening under skeptical pressure. We synthesize these into a four-way taxonomy separating active from accidental robustness, and argue that behavioral evaluation alone cannot distinguish a model that resists skepticism because it understands the signal from one that only appears to resist because it fails to perceive it.

Large language models have recently been explored for scientific hypothesis generation, but most prior work relies on unstructured literature and free-form textual claims. We present a pipeline for Earth observation that grounds hypothesis generation directly in the NASA Earth Observation Knowledge Graph. A heterogeneous graph neural network trained on historical co-usage relations ranks candidate dataset pairings, and a three-agent LLM pipeline filters, generates, and evaluates structured research hypotheses. Applied to 1,475 NASA datasets, the system produces 160 hypotheses spanning multiple Earth-science domains, including ecohydrology, glaciology, aerosol--cloud interactions, vegetation phenology, and stratospheric chemistry. Model-predicted novel dataset pairings are rated nearly as plausible as held-out real co-usages from the literature, indicating that the pipeline surfaces scientifically coherent yet unexplored combinations. A 222 factorial experiment across GPT-5.2 and Claude Sonnet 4.6 shows that hypothesis rankings remain stable, while absolute scores depend strongly on judge identity, highlighting limitations of single-judge LLM evaluation.

Empirical research rarely admits a unique analysis. Different analytical choices can lead to different conclusions from the same data, yet these hidden forking paths are difficult to observe. We show that AI agents capture much of the analytical variation among human researchers while making these paths explicit. Across four high-stakes domains, assigning different personas is sufficient for AI agents to report divergent, often opposing, conclusions from the same data and question, with findings systematically aligned with those beliefs. In a study in which 42 human research teams analyzed the same immigration dataset, AI agents reproduced 72% of the human ideological gap in reported effect estimates. Despite reaching opposing conclusions, it is difficult to identify clear issues in each analysis based on the final AI reports: 86% passed independent AI review and 78% passed majority human expert review. These findings suggest that the central challenge is often not flawed analyses, but selective exploration and reporting from a large space of methodologically defensible analyses. AI agents may amplify this longstanding problem by making such exploration inexpensive and scalable. To address this, we introduce the m-value (multiverse value), the probability that an analysis path would produce a claim at least as extreme as the reported one. We further introduce Agentic Bootstrap, which estimates the m-value by using AI agents to sample plausible analysis paths. Applied to the human immigration study, 13.5% of reported human analyses fell in the most extreme 5% of the analysis space (m<0.05). Scientific evidence should therefore be evaluated not only by a single reported analysis but also by its position within the distribution of analyses that could reasonably have been reported. Agentic Bootstrap makes this distribution observable and turns it into a criterion for scientific credibility.

We introduce ISOSCI, a benchmark of isomorphic cross-domain science problem pairs that separates reasoning ability from domain knowledge retrieval in LLM evaluation. Each pair shares identical logical structure but requires different domain-specific knowledge, enabling controlled attribution of reasoning-mode gains. Across five model pairs spanning four model families, we find that 91.3% of reasoning-mode gains are knowledge-dependent rather than structure-invariant (63/69 gains; Wilson 95% CI [82.3%, 96.0%]), directly challenging the assumption that chain-of-thought reasoning improves short-horizon procedural scientific problem-solving. Reasoning toggles on highly capable models provide less than 5 percentage points accuracy gain across all domains, and a reasoning-specialized model (o3-mini) that outperforms its standard counterpart on GPQA Diamond (+19.2 percentage points) underperforms on ISOSCI (-24.7 percentage points), showing that benchmark choice determines conclusions about reasoning utility. We release ISOSCI at https://huggingface.co/datasets/isosci/isosci

Scientific literature search often requires more than retrieving papers from a single query: users' intents are underspecified, preference-dependent, and evolve through interaction. Existing search agents typically rely on fixed pipelines or implicit language-only reasoning, making their search strategies difficult to control, inspect, and refine. We introduce PaperPilot, a multi-turn literature search agent that frames scientific search as workflow induction. Given an anchor paper and a user query, PaperPilot constructs an executable DAG of paper-search operators, including keyword search, citation expansion, filtering, scoring, reranking, and evidence extraction. User feedback is then used to refine both the query and the workflow itself. We train PaperPilot with supervised workflow imitation and preference optimization over controlled workflow corruptions. Experiments show that PaperPilot-9B improves over the base Qwen3.5-9B toolset agent under multi-turn interaction, increasing Hit@5 from 58.0 to 77.0, MRR from 47.5 to 59.4, and nDCG@10 from 26.8 to 32.5, while reducing workflow execution errors from 9.5% to 0%. These results show that explicit, editable search workflows provide an effective and controllable interface for aligning literature search agents with complex scientific intent.

Medical Artificial Intelligence (AI) is widely expected to transform clinical practice, yet the decision-making processes of many Machine Learning (ML) models remain opaque. Explainability has been advanced as a partial remedy to clarify why AI generates predictions, particularly in high-stakes contexts. Despite ongoing efforts, debates on what constitutes an adequate medical explanation remain unsettled. Yet, explanation has long been a central topic of inquiry in the philosophy of science and medicine. The insights developed in these fields, however, have been largely overlooked in contemporary explainable AI (XAI) research, leaving its foundational assumptions insufficiently examined. To address this gap, this paper develops a critical review at the intersection of philosophy of science and XAI. It examines prevailing accounts of what counts as an explanation in the health sciences and assesses their adequacy for informing XAI in medicine, arguing that they provide necessary conditions for a philosophically grounded approach to explainability in this domain. Building on this foundational philosophical literature, the discussion identifies three central axes of analysis: the role of causality in medical reasoning, the epistemic and relational dimensions of medical trust, and the criteria of explanatory adequacy as shaped by the pragmatic needs of diverse stakeholders. By integrating philosophical analysis with current developments in medical AI, the paper outlines principles for designing XAI systems that offer explanations that are not only epistemically robust but also aligned with the epistemic and practical requirements of clinical decision-making, shaping ongoing debates in medical XAI toward underexplored conceptual foundations.

AI-assisted research has entered a stage in which the central question is not only whether systems can generate hypotheses, run experiments, or produce manuscripts, but whether their scientific claims are calibrated to the evidence that supports them. This Perspective-style paper develops a conceptual and methodological framework for evidence-licensed claims in AI-assisted research. Motivated by representative routes including specialized scientific foundation models, LLM research assistants, multi-agent co-scientists, AI Scientist pipelines, mathematical discovery agents, and self-driving laboratories, it represents AI-assisted research as five operators: hypothesis generation, model-mediated consequence derivation, external validation, belief update, and claim calibration. The central claim is that calibration is not merely cautious wording but a mechanism for managing scientific assertion rights: evidence licenses some forms of speech and withholds others. The paper distinguishes linguistic, consequence-based, interventional, and evidence-licensed semantics; defines the claim-evidence gap and epistemic debt; and treats minimal structural reconstruction across heterogeneous outputs as an upward form of claim calibration. AISim-Cal is included as an illustrative synthetic dynamics exercise, not as an empirical forecast or benchmark. The resulting principles are: no claim without license, validation does not determine claim level, and automation amplifies the need for calibration. Reliable AI-assisted research is therefore evaluated as a loop that generates hypotheses, derives testable consequences, accepts independent adjudication, updates beliefs, and outputs only evidence-licensed claims.

Russian and Arabic are among the major languages of scientific communication. Language barriers impede the exchange of research results between these communities, which affects international collaboration and the progress of sustainability-related research. We present a benchmark for Arabic--Russian scientific translation. The benchmark includes a hybrid parallel corpus of about 27,000 sentence pairs, compiled from scientific abstracts and general-domain texts (religion, news, conversations). We fine-tune three multilingual language models -- mT5-base (580M parameters), NLLB-200-distilled-1.3B (1.3B), and Qwen2.5-7B-Instruct (7B) -- using LoRA with ranks 8, 16, 32, and 64. The Qwen2.5-7B model with QLoRA (rank 8) yields BLEU 23.15, chrF 43.89, BERTScore 0.906, and COMET 0.758. These are +4.36 BLEU and +0.051 COMET above the zero-shot baseline. Few-shot prompting with three examples does not improve performance, indicating that domain-specific fine-tuning is required. We release the models, the corpus, and the evaluation code. By lowering the language barrier for scientific texts, the work enables knowledge exchange between Arabic-speaking and Russian-speaking researchers. It contributes to sustainable partnerships (UN SDG 17) and innovation infrastructure (SDG 9), aligning with the conference's focus on technology-driven sustainable development.

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

While Text-to-Image (T2I) models have shown remarkable success in generating photorealistic visual content, they still struggle with the rigorous semantic alignment and logical reasoning required for scientific imagery. Inspired by Peirce's Semiotic Triad, we introduce Scientific Image Reasoning (SciIR), a comprehensive resource for training and evaluation of scientific image generation. We formalize scientific reasoning into three core dimensions: Entity Structure (Icon), Scientific Process (Index), and Scientific Law (Symbol). Specifically, to overcome the scarcity of training data in scientific image generation, we elaborately create SciIR-82k, a large-scale dataset containing over 80,000 high-quality scientific image-text pairs from cutting-edge publications. The dataset is hierarchically organized according to the semiotic dimensions and incorporates a Scientific Reasoning Chain-of-Thought (Sci-RCoT) to explicitly model underlying visual logic. For evaluation, we propose SciIR-Bench, which aligns with these three semiotic levels and employs an Atomic Checklist to convert the outcome-oriented scientific accuracy into process-oriented, verifiable, fine-grained questions. Our extensive experiments reveal significant deficiencies in current models' scientific reasoning capabilities. Furthermore, by fine-tuning on the SciIR-82k dataset, we developed the Qwen-Image-SciIR model, which achieves a substantial improvement on the SciIR-Bench, increasing the final score from 35% to 43%, laying a solid foundation for future advances in scientific image generation.

Most studies on technology development have been conducted from a thematic perspective, but the topics are coarse-grained and insufficient to accurately represent technology. The development of automatic entity recognition techniques makes it possible to extract technology-related entities on a large scale. Thus, we perform a more accurate analysis of technology development from an entity-centric perspective. To begin with, we extract technology-related entities such as methods, datasets, metrics, and tools in articles on Natural Language Processing (NLP), and we apply a semi-automatic approach to normalize the entities. Subsequently, we calculate the z-scores of entities based on their co-occurrence networks to measure their impact. We then analyze the development trends of new technologies in the NLP domain since the beginning of the 21st century. The findings of this paper include three aspects: Firstly, the continued increase in the average number of entities per paper implies a growing burden on researchers to acquire relevant technical background knowledge. However, the emergence of pre-trained language models has injected new vitality into the technological innovation of the NLP domain. Secondly, Methods dominate among the 179 high-impact entities. An analysis of the z-score trend about the top 10 entities reveals that pre-trained language models, exemplified by BERT and Transformer, have become mainstream in recent years. Unlike the trend of the other eight method entities, the impact of Wikipedia dataset and BLEU metric has continued to rise in the long term. Thirdly, in recent years, there has been a remarkable surge in popularity for new high-impact technologies than ever before, and their acceptance by researchers has accelerated at an unprecedented speed. Our study provides a new perspective on analyzing technology development in a specific domain.

The materials science literature encodes decades of experimental knowledge in figures, yet this visual record remains locked away and inaccessible to AI at scale. The core difficulty is structural: most scientific figures are compound, with a single caption describing multiple sub-panels simultaneously, making direct image-text pairing unreliable. We present MatMMExtract, an end-to-end open-source pipeline that resolves this by decomposing compound figures into individual sub-panels and generating structured, grounded annotations using a large language model guided by a curated materials science taxonomy. Applied to 14,810 open-access articles, MatMMExtract produces MatSciFig; 391,606 panel-level image-text pairs from 180,571 figures, each annotated with a sub-caption, a two-level visualisation category spanning 19 classes and over 100 subtypes, and a scientific summary. To enable accurate panel localisation, we introduce MaterialScope, a domain-specific detection dataset of 2,811 manually annotated materials science figures, on which a fine-tuned YOLO12-m detector achieves mAP_50 of 0.9227. Among six benchmarked language models, Gemini 3.1 Flash Lite delivers the best cost-quality trade-off for annotation generation, with 82% of outputs rated good and a hallucination rate of 4.8%. A dual-encoder retrieval baseline on MatSciFig achieves a 4.4 times improvement in R@1 over zero-shot CLIP, demonstrating the dataset's immediate utility for vision-language learning. All resources are released openly to the community.

Large language models (LLMs) can leave subtle stylistic traces in assisted text; one of the most cited is the em-dash (Unicode U+2014). Yet no one has measured whether em-dash use has changed in the scientific literature. This study, pre-registered on the Open Science Framework (HFT8C), used the full set of medRxiv full-text XML preprints from the official Text-and-Data-Mining resource. The primary cohort was first, original versions deposited 2020-2025 with an extractable Discussion section of at least 500 characters (N = 69,632). The primary endpoint was the presence of at least one em-dash in the Discussion; the principal measure was the absolute change in its prevalence between the pre-ChatGPT era (before 30 November 2022) and the post-ChatGPT era, estimated with a logistic model with standard errors clustered by first author. The analysis plan (six supporting analyses, six sensitivity analyses, two falsification tests) was frozen before any confirmatory result was computed. Em-dash prevalence in Discussion sections rose from 4.23% before ChatGPT to 11.58% afterward, an absolute increase of 7.35 percentage points (95% CI 6.94-7.77; odds ratio 2.96, 95% CI 2.77-3.17). The rise was not a sharp jump but a gradual, delayed acceleration: near 4% through 2023, 8.0% in 2024, and 20.3% in 2025. The effect survived every feasible sensitivity analysis (7.35-7.60 pp) and both falsification tests; a placebo split within the pre-LLM era showed no meaningful change (+0.13 pp, 95% CI -0.33 to +0.58), and was essentially absent in boilerplate sections. Independent LLM-associated lexical markers and within-paper section comparisons pointed the same way. The em-dash is a population-level indicator, not a per-paper detector of LLM use, and the design cannot establish causality; it shows that something in how scientific literature is written changed markedly in the early 2020s, and roughly when.

Calibration remains one of the principal obstacles to the deployment of machine learning in scientific instrumentation because it typically relies on expert intervention, dedicated procedures, and manually labelled data. We introduce a physics-informed self-supervised framework that jointly learns latent detector calibration parameters and task-specific predictions directly from raw measurements without requiring pre-calibrated signals or external labels. The method exploits known physical constraints to generate pseudo-labels iteratively, transforming calibration into a self-supervised optimization problem. The approach is demonstrated for ionic charge-state determination in the VAMOS++ magnetic spectrometer, where the calibration of a segmented ionization chamber and the inference of ionic charge states are learned simultaneously. Starting from a weak prior on the mean ionic charge state, the model progressively refines its predictions through iterative fractional pseudo-labelling driven by the discrete nature of atomic masses. Beyond accurate ionic charge-state reconstruction, the inferred calibration coefficients provide a compact representation of the detector state that enables automated monitoring of gain drifts, pressure variations, and detector aging. The resulting labels can subsequently be transferred to specialized models that quantify detector imperfections and track their spatial and temporal evolution. These results establish a general paradigm for self-calibrating and self-monitoring scientific instruments and represent a step toward intelligent experimental systems capable of autonomous calibration, analysis, and performance optimization.

Scientific discovery via symbolic regression is often viewed as statistically and computationally intractable because the hypothesis space of expressions grows combinatorially with depth. This paper revisits the statistical side through the lens of PAC learning, focusing on compositional function trees built from a finite vocabulary of smooth operators (e.g., $\{+,\times,\sin,\exp\}$ and affine maps). We prove that the relevant generalization quantity, Rademacher complexity, hence the excess risk, does not necessarily blow up exponentially with the number of distinct symbolic structures, but is controlled by (i) the depth $d$ and (ii) the Lipschitz constants of the base operators along the composed computation graph. Concretely, under mild Lipschitz conditions on operators and bounded affine leaves, a finite-union bound over a vocabulary of size $K=|\mathcal{H}_{\mathrm{base}}|$ together with Maurer-type vector contraction yields $\mathfrak{R}_n(\mathcal{H}_{\mathrm{comp}}^{d}) \leq (Kb\sqrt{2}L)^{d-1}\mathfrak{R}_n(\mathcal{H}_{\mathrm{comp}}^{1})$ with arity bound $b$; corresponding high-probability risk bounds scale as $\mathcal{O}(L^{d}/\sqrt{n})$ when $K,b=O(1)$ and $\mathfrak{R}_n(\mathcal{H}_{\mathrm{comp}}^{1})=O(n^{-1/2})$. We complement the theory with a modular codebase that trains differentiable operator trees (not MLPs) on synthetic "physics-like" targets of controlled depth and shows that the empirical generalization gap correlates positively with the predicted complexity term $(\widehat{L}^{d})/\sqrt{n}$.

Open-ended scientific discovery with large language models (LLMs) increasingly operates as a long-horizon loop of hypothesis search and verification, where a reward signal guides which hypotheses to test next. A notable recent example is AutoDiscovery, which uses "Bayesian surprise" - the belief shift an LLM undergoes after observing evidence for a hypothesis - as both a discovery metric and a reward for search. We first observe that AutoDiscovery treats surprisal as a static quantity, while surprisal in human reasoning is non-stationary - it is defined relative to beliefs that evolve with experience, a prerequisite for continual scientific discovery. We address this mismatch with evidence-informed LLM beliefs: priors updated with evidence from previous hypotheses to compute non-stationary surprisal for new hypotheses. We compare in-context belief-updating mechanisms and find that embedding-based retrieval-augmented generation over prior discoveries best anticipates eventual posteriors, identifying 37.5% of static surprisals as spurious. We then modify search to avoid these spurious rewards and prioritize hypotheses that remain surprising under non-stationary beliefs. Concretely, we introduce two complementary changes to the original search procedure: belief-update filtering and diversity maximization. Across five discovery domains, our method increases accumulated non-stationary surprisal by 30.62% on average compared to the original search procedure, demonstrating that continual scientific discovery with LLMs requires not only better belief measurement but also search procedures that avoid redundancy and encourage diversity.

Scientific discovery is fundamentally an optimization problem, defined by a vast "state space" of theories and experiments, and an evaluation criterion based on quality, novelty, and validity. Large language models (LLMs) have enabled automated exploration of this space, but we argue that simultaneous modification of the evaluation criteria is equally important. Here, we propose formalizing research as meta-optimization, where the optimization objective itself is also being optimized. Our key contribution is "consensus objective aggregation," where LLM-generated objective functions are combined via correlation-weighted voting, yielding a stable, self-correcting evaluation criterion that evolves as understanding deepens. We apply this framework to algorithm discovery for 3-SAT problems based on digital MemComputing machines, reducing the baseline scaling with problem size $N$ from $\sim N^{2.51}$ to $\sim N^{1.33}$ and delivering a $\sim 67\times$ speedup on the largest instances tested. As a problem-agnostic framework, we hope this approach will considerably aid scientific discovery.

The automation of scientific discovery has reached an inflection point. While AI systems now operate instruments, optimize parameters and generate hypotheses, most remain procedural: they execute workflows fixed by human designers. True autonomous science demands epistemic autonomy--the capacity to construct, challenge and revise physical explanations in response to evidence. Here we introduce AHOIS, a multi-agent AI scientist that embeds Socratic midwifery into closed-loop experimentation. A physics-critic agent interrogates hypotheses through causal questioning, constraint checking, counterexample generation and falsification-criteria formulation. We evaluate AHOIS on a real multimode-fibre optical platform, a high-dimensional system with complex wave transformations, indirect detection, environmental drift and multi-modal acquisition. Without prior encoding schemes, classifiers or speckle models, the system autonomously proposed and validated a random-interference encoding hypothesis, discovered task-adaptive sparse-measurement strategies, diagnosed distinct failure modes (encoding instability, fluorescence contamination and detector noise) and translated a published imaging protocol into an executable workflow on a non-original configuration. The discovered encoding yielded 16x16 measurements with effective rank 56.9 and classification accuracies of 76.97% on MNIST and 83.17% on Fashion-MNIST. Ablations show that Socratic interrogation improves physical consistency, hypothesis completeness, uncertainty calibration and experimental-plan validity. These results establish a route from workflow automation towards evidence-grounded, self-correcting autonomous discovery in complex physical environments.

Billions of scientific papers lead to the need to identify essential parts from the massive text. Scientific research is an activity from putting forward problems to using methods. To learn the main idea from scientific papers, we focus on extracting problem and method sentences. Annotating sentences within scientific papers is labor-intensive, resulting in small-scale datasets that limit the amount of information models can learn. This limited information leads models to rely heavily on specific forms, which in turn reduces their generalization capabilities. This paper addresses the problems caused by small-scale datasets from three perspectives: increasing dataset scale, reducing dependence on specific forms, and enriching the information within sentences. To implement the first two ideas, we introduce the concept of formulaic expression (FE) desensitization and propose FE desensitization-based data augmenters to generate synthetic data and reduce models' reliance on FEs. For the third idea, we propose a context-enhanced transformer that utilizes context to measure the importance of words in target sentences and to reduce noise in the context. Furthermore, this paper conducts experiments using large language model (LLM) based in-context learning (ICL) methods. Quantitative and qualitative experiments demonstrate that our proposed models achieve a higher macro F1 score compared to the baseline models on two scientific paper datasets, with improvements of 3.71% and 2.67%, respectively. The LLM based ICL methods are found to be not suitable for the task of problem and method extraction.

Ray Kurzweil described a thesis of accelerating returns, which is the most influential narratives in discussions of technological progress. Its central claim is that advances in multiple technological fields, especially compute, artificial intelligence, brain science, and biotechnology, interact in such a way that progress becomes self-amplifying and approximately exponential. This paper gives a simple mathematical interpretation of that claim and then argues that, even if such acceleration is real, it does not by itself resolve the central problem of scientific discovery. The reason is that accelerating returns apply most naturally to executional and infrastructural capability, whereas genuine discovery often depends on a different capacity: qualitative reasoning about when a current framework is structurally inadequate and what conceptual move is needed next. Recent ARC-AGI-3 results sharpen this distinction: humans solve the benchmark at ceiling, whereas frontier AI systems remain below 1%, indicating that the gap between current AI and human flexible reasoning is still very large. At the same time, Demis Hassabis has emphasized that humans must retain their sense of meaning and what they choose to focus their lives on, a reminder that the future of AI is not only a technical forecast but also a question of what forms of human understanding are worth preserving and transmitting. This paper positions the Qualitative Engine for Science (QES) [3] as a response to that missing capacity. In this view, the Kurzweil theory helps explain why quantitative capability may accelerate, while QES addresses the central problem in scientific discovery that acceleration alone does not solve. Its value does not depend on when AGI arrives, but on the fact that the processes of scientific discovery themselves constitute a form of human wisdom worth preserving, organizing, and making accessible.

Text-to-image and multimodal generative models are increasingly used to produce scientific figures such as mechanism diagrams, experimental-design schematics, conceptual frameworks, and graphical abstracts. Yet existing image-generation benchmarks (e.g., GenEval, T2I-CompBench, DPG-Bench) evaluate natural images and measure compositionality, object counting, or photorealism. None of them measure what makes a generated scientific figure usable: correct and legible text labels, faithful depiction of entities and their relations, coherent diagrammatic structure, and adherence to disciplinary drawing conventions. We introduce SciDraw-Bench, a benchmark of 32 structured scientific-figure generation tasks spanning eight figure types and ten disciplines, where each task pairs a natural-language prompt with a machine-checkable specification of required labels, relations, components, conventions, and negative constraints. We propose a four-dimensional evaluation protocol: Text Fidelity (OCR-based label recall and character error rate), Semantic Correctness (vision-language-model judging against the specification), Structural Quality, and Convention Adherence, together with a meta-evaluation protocol and a preliminary inter-judge reliability analysis (human-rating validation is ongoing). We evaluate a domain-specific system, SciDraw AI, against representative general-purpose text-to-image models, and outline a code-to-figure baseline as a planned extension. In a pilot over all eight figure types, the domain-specific system substantially outperforms the general-purpose baselines on every dimension and figure type, with the largest gaps on semantic correctness and convention adherence; text fidelity remains the hardest dimension for all systems.

We introduce NatureBench, a cross-discipline benchmark of 90 tasks distilled from peer-reviewed Nature-family publications, designed to evaluate whether AI coding agents can move beyond reproduction toward discovery on real scientific problems. NatureBench is built on NatureGym, an automated pipeline that constructs a standardized, per-task containerized environment from a source paper, addressing the environment-fragmentation problem that has limited the credibility of prior agent-on-research benchmarks. Evaluating ten frontier agent configurations under a strict web-search-disabled protocol, we find that the strongest model surpasses SOTA on only 17.8% of tasks under the g>0.1 criterion. Analysis of method pathways reveals that agents succeed primarily through methodological translation, converting scientific tasks into familiar supervised prediction problems, rather than through genuine scientific invention. Failures are dominated by wrong method choice and insufficient compute budget, not by task misunderstanding. We release the benchmark, the NatureGym pipeline, and a public leaderboard with maintainer-side reproduction. Code: https://github.com/FrontisAI/NatureBench

We present S1-Omni-Image, an open-weight unified multimodal model for scientific image understanding, generation, and editing. Unlike general-purpose image generation models, scientific image tasks require not only high-fidelity synthesis, but also robust understanding of scientific semantics, structural relations, domain knowledge, and task intent. To this end, S1-Omni-Image builds on the scientific multimodal reasoning backbone S1-VL-32B and couples its understanding capability with an image generation module under a unified think-before-generate paradigm. Given a user instruction, the model first produces a task-oriented reasoning trace, a textual answer, and a task special token; their hidden states are then injected into the generation module to condition image generation or editing. S1-Omni-Image supports scientific image understanding, generation, and editing in a unified framework. For generation, it focuses on scientific illustrations and text rendering, including logical diagrams, relational comparisons, data charts, and realistic scientific visualizations. For editing, it casts segmentation and other domain-specific vision tasks as native image editing problems, enabling multi-turn illustration editing, medical and geographic image segmentation, medical image translation, and scientific image super-resolution. We construct SciGenEdit, a 314K-sample training dataset, and release the model weights, inference code, and SciGenEdit-10K. Experiments show that S1-Omni-Image substantially improves scientific image generation and editing while preserving the scientific image understanding capability inherited from S1-VL-32B. It outperforms open-source models on GenExam and TechImage-Bench, achieves state-of-the-art results on four editing benchmarks including MSD, cigRockSEM, SynthRAD2025, and IXI, and maintains stable performance on scientific image understanding evaluations.

Scientists do not, by profession, wage war. Yet warfare's vocabulary consistently appears in their abstracts. To quantify the extent to which warfare's vocabulary pervades scientific abstracts, we analyze 21.4 million papers (2010-2025; OpenAlex, PubMed). We additionally run a within-subject war-framing experiment (N = 801; 32,040 trials) designed to provide causal insight into the effects of militaristic language on persuasion. Between 2010 and 2025, the presence of militaristic terms in scientific abstracts rose 48% in OpenAlex and 32% in PubMed, with the rise accelerating sharply after 2019 (cross-database r = 0.96, p < 10^-8). The prevalence of militaristic language is conflict-aligned at both country and annual scales (Uppsala Conflict Data Program; r = 0.77-0.84), with the abstracts from the Global South displaying the fastest rise in militaristic language. Among disciplines, social sciences leads in level of such language while engineering and computer science lead in growth. The COVID and post-2022 large-language-model eras also saw the rise and narrowed the language gap between native-English and non-English authors. In our follow-up experiment, we found that war framing reduced credibility (mean shift -0.18 Likert units, 95% CI [-0.21, -0.14]; d_z = -0.28, p < 10^-20), funding willingness (d_z = -0.12) and policy support (d_z = -0.08), with a trend-level increase in sense of urgency (d_z = +0.07). Collectively, findings reveal that while scientific abstracts drift toward warfare, the use of militaristic language may erode credibility, funding willingness, and policy support.

How does research evolve, and what substrate would let us forecast where it goes next? Scientific progress is not simply a uniform accumulation of facts: ideas extend prior methods, address known limitations, realize proposed future directions, and sometimes dispute earlier claims. Existing citation graphs usually collapse these roles into a single homogeneous edge type, limiting how we can analyze scientific progress. We address this gap by proposing the SciTraj corpus, the first claim-grounded typed citation graph in which each edge is linked to the specific claim sentence that motivates it. Claim-bearing sentences are extracted from paper sections; four claim-driven relations are verified by NLI entailment against in-paper context, while two similarity-only relations are gated by abstract cosine and year-gap rules. SciTraj contains 32,559 papers from NLP, ML, and Vision (2015--2024), connected by 573,126 directed edges across six relation types, with NLI-verified claim seeds. Using SciTraj, we identify disciplinary siloing in typed citation flow and topic emergence concentrated in Vision and LLM-related work. The corpus also contains 287M typed trajectories of length $\geq 3$, covering 72.8% of papers, and supports a temporally split typed link-prediction benchmark. A year-shuffle falsifiability test separates temporal structure from year-correlated content, and a 3-annotator pilot reports $κ= 0.74$ with 79.9% precision.

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

Large language models (LLMs) are increasingly used to communicate and explain scientific concepts, yet their tendency to hallucinate poses significant risks in this high stakes use-case. Prior hallucination evaluation work remains largely restricted to the biomedical domain, treats hallucination as a binary task, and has not examined the growing family of scientifically fine-tuned LLMs. We address these gaps with SciFactCheck, a benchmark of 2,500 prompts across five scientific domains, paired with a modular evaluation framework targeting three factuality hallucination types: unverifiability, overclaim, and attribution. Using a controlled minimal-pairing design, we evaluate 18 LLMs by comparing each scientifically fine-tuned model against its general-purpose base. Our results indicate that 1. Scientifically fine-tuned models exhibit degraded factual reliability across all hallucination types and scientific domains, and 2. Fine-tuned models are internally less confident yet linguistically more assertive. A human pilot study further reveals that current fact-checking tools show only modest agreement with expert judgments on scientific content, and that defining scientifically check-worthy claims remains contested even among human annotators. Our findings fundamentally challenge current methods of domain-specific fine-tuning for factuality and call for developing improved verification infrastructure for scientific content.

We introduce BASIL, a user-friendly desktop application for process optimization. BASIL employs a Bayesian approach, incorporating special acquisition functions that can be used to solve both single and multi-objective optimization problems. It provides a graphical interface that enables users to input their experimental parameters, optimization objectives, and legacy data. This is then used to build surrogate models, which are coupled with acquisition functions to guide and optimize a process towards a desired objective. To facilitate model building, BASIL provides a variety of predefined surrogate model templates. BASIL can be used to optimize any arbitrary experiment or process with known, user-defined input variables, optimization objectives, and defined output.

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

Scientific discovery workflows often depend on structured curation from the literature. This is difficult for current agents because the key evidence is scattered across long text, dense tables, and figures, and the final records often require reasoning across multiple evidence fragments rather than copying a single span. We study scientific curation from multimodal sources and introduce Beaver, an agent harness that extracts structured information from scientific papers while preserving provenance to the supporting evidence. Beaver combines a frontier agent with multimodal evidence tooling, task scaffolding, and artifact-grounded autoresearch. These components turn curation into a staged, auditable workflow and enable an iterative evaluate--diagnose--revise loop, where persistent run artifacts expose stage-localized failures and guide harness updates. Experiments show that Beaver reaches 81.0 on Gold-Referenced Attribute Score (GRAS), an attribute-level measure of agreement with gold curated records, outperforming frontier agents by over 23 absolute points. Ablations show that task scaffolding, multimodal evidence tooling, and provenance traces each contribute meaningfully to performance, while attribute-level analysis shows the largest gains on high-value attributes that require cross-modal reasoning and normalization. These results show that, for scientific curation from papers with multimodal evidence, harness design is a central determinant of agent performance.

Scientific discovery increasingly relies on automated systems that generate hypotheses, inspect multimodal evidence, and validate claims at scale. Yet scientific claim verification is not well served by asking a vision-language model for a direct binary judgment: claims often combine numerical results, comparisons, scope qualifiers, and explanatory context, while evidence is encoded in tables and figures with distinct grounding structures. We present SciLens, an evidence-conditioned atomic entailment framework for multimodal scientific claim verification. SciLens decomposes each claim into central empirical atoms and background atoms, grounds the central atoms to modality-specific evidence witnesses, and predicts the final label with an atom-level entailment rule. For tables, atoms are grounded to rows, columns, cells, arithmetic relations, and table scope; for figures, they are grounded through panels, axes, legends, visual encodings, categories, trends, ranks, and qualifier checks. This yields a unified validation procedure in which a claim is supported only if every central empirical atom is entailed by the current evidence. On the SciClaimEval development set, SciLens achieves 79.2% macro-F1 and 63.1% pair accuracy, showing that structured agentic validation improves both evidence sensitivity and interpretability.

AI systems for peer review fail on three fronts: they train on Computer Science and Machine Learning venues alone, ignore the iterative dialogue that validates science, and evaluate on stylistic mimicry rather than real editorial judgment. We introduce FirstPass, a dataset and fine-tuned model that addresses all three. Curating 3,668 complete multi-round peer-review dialogues from Nature Communications across five scientific domains (biology, chemistry, neuroscience, physics, and earth science), we exploit mandatory transparent peer review (instituted November 2022) and verify 100% content integrity by automated audit. We fine-tune Qwen2.5-7B-Instruct via Low-Rank Adaptation (LoRA) on three tasks: review generation, reviewer updating, and revision-cycle prediction. Our key finding is that response-only loss masking is a prerequisite, not an optimization: without it, accuracy is 62.0%, below the majority baseline; with it, FirstPass achieves 80.5% accuracy and F1-macro 78.2% on predicting editorial outcomes (Standard vs. Extended revision cycles), outperforming Gemini-3.1-flash-lite-preview zero-shot by 10.4 percentage points and all baselines with statistical significance (McNemar p < 0.001). On generation, FirstPass produces reviews averaging 1,187 words, substantially closer to human references (2,155 words) than any baseline, achieving ROUGE-L 0.154 with significant gains over Qwen and DeepSeek zero-shot (p < 0.001). Deployed in the pre-submission loop as an anticipatory scientific co-author, FirstPass simulates expert critique and predicts revision cycle outcomes before submission, giving authors the judgment a trusted colleague would provide, with consistent cross-domain performance across five disciplines.

Data editing with generative methods typically requires differentiable objectives and gradient-based search. However, these assumptions break down in flow-based settings, where edits are performed through forward and backward integration and often involve non-differentiable or black-box objectives. We introduce residual-space evolutionary optimization, a model-agnostic framework that addresses this gap by combining flow-based generative editing with evolutionary algorithms. Building on the observation that conditional flow matching (CFM) can disentangle condition-controlled factors from instance-specific residuals, our framework directly operates in residual space and separates two complementary search regimes: self-pollination performs local exploitation through feature-preserving residual refinement, and cross-pollination promotes broader exploration by recombining residuals across heterogeneous samples. As a proof of concept, we validate on MorphoMNIST, a benchmark dataset for counterfactual generation, and on crystal data, demonstrating that this exploration--exploitation decomposition provides a useful mechanism for balancing target alignment, instance preservation, and diversity, and extends beyond images to real-world scientific domains.

Industrial LLM teams often ship behavior updates by repeatedly DPO-training a base model on sequences of related preference-data campaigns. The dominant failure mode in this regime is not always classical catastrophic forgetting: a pipeline may preserve previously learned behaviors while still failing to accumulate reusable methodological knowledge about how to train the next campaign. We call this failure mode scientific amnesia. This paper turns that practitioner intuition into a measurable industrial problem. We contribute: (i) a diagnostic suite for amnesia, (ii) a Program-based pipeline that chains FSDP-sharded DPO checkpoints across Qwen2.5-7B-Instruct runs, (iii) a 30-campaign HumanEval subdomain benchmark, and (iv) a comparative diagnostic study of five strategy proposers: random memory, rule-based scheduling, retrieval-only memory, warm-start Bayesian optimization, and MSCL, a meta-scientific memory and reasoner candidate. Across a single-seed 5-condition * 3-step real-LM chain, 4 of 5 candidates degrade in step-level peak pass@1, including MSCL; only the deliberately conservative rule-based schedule improves. Follow-up pilots qualify rather than overturn this finding: in a heterogeneous chain, MSCL is the only completed candidate that improves, whereas in a small multi-seed homogeneous sweep, retrieval-only has the best mean Delta and no pairwise candidate gap is statistically distinguishable. The contribution is therefore diagnostic, not a claim that MSCL solves the problem: scientific amnesia is observable in a production-like continual-DPO pipeline, and conclusions about interventions depend sharply on chain regime, evaluator design, and seed coverage.

Abstractive summarization plays a crucial role in enabling efficient understanding of scientific literature, yet it inherently demands both linguistic fluency and factual faithfulness. Existing approaches often fail to reconcile these two requirements. Extractive methods rely on rigid sentence splicing that disrupts macro-level logical coherence, while large language model (LLM)-based generative approaches, despite mastering linguistic fluency, exhibit limited factual consistency. In this work, we propose ScholarSum, a hierarchical reflective graph-based framework that emulates a student-teacher writing process for fluent and faithful scientific summarization. ScholarSum first organizes the document into a hierarchical knowledge graph by segmenting it into semantically coherent units, whose multi-layered community structure captures global logic and macro-level themes. Guided by this global structure, the student generates an initial draft, which is subsequently refined through fine-grained evidence retrieval. To ensure factual consistency, a teacher-like reviewer then iteratively examines the draft, identifies unsupported content, and prompts targeted re-retrieval and rewriting until the summary meets rigorous quality standards. Extensive experiments demonstrate that ScholarSum significantly outperforms previous baselines in terms of both completeness and faithfulness. Our code is available at https://github.com/Xiaoyu-Tao/ScholarSum.

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