Model Discovery

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7 papers in the last four weeks, level with the four weeks before. 0.1% of all new papers.

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Latest papers 84

Oct 1, 2026cs.LG

Are We Recovering Mechanisms? Objective-Level Recovery Gaps in Mechanistic Interpretability

Mechanistic interpretability aims to recover the internal computations responsible for model behavior. Progress in automated circuit discovery is often framed as a search problem: better attribution or optimization should identify better mechanisms. This assumes that the evaluation objective can recognize a better circuit once it is found. We show that intervention-defined faithfulness can instead prefer an equally sized circuit that reproduces the model's behavior less well, creating an objective-level recovery gap. Across four human-reference tasks and InterpBench, we compare validation faithfulness with behavior on held-out prompts under fixed ordinary resampling. The behavioral criterion is agreement with the intact model, including its mistakes, except on Greater-Than, where we use semantic accuracy. Controlled reference edits reveal misranking without any discovery algorithm, and outputs of EAP, EAP-IG, ACDC, and Edge-SP exhibit the same failure. Under resampling, KL misranks 9.4%-41.2% of candidate pairs across these methods on the human-reference tasks. We investigate context distortion as an explanation: replacing excluded signals changes the inputs on which retained components operate. Restoring selected signals from the recipient's intact-model execution repairs 96 of 100 persistent KL misrankings from the discovery pool on both validation and held-out prompts. The circuits and their original behavioral scores remain unchanged. These findings show why better discovery alone is insufficient when its objective rewards the wrong candidate.

Chuqin Geng, Li Zhang, Haolin Ye +3

University of Toronto · McGill University

Mechanistic Interpretability Model Discovery Circuits

Sep 30, 2026cs.LG

WOMBAT: Whitebox Oracle for Molecular Benchmarking and Attribution Testing

When a graph neural network (GNN) explainer produces an unexpected attribution on a molecule, the attribution alone cannot reveal whether the explainer has failed or the model has learned a shortcut. We introduce WOMBAT, a benchmark of 14 whitebox GNNs, each with message-passing weights set by hand to detect a specific SMARTS motif. Each model's decision rule is known by construction, providing attribution ground truth against which explainer errors can be identified and studied. We validate the models on millions of PubChem molecules and evaluate post-hoc explainers including GNNExplainer, PGExplainer, and Integrated Gradients. Guided by our qualitative analysis, we construct a model that causes Integrated Gradients to spread attribution across the graph, even though the model reliably detects the intended motif. We release the dataset, models, and evaluation code to help researchers in the development of newer XAI tools for GNNs.

Dominik Matuszek, Bartosz Zieliński, Tomasz Danel +1

Jagiellonian University, Faculty of Mathematics and Computer Science · Jagiellonian University, Doctoral School of Exact and Natural Sciences · Jagiellonian University, Jagiellonian Center for Artificial Intelligence +2

Graph Neural Networks Explainable AI Methods Black Box Model Discovery Ground Truth Oracles+1

Sep 30, 2026cs.LG

Initialization Improves LLM-Driven Discovery

Large Language Models (LLMs) have been used for novel discovery of algorithms, theorems, drugs, and other tasks through the use of harnesses that prompt an LLM to iteratively optimize an objective. In this work, we study the relationship between the population of previous iterates and eventual discovery success. We generalize past work on harness design to develop a suite of 12 harnesses called 'Modular' and characterize their performance across 5 diverse discovery tasks, finding that discovery success is brittle and sensitive to harness design. We uncover mode collapse, characterized by a dramatic drop in the diversity of iterates, as a common failure mode. We find that popular state-of-the-art harnesses and diversity-inducing harness interventions, which aim to prolong this collapse, yield inconsistent gains. Our results instead uncover that the performance of early discoveries is predictive of eventual success. We therefore propose a universally applicable intervention that performs an initial stage of parallel exploration in order to initialize subsequent iterative optimization. Our method provides consistent gains across many harnesses and target applications, confirming the importance of initialization in LLM-driven discovery.

Mansi Sakarvadia, Marco Ciccone, Colin Raffel

University of Chicago · Vector Institute · University of Toronto

Model Discovery

Sep 29, 2026hep-ph

Searching for BSM Experimental Signatures with Large Lagrangian Models

The search for physics Beyond the Standard Model (BSM) is generally limited not by the supply of theory descriptions but by the lack of discriminating experimental observations. A case in point is dark matter, where the overwhelming gravitational evidence only goes so far in distinguishing between models within a vast theory space. Exploring the space of testable model signatures may help identify overlooked experimental observables and indicate the utility of future experiments. A challenge is designing a search through model signatures outside what is found in the literature. Our primary contribution is hAIthem, a framework that combines the self-guided exploration of reinforcement learning (RL) with the broad literature-derived knowledge of LLMs. We build an RL agent that learns to find which portions of a theory's high-dimensional parameter space are not excluded under some subset of constraints by playing a Battleship-style "game" against a suite of phenomenology tools. The agent is built as a Large Lagrangian Model (LLaM), an autoregressive transformer that reads a tokenized Lagrangian, is pretrained at scale (here on ~1 billion tokens from ~10,000 Lagrangians), and is fine-tuned in a live environment. The framework then constructs a decision tree that separates RL-found regions using observables computed with established tools, and passes the remaining degenerate regions to a set of LLM agents that compete to produce realistic signatures. In this proof of concept, RL-search outperforms an evolutionary-algorithm baseline, finding more viable regions with greater physical diversity. In a restricted space of single dark scalar multiplet models, we find that hAIthem proposes interesting combinations of previously studied observables, such as the application of a halo-independent kinematic ratio to paleo-detectors.

Ibrahim Elsharkawy, Victoria Knapp-Perez, Wahid Bhimji +1

Department of Physics, University of Toronto and Vector Institute, Toronto, ON, Canada · NERSC, Lawrence Berkeley National Laboratory, Berkeley, California, USA · Department of Physics and Astronomy, University of California, Irvine, CA 92697 +3

Model Discovery General Relativity Lagrangian Methods Kinematics

Sep 28, 2026cs.LG

SleuthBench: Benchmarking Statistical LLM Evaluation Using Tabular Hidden Signals

Evaluating statistical discovery by large language model (LLM) agents requires verifiable analytical ground truth. Establishing such ground truth for real-world datasets is costly, and prior knowledge of public datasets can influence agent responses. We introduce SLEUTHBENCH, a benchmark that addresses both problems by injecting controlled data-quality problems and feature effects into public tabular datasets: the injected pattern determines the answer, so reference answers are computed automatically and memorized knowledge of the original table is insufficient, while the table keeps its background structure. The injected patterns are modeled on phenomena reported in real data analyses. The benchmark defines 17 question templates in two families: data-quality questions and feature-contribution questions. We evaluate six state-of-the-art LLMs that analyze the data using a Python coding tool, on data-science and business phrasings of 70 validated dataset-template combinations, yielding 1680 graded responses in total. The models detect data-quality problems reliably (83.8% accuracy) but recover feature contributions poorly (41.9%). Finding how features shape the target requires searching over both candidate variables and analytical procedures. To address this issue, we propose the Empirical Layer, a set of precomputed statistical artifacts comprising summaries, fitted feature and interaction effects, and dataset descriptions, which exposes candidate patterns for direct inspection. Access to these artifacts raises feature-contribution accuracy from 41.9% to 68.0%.

Jingyun Jia, Antoine Remond-Tiedrez, Aaron Alvarez +3

University of Wisconsin–Madison, Intelligible · Intelligible · University of Cincinnati

Large Language Model Evaluation Model Discovery Data Quality

Sep 27, 2026quant-ph

Autonomous phase discovery

Understanding quantum phases of matter has long relied on physicists' intuition and mathematical tools such as symmetry and topology. Remarkably successful as these approaches have been, they provide no universal way to explore a Hamiltonian space whose organizing principle is not known in advance. In this work, we introduce a fully autonomous system combining differentiable programming and unsupervised learning for quantum phase discovery. The search evaluates ground-state data along an adaptive trajectory rather than on a predetermined parameter grid. We demonstrate the system with three different solvers and benchmark it against random sampling at equal ground-state-evaluation budgets. On a generalized cluster chain hosting up to

200

distinct phases, the search finds up to

25

more phases at the same budget, and matches random sampling given thirty times its budget. On a

50

-parameter Chern insulator, it reaches sectors not obtained by the simple harmonic constructions considered here, in a family whose inverse problem remains open, while recovering all sectors found by sampling. Our results establish autonomous, gradient-driven exploration of Hamiltonian space as a practical route to discovering quantum phases without phase labels or a prescribed target phase.

Shiyu Zhou, Yuxuan Zhang, Sebastian Wetzel +2

Perimeter Institute for Theoretical Physics, Waterloo, Ontario N2L 2Y5, Canada · Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA · Institute of Physics, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland +2

Quantum Phases Quantum Annealing Model Discovery Hamiltonian

Sep 17, 2026cs.AI

AutoData: Agentic Search for Pre-training Data Selection

LLM agents have recently shown promise in automating machine learning engineering by editing model and training code under execution feedback. Data, however, remains largely outside this agentic optimisation loop. We frame pre-training data selection as heuristic engineering over per-document features, i.e., lexical statistics, categorical labels, and perplexity. We introduce AutoData, an agent that searches directly over executable selection algorithms. Unlike prior data mixture methods that optimise weights over a fixed set of domains, AutoData searches a richer program space of scoring, stratification, and stochastic selection rules, discovering feature interactions automatically by iteratively refining algorithms with validation feedback from a proxy model. Within an overnight search, AutoData discovers a selection algorithm that outperforms existing human-designed curation pipelines. Despite being searched only on this small proxy, the discovered recipe transfers to larger scales and improves the downstream metric CORE. These results suggest that data engineering can be treated as an agentic machine learning problem, extending autonomous research from model and training-code optimization to the data.

Yan Meng, Dhruv Srikanth, Bingchen Zhao +2

University of Amsterdam · Weco AI

Data Science Agents Mle-Bench Lite Model Discovery Data-Curation Agentic Search

Sep 14, 2026cs.CL

Discovery Foundation Models: Toward Open-Ended Discovery Intelligence

Foundation models have progressed from learning and reasoning over existing knowledge, to increasingly learning through action, tool use, and outcome feedback. We argue that the next frontier is a further transition: from solving and acting within problems specified by humans to participating in the process by which new problems, representations, explanations, and knowledge are created. We refer to this capability as Discovery Intelligence. We formulate Discovery Foundation Models (DFMs) as general-purpose model systems for open-ended discovery. A DFM operates over a revisable research state and supports seven coupled capabilities spanning problem discovery, formulation, representation construction, hypothesis formation, intervention, evidence-grounded revision, and continual discovery improvement. We instantiate this framework with Zetema, which couples explicit research-state dynamics, verification and experimental gating, external grounding, and cross-task Discovery Skill evolution. We further ground the framework with GALILEO, a real therapeutic-discovery system in which Dry-Lab reasoning, robotic and hands-on Wet-Lab experimentation, external biological evidence, and iterative hypothesis and design revision form a closed physical discovery loop. We then formulate a unified approach to capability formation and process-centered evaluation, enabling discovery behavior to be trained, improved, and measured beyond final-answer performance. Together, these components establish discovery as a learnable, executable, and evaluable capability of foundation-model systems. We view this shift as a broader progression in intelligence scaling: from learning over existing knowledge, to learning from action outcomes, and ultimately to participating in the construction, testing, and revision of the structures through which new knowledge is discovered. Code: https://github.com/Gen-Verse/DFM-Plans

Ling Yang, Zhenfei Yin, Yingcheng Wu

DFM Scientist Collaboration Program

Model Discovery Discovery Wireless Foundation Models Intelligence Unsupervised Skill Discovery

Sep 14, 2026cs.CL

Automated Detection and Structuring of Social Tipping Point Evidence in Climate related Documents: A Modular AI Framework

The climate literature has grown faster than review teams can read it. That gap matters most for a concept like the environmental social tipping point, the threshold at which a small change triggers rapid, self-reinforcing change in a social system. Evidence of this kind of shift is usually contained in one or two paragraphs within a longer document. As a result, existing text mining tools-which categorize entire documents by topic or highlight isolated claims-leave an expanding set of important evidence without any systematic method for discovery or organization. This paper presents an open and modular transformer-based framework that detects and structures social tipping point evidence at the passage level. The framework joins five components into a single deployable workflow: a DistilBERT boundary splitter for segmentation, an iteratively augmented RoBERTa classifier for detection, a Mistral 7B model that rewrites each detected passage for clarity, a LLaMA 3.2 3B model that rates the passage against five published social tipping point criteria, and a Milvus vector store for semantic retrieval. The system is wrapped in a Streamlit interface backed by MinIO object storage. Evaluated on a 163-passage benchmark labelled by GPT-4.1 and a 51-passage set reviewed by experts, the splitter surpassed three competing methods on a nine-metric composite score (6.137). The tuned RoBERTa model achieved 71.4 percent accuracy with a Cohen's kappa of 0.337 on the full benchmark, and 87.5 percent accuracy with a kappa of 0.742 on passages with labels, outperforming both a climate-focused model and untuned language models.

Kavindu Perera, Mohammad Abaeiani, Ekaterina Gilman +14

Center for Applied Computing, University of Oulu, Oulu, 90570, North Ostrobothnia, Finland. · Center for Machine Vision and Signal Analysis, University of Oulu, Oulu, 90570, North Ostrobothnia, Finland. · ITML CY, 185 Arch. Makariou III Ave, Limassol, 3095, Cyprus. +6

Large Language Model Classification Bert-Based Models Model Discovery Climate Document Ai-Based Framework+1

Sep 12, 2026q-bio.QM

Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens

Many biological discovery problems require experiments to be selected sequentially under constrained budgets. CRISPR screening is a prominent example, as exhaustive perturbation testing is often infeasible and candidate perturbations must instead be prioritized over multiple experimental rounds. Despite the importance of this problem, existing benchmarks for adaptive hit discovery remain limited in scale and diversity. Here, we introduce AssayBench-Loop, a large-scale benchmark for adaptive hit discovery comprising 1,389 CRISPR screens across five phenotype categories. Beyond enabling systematic evaluation, its scale makes it possible to learn acquisition strategies across historical experiments. Building on this resource, we introduce AssayLoop, a sequential experimental design framework combining AssayFormer, a transformer-based amortized acquisition policy trained across historical screens to adapt from experimental feedback, with LLM-derived biological priors through an adaptive handoff. In this view, completed experiments become training data for learning how accumulated evidence should guide what to test next, while LLMs provide prior biological knowledge to seed the search. We further introduce AssayLLM, showing that the same principle can be extended directly to an LLM through task-specific post-training. On temporally held-out screens, AssayLoop achieves a 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying approximately 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs, and AssayFormer alone. Performance improves with increasing historical training data and transfers to phenotype categories excluded from training. These results demonstrate the value of learning acquisition policies across historical experiments and combining them with broad biological priors for efficient adaptive hit discovery.

Carl Edwards, Edward De Brouwer, Xiner Li +5

Genentech, South San Francisco, CA, USA

Screening Drug Discovery Model Discovery Discovery

Sep 10, 2026cs.LG

CausalArena: Benchmarking Causal Discovery in the Foundation Model Era

Causal discovery aims to uncover causal structures from data and is fundamental to scientific reasoning and intervention-based decision making. Its evaluation relies heavily on structural causal models (SCMs), which specify a causal graph together with the mechanisms that generate data, yet existing studies differ substantially in graph families, mechanisms, and evaluation protocols. The emergence of causal discovery foundation models (CDFMs) further complicates evaluation: performance may reflect not only causal discovery ability, but also overlap between pretraining environments and test SCMs, making results on fixed synthetic benchmarks difficult to interpret. We introduce CausalArena, a unified and evolvable benchmark for causal discovery under a common protocol. Synthetic SCMs supply controlled breadth over structures and mechanisms; semantic operational SCMs provide human-auditable, semantically grounded environments beyond standard synthetic generators; and formula-grounded SCMs test discovery under explicit scientific mechanisms. Public real-world datasets provide an additional external-validity check. Experiments across classical, neural, and pretrained methods reveal substantial ranking shifts across SCM families and protocols, showing that strong performance in one benchmark regime does not reliably transfer to others. These results highlight benchmark diversity and pretraining--evaluation overlap as central challenges for evaluating causal discovery in the foundation model era.

Zi-Rong Li, Si-Yang Liu, Tian-Zuo Wang +1

School of Artificial Intelligence, Nanjing University

Causal Discovery Methods Causal Synthetic Benchmark Model Discovery Discovery Foundation Model

Sep 4, 2026cs.LG

SMILE: Bridging Continuous Optimization and Discrete Symbolic Recovery

Symbolic regression (SR) discovers closed-form mathematical expressions from data, offering interpretability beyond black-box models. Existing methods suffer from slow convergence in combinatorial search spaces and lack mechanisms to exploit compositional structure in the data. We introduce SMILE (Sine, Multiplication, Identity, Logarithm, Exponential), a hybrid framework that unifies continuous gradient-based optimization with discrete symbolic recovery through three stages: structural analysis of the data to identify the compositional hierarchy of the target expression, continuous optimization to learn parameters of a network that encodes the target expression using interpretable activations, and symbolic recovery through structured pruning, coefficient optimization, and rounding. This final stage distills the learned network into a compact expression with exact symbolic constants. We evaluate SMILE on SRBench across ground-truth and black-box datasets, with ablation studies validating each component. SMILE achieves the highest symbolic solution rate at the largest noise levels, demonstrating strong robustness where competing methods degrade substantially. It consistently lies on the Pareto front of accuracy versus complexity, recovering significantly simpler expressions in a fraction of the time required by the competing methods.

Mansooreh Montazerin, Antonio Ortega, Ajitesh Srivastava

Department of Electrical and Computer Engineering University of Southern California

Symbolic Regression Model Discovery Exponents Model Activations

Aug 16, 2026cs.LG

Large Discovery Models: Empirically-grounded Model-Based Open-Ended Search

Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a

2.4\times

greater reduction in validation BPB, an

18.2\%

relative decrease in binding energy, and more than

60\%

relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.

Zhongwei Yu, Yan Song, Xue Yan +9

The Hong Kong University of Science and Technology (GZ) · University College London · AI Lab, The Yangtze River Delta +3

Model Discovery Discovery Generative Models Antibody Multi-Objective Optimization

Aug 10, 2026cs.CV

Multimodal Model Diffing for Feature Discovery and Control

Multimodal Large Language Models (MLLMs) exhibit strong visual understanding, yet the internal features that cause these behaviors remain difficult to identify, audit, or control. While applicable to post-hoc inspection, hidden states that are decomposed into interpretable feature directions using sparse autoencoders (SAEs) neither readily isolate which features are changed by multimodal training, nor are they directly useful for targeted control. We introduce MMDiff, a multimodal model-diffing framework that trains multimodal SAEs and turns them into feature-level interfaces for discovering and controlling multimodal behavior. MMDiff supports three uses: (i) feature isolation, by diffing a base-LM SAE against its multimodal-adapted counterpart to identify features altered by multimodal training; (ii) task-specific feature detection, via per-token contrastive firing analysis that isolates causal features; and (iii) feature-level control, by causally removing or steering the discovered feature directions. We train multimodal SAEs for three MLLM families, LLaVA-MORE, PaliGemma 2, and InternVL3.5, and evaluate on visual-spatial understanding, multimodal safety, and OCR. MMDiff discovers sparse, causally specific features whose removal selectively degrades target behaviors by an average of 12% on spatial tasks and 17% on OCR, and reduces attack success rate by 24% on multimodal safety attacks, with no impact on VQA performance. Steering these features improves spatial and OCR accuracy by +3.6% and +1.8% on average over a standard single-layer steering baseline. These results show that multimodal SAEs can serve not only as interpretability tools, but as mechanisms for auditing, steering, and controlling MLLMs behavior toward safer and more capable generations.

Hunar Batra, Lachin Naghashyar, Ashkan Khakzar +4

University of Oxford · Microsoft

Multimodal Large Language Models Multimodal Model Contrastive Learning Model Discovery Discovery

Aug 10, 2026cs.AI

Model Discovery Agent: LLM-assisted Bayesian experiment design for data-efficient discovery of mechanistic world models

A primary goal of science is to learn mechanistic world models from limited experimental data, both to explain observations and to predict novel interventions. We introduce the Model Discovery Agent (MDA), which combines LLM proposals for

\mathcal M

-open model discovery, experiment design based on Value of Information, and approximate Bayesian inference over model structures, parameters, and stochastic latent trajectories. We apply MDA to learn symbolic reaction rate laws for ChemBench \citep{kabra2026autoscilab}, partially observed ODE models for GlucoseBench \citep{xie2018simglucose,kovatchev2009insilico}, and partially observed SDE models for a new stochastic single-neuron simulator we create. In the appendix, we also show results on various other domains from BoxingGym \citep{gandhi2025boxinggym}. We show that MDA has improved sample efficiency compared to various baseline methods, and the learned models are good predictors but also provide interpretable abstractions of each domain.

Kevin Murphy

Dept. Computer Science Univ. British Columbia, Canada.

Model Discovery Agentic Discovery Bayesian Experimental Design Artificial Intelligence Models Latent World Models World Models

Aug 7, 2026cs.AI

DocMemo: Dynamic Evidence Discovery via Probabilistic Memory-Guided Retrieval for Multi-Modal Document Understanding

Long-document understanding requires locating sparse and heterogeneous evidence across hundreds of pages, yet existing systems remain limited by static retrieval and fragile cross-round memory. Mainstream single-round methods commit to a fixed top-

k

page set at the outset and struggle to recover from early retrieval errors; recent iterative approaches allow multi-round evidence acquisition, but they do not investigate the propagation mechanism of cross-round states, making it difficult to track the dynamic changes in page relevance. To address these limitations, we propose DocMemo, a memory-guided framework that formulates long-document reasoning as dynamic evidence exploration. DocMemo maintains a tri-level retrieval state consisting of Document Schema Memory, Page Belief Memory, and Question Episodic Memory, which respectively capture structural priors, dynamic relevance estimation, and query-specific reasoning trajectories. During reasoning, DocMemo continuously refines cross-round page selection through Bayesian page belief updating with Thompson sampling, spatial proximity propagation, and structure-aware adaptive-granularity evidence access, while supplementing page-level evidence with fine-grained visual regions. Experiments on 3 benchmarks show that DocMemo achieves state-of-the-art performance and validate the efficacy of structured memory and dynamic page belief updating. Code is available at https://github.com/Harrygof/DocMemo.

Hanshu Yao, Janfeng Zhong, Niu Lian +1

1Harbin Institute of Technology, Shenzhen · 2Tsinghua Shenzhen International Graduate School, Tsinghua University

Document Multi-Hop Reasoning Peak Memory Model Discovery Probabilistic Model

Aug 7, 2026cs.AI

Science Edge Evaluation: SEE the Missing Step Toward Real Scientific Discovery

Large language models (LLMs) are increasingly involved in scientific discovery, yet it remains unclear whether they can support complex real laboratory science. Here we introduce Science Edge Evaluation (SEE), a multimodal benchmark of expert-curated questions grounded in peer-reviewed literature and experimental practice in chemistry, biology, and materials science. Evaluation of 19 multimodal large language models (MLLMs) shows that even the best-performing model reaches only 48.7% accuracy. Moreover, general-purpose models outperform science-specialized models on average. In the visual-agent evaluation, the use of tools increases the best accuracy to 52.7%. Tool use can expand the information available to models, but more information does not necessarily lead to reliable scientific reasoning. The key challenge is whether models can manage tool-derived information within the boundaries of the original experimental evidence. Together, these findings reveal that current MLLMs still cannot reliably make justified and evidence-bounded inferences from experimental results, which is an essential capability in real scientific discovery. Bridging this gap requires MLLMs to transition from explaining established scientific concepts to deriving novel and evidence-based insights from experimental data.

Taolin Han, Yuchen Zhang, Jinghang Wang +22

1Alibaba Group · University of Chinese Academy of Sciences · Taolin Han1,3* +28

Scientific Discovery Model Discovery Multimodal Large Language Models

Aug 5, 2026cs.LG

DASyR-LLM: Domain-Aware Symbolic Regression with LLMs for Kinetic Model Discovery

Kinetic model discovery is a central challenge in chemical engineering, as accurate rate expressions are essential for understanding and controlling chemical and biological processes. Symbolic regression (SR) has emerged as a powerful data-driven approach for identifying interpretable kinetic models, but usually operates without domain knowledge, often exploring physicochemically implausible models. Large language models (LLMs) offer a promising avenue for injecting domain expertise into this search. Here, we introduce an LLM-guided SR framework, embedding an LLM module within an iterative SR algorithm for automated kinetic model discovery. The LLM performs two roles at each iteration: (1) a qualitative physicochemical critique of the best SR candidates, and (2) the proposal of new candidate rate expressions guided by the SR-generated models and embedded chemical knowledge. Our framework is evaluated on four in silico case studies of increasing complexity, spanning heterogeneous catalysis and bioprocess systems. Results show the LLM-guided framework reduces iterations to identify the ground-truth model by

41.7-79.3\%

versus a state-of-the-art SR framework, with the LLM directly proposing the correct model structure in over half of the guided runs. In practical settings, where each iteration typically requires a new wet-lab experiment, this translates into a substantial reduction in experimental effort. Predictive performance on an independent validation set is equivalent between both approaches, with

R^2>0.98

in all case studies. Ablation studies indicate that both the SR component and the LLM scale contribute to this performance, with a reduced-size LLM largely retaining discovery efficiency. These findings demonstrate that LLMs can effectively inject domain knowledge into scientific model discovery, paving the way toward fully automated, domain-aware kinetic modelling pipelines.

Roberto Aliaga Medina, Paulina Quintanilla, Antonio del Rio Chanona

Department of Chemical Engineering Imperial College London South Kensington, London, SW7 2AZ, UK · Department of Chemical Engineering, Biotechnology, and Materials University of Chile, Santiago, Chile · Department of Chemical Engineering University College London Gower Street, London, WC1E 6BT, UK

Symbolic Regression Chemical Process Systems Model Discovery Large Language Models(Llms Small Large Language Models Discovery

Aug 3, 2026cs.NE

Towards Autonomous Formulaic Alpha Discovery: An Evolutionary Computation Perspective

Automated formulaic alpha discovery aims to generate predictive and interpretable trading signals from large symbolic factor spaces. Its effectiveness is constrained by noisy fitness estimates, market nonstationarity, costly backtesting, semantic redundancy, and conflicting practical objectives. Existing studies employ diverse techniques, including genetic programming (GP), evolutionary algorithms (EAs), reinforcement learning (RL), generative flow networks (GFlowNets), Monte Carlo tree search (MCTS), large language models (LLMs), and agentic workflows, but generally examine them as separate algorithmic families. This article introduces, for the first time, a unified evolutionary computation (EC) perspective on automated formulaic alpha discovery, formulating it as a noisy, dynamic, and multiobjective symbolic evolutionary optimization problem. A six-component analytical framework is developed to characterize existing methods through representation, variation, fitness evaluation, selection, memory, and adaptation. Furthermore, an eight-dimensional, autonomy-oriented evaluation framework is proposed, covering search efficiency, fitness reliability, residual alpha quality, economic diversity, tradability, evolutionary autonomy, robustness to nonstationarity, and reproducibility. Together, these frameworks provide a systematic foundation for unifying heterogeneous approaches, diagnosing component-level limitations, and guiding the development of reliable, adaptive, interpretable, and reproducible autonomous alpha discovery systems.

Xinwei Yu, Yiyang Fu, Mingcheng Fan +3

Xi’an Jiaotong-Liverpool University, Suzhou 215123, China · Shanghai University, Shanghai 200444, China

Evolutionary Optimization Model Discovery Genetic Algorithms Algorithmic Cores

Aug 1, 2026cs.LG

Verifier-Guided Model Discovery for Physical Dynamical Systems with Pretrained Symbolic Transformers

Reliable forecasting of nonlinear physical systems underpins scientific discovery and engineering decision-making. Yet high-fidelity simulations are prohibitively costly, and machine-learning surrogates can be opaque and encode assumptions about system dynamics, limiting generalizability. Pretrained transformers mapping synthetic ODE trajectories to equations offer interpretable alternatives, promising transfer without system-specific equation knowledge. Transferring them reliably to high-dimensional physical data, however, remains an open challenge. We develop a verifier-guided (VG) workflow around ODEFormer as a symbolic backbone, using dynamical and physical-admissibility criteria to select from a multi-trajectory candidate equation pool, enabling transfer. On canonical Van der Pol oscillators, VG outperforms the original ODEFormer workflow across held-out initial conditions. We then address vortex shedding, a phenomenon occurring in atmospheric and plasma systems of societal relevance, through coordinate reduction and symbolic discovery at fixed and varying Reynolds numbers. VG discovers fixed-parameter reduced-order equations that recover the fundamental shedding oscillator and higher harmonics without a wake-specific candidate library or prescribed Navier-Stokes structure, while the cross-parameter model generalizes to withheld regimes. Reconstruction fidelity alone did not determine symbolic discoverability, highlighting the importance of compatibility between latent dynamics and the backbone's pretraining distribution. This work establishes a verifier-guided neural-to-symbolic methodology for interpretable and physically auditable forecasting in the natural sciences.

Farbod Faraji, Francesco Belardinelli

Department of Computing, Huxley Building, Imperial College London 180 Queen’s Gate, South Kensington, London SW7 2RH, United Kingdom

Vortex Dynamical Systems Nonlinear Dynamics Model Discovery Neuro-Symbolic Framework Generative Pretrained Transformers

Jul 25, 2026cs.AI

Adaptive Graph-of-Islands Evolution for Automatic Feature Engineering with LLMs

Automatic feature engineering (AutoFE) for tabular data requires discovering informative transformations from a large program space. Existing approaches suffer from three limitations: classical methods rely on fixed operator libraries with limited expressivity, LLM-based methods generate proposals from static prompts without retaining search experience, and evolutionary methods use fixed migration policies that ignore task-specific cross-family transfer utility. We introduce TOPOFE, a framework that formulates AutoFE as graph-structured multi-island evolutionary program search. The transformation space is partitioned into semantically coherent families, each explored by an island through LLM-guided mutation and crossover. Each island maintains a Prompt Adaptation Memory that accumulates accept/reject feedback to steer proposals toward productive regions without parameter updates. To coordinate global exploration, TOPOFE dynamically learns a directed topology graph whose edge weights encode transfer utility between transformation families. Cross-island transfer is triggered by adaptive saturation detection and performed through LLM-mediated hybrid synthesis, enabling discovery of compositional feature programs that cannot emerge from isolated local search. Experiments on 29 tabular datasets show that TOPOFE consistently outperforms most state-of-the-art AutoFE methods on classification and regression tasks. Beyond predictive performance, TOPOFE produces feature sets with lower redundancy and higher representational coverage, while the learned topology graph acquires meaningful task-specific transfer structure correlated with downstream gains. The discovered feature programs transfer reliably across diverse predictors and LLM backbones, demonstrating that improvements arise from TOPOFE's structured search and adaptive coordination rather than backbone-specific generation capability.

Sha Li, Naren Ramakrishnan

Department of Computer Science Virginia Tech Blacksburg, VA 24060 · Department of Computer Science Virginia Tech Alexandria, VA 22305

Feature Engineering Tabular Learning Model Discovery Large Language Model Pipelines Topology Automated

Jul 22, 2026hep-ex

Machine Can Automatically Discover Parametric Functions to Model HEP Data

In HEP data analyses, finding an adequate function to model binned data has largely relied on a manual process: guess a functional form by intuition, fit, examine, then repeat until successful. We show that this iterative process can be automated by a machine using symbolic regression, which performs a data-driven search over function space without requiring prior knowledge of what an adequate function should look like. We present the SymbolFit package, which pairs symbolic regression with uncertainty modeling to target HEP analysis use cases, and demonstrate it on the CMS and ATLAS Run 2 dijet spectra: 560 independent seeded runs across seven simple fit configurations generated over 1000 functions fitting the spectra with

χ^2/\text{NDF}\approx 1

, and 111 of the runs rediscovered the very dijet and UA2 functions used in published dijet searches.

Ho Fung Tsoi, Dylan Rankin, Cecile Caillol +5

University of Pennsylvania, USA · European Organization for Nuclear Research (CERN), Switzerland · University of Cambridge, UK +4

Symbolic Regression Symbol-Model Discovery Unified Path-Integral Update S-Jepa

Jul 21, 2026cs.LG

CircuitKIT : Circuit Discovery, Evaluation, and Application Toolkit for Mechanistic Interpretability

Circuit analysis can support not only model explanation but also downstream interventions such as pruning, editing, steering, and selective fine-tuning. However, conducting such analyses currently requires stitching together separate implementations for discovery, evaluation, and intervention, as well as hand-authoring the contrastive prompts required by many discovery methods. This fragmentation makes methods difficult to compare and limits their application beyond canonical tasks. We introduce CircuitKIT, a source-available library that connects the circuit-analysis workflow through a typed, serializable representation. CircuitKIT provides a suite of discovery algorithms, declarative interfaces for mapping structured data into discovery tasks, complementary circuit diagnostics, and downstream application modules. Together, these components provide common infrastructure for conducting and comparing circuit analyses. The library, examples, notebooks, and documentation are released at https://github.com/Lexsi-Labs/CircuitKIT .

Pratinav Seth, Hem Gosalia, Aditya Kasliwal +1

Lexsi Labs

Circuits Model Discovery Discovery

Jul 20, 2026cs.CL

Automated Discovery Has No Universally Superior Harness

Autonomous discovery systems such as OpenEvolve and TTT-Discover are often used as general-purpose harnesses. However, in practice these are composite systems combining several design choices about archives, parent selection, exploration, and budget allocation into a single recipe. Because discovery runs are expensive and inherently stochastic, existing harnesses are often compared using too few independent trials to distinguish key methodological improvements from run-to-run variance. We systematically decompose OpenEvolve-style evolutionary search and the TTT-Discover search harness into its constituent components and systematically evaluate 30 budget-matched harnesses across 12 model-problem pairs using more than 3.1 million LLM rollouts and repeated-trial statistical analysis. Our results show that discovery harnesses have a generalization problem: No fixed harness is reliably superior across the evaluated model-problem pairs, and variants of OpenEvolve generally underperform simpler alternatives. Thus, harness choice is better viewed as a hyperparameter rather than as a universal recipe, and should be tailored to the specific problem and underlying model. We also find that early discovery progress predicts final performance, and use this property to present a budget-matched adaptive-allocation experiment that starts multiple harnesses, prunes weak partial runs, and reallocates compute to stronger survivors, outperforming both commitment to a randomly sampled fixed harness and a non-adaptive harness ensemble. Together, these results motivate shifting from fixed harness selection to online adaptation guided by early performance. We release all run pools including baseline null distributions for every model-problem pair as reusable statistical infrastructure against for future harness proposals.

Akshat Gupta, Jermaine Lei, Alexander Lu +2

UC Berkeley · MIT, MIT-IBM Watson AI Lab

Evolutionary Search Model Discovery Discovery Token Budget Allocation

Jul 15, 2026cs.AI

Automatic Ordinary Differential Equations Discovery For Biological Systems Using Large Language Model Powered Agentic System

Automatic scientific discovery has long been a goal of computational scholars - a machine that can discover nature's secrets on its own, moving computational systems beyond data-fitting tools toward the generation and refinement of mechanistic models of the universe. Recent advances in symbolic regression (SR) and large-language-model (LLM)-based agents suggest that such systems can recover equations from data, incorporate domain priors, and automate parts of the research workflow. However, most existing approaches either focus on narrow equation-discovery benchmarks or broad end-to-end automation pipelines, while biological systems remain comparatively underexplored. Here, we introduce the MEDA system, an LLM- and SR-powered agentic framework for discovering ordinary-differential-equation (ODE) models of biological and biologically inspired dynamical systems. MEDA retrieves background knowledge, defines admissible variables, generates mechanistic constraints, proposes candidate ODEs, and fits and evaluates them. We evaluate it across canonical model retrieval, reasoning-based extrapolation to unseen variants, and open-ended discovery, with and without experimental data. Across these settings, MEDA recovered the correct state variables, achieved strong structural recovery in retrieval and extrapolation tasks, and produced biologically plausible discovery-oriented models. Ablation and robustness analyses show that knowledge-guided formalization and mechanistic constraints are load-bearing components, whereas numerical fitting alone can preserve trajectory-compatible but biologically incorrect equations.

David Krongauz, Arad Zulti, Eran Segal +1

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel · Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel · Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates +2

Model Discovery Ordinary Differential Equations Symbolic Regression Drug Discovery Large Language Model Agents

Jul 14, 2026cs.AI

From Observation to Insight: Mechanistic World Models and the Quest for Autonomous Discovery

Recent advances in foundation models have transformed AI for Science, enabling remarkably accurate predictive performance across domains ranging from protein folding to weather forecasting. Yet prediction alone does not constitute scientific discovery. Scientific understanding depends on uncovering the reusable explanatory mechanisms that generate observations, whereas contemporary machine learning remains fundamentally organised around predictive mappings rather than explanatory structure. In this paper, we argue that scientific discovery is fundamentally a problem of knowledge organisation. To this end, we introduce Mechanistic World Models, a new design paradigm that places reusable mechanisms at the centre of representation, computation and learning. Drawing on insights from the philosophy of science, we derive the computational capabilities required for discovery, identify the design principles and inductive pressures that encourage explanatory knowledge to emerge, and formalise the anatomy of a mechanism-centric world model. Finally, we show how diverse research directions including mechanistic interpretability, causal representation learning, equation discovery and modular architectures capture complementary ingredients of this paradigm while lacking a unified framework. We propose Mechanistic World Models as a conceptual foundation and computational blueprint for moving AI beyond predictive forecasting towards autonomous scientific discovery.

Ingmar Posner, Anson Lei, Bernhard Schölkopf

Applied AI Lab., University of Oxford, United Kingdom. · MPI for Intelligent Systems & ELLIS Institute, Tübingen, Germany.

Model Discovery Mechanistic Interpretability Artificial Intelligence Models Discovery World Models

Jul 13, 2026cs.LG

DAG-FM: A Foundation Model for Causal Discovery under Heterogeneous Causal Mechanisms

Causal discovery from observational tabular data remains fundamentally challenging, primarily due to the heterogeneity of underlying causal mechanisms and the high-dimensional combinatorial search space of Directed Acyclic Graphs (DAGs). In this paper, we propose \textbf{DAG-FM}, a novel foundation model architecture that amortizes causal discovery. Unlike direct matrix prediction, DAG-FM decomposes the causal discovery process into two auto-regressive stages using two specialized Transformer-based sub-modules: a leaf-node predictor and a parent-node predictor. To effectively model complex row-column interactions, we adopt a robust tabular interaction block to output feature-wise representations. Crucially, to handle diverse and unknown Functional Causal Model (FCM) assumptions in real-world scenarios, we introduce Mixture-of-Leaf-Experts (MoLE), allowing the model to dynamically route and adapt to identifiable mechanism families. Through an iterative inference algorithm, DAG-FM seamlessly extracts causal orderings and constructs valid DAGs. Extensive experiments demonstrate that DAG-FM achieves state-of-the-art performance on both synthetic benchmarks and complex real-world datasets, significantly outperforming traditional classical algorithms and recent foundation models in both accuracy and scalability.

Yikang Chen, Zhengkang Guan, Haoyuan Qian +3

1Zhejiang University · 2Tsinghua University

Causal Discovery Methods Causal Modeling Directed Acyclic Graph Causal Attention Model Discovery Twitter-Fmnerg Benchmarks+1

Jul 13, 2026cs.LG

CDFM: Towards a General-Purpose Causal Discovery Foundation Model

Causal discovery, the process of recovering underlying causal structures from observational data, is a fundamental pursuit across scientific disciplines. Over the past decades, numerous algorithms have been developed to tackle this challenge through workflows tailored to the specific causal mechanisms underlying each type of dataset, demonstrating effectiveness across a wide range of applications. However, as the volume and heterogeneity of real-world data continue to grow, this dataset-specific approach inevitably leads to a fragmented, test-driven paradigm that struggles to scale to the demands of modern scientific discovery. To address this, we formulate the Causal Discovery Foundation Model (CDFM) as a unified, general-purpose framework for zero-shot structural inference. To ensure reliable generalization across unknown domains, we first investigate the theoretical boundaries of causal identifiability, revealing the indispensable role of causal prior mechanisms in this process. Building on these insights, we formulate a principled variational framework that treats unknown causal mechanisms as latent variables and mathematically decomposes the intractable marginal likelihood into distinct, tractable learning modules. The variational decomposition provides a conceptual design principle for the architecture design of CDFM, while comprehensive causal knowledge guides the large-scale synthesis of our pretraining data. By pretraining on a massive, highly diverse space of synthetic structural causal models, CDFM successfully internalizes complex statistical asymmetries. Extensive experiments demonstrate that CDFM consistently outperforms traditional algorithms, driving a paradigm shift toward a general-purpose causal discovery foundation model.

Jie Qiao, Ruichu Cai, Zijian Li +6

School of Computer Science, Guangdong University of Technology, Guangzhou, China · College of Mathematics and Computer, Shantou University, Shantou, China · Department of Computer Science and Technology, Tsinghua University, Beijing, China

Causal Discovery Methods Model Discovery Variational

Jul 12, 2026cs.AI

Imaging-101: Benchmarking LLM Coding Agents on Scientific Computational Imaging

Computational imaging, which recovers hidden signals from indirect, noisy measurements, underpins quantitative discovery across scientific disciplines, yet building a correct reconstruction pipeline demands deep domain expertise and remains laborious even for domain scientists. We introduce Imaging-101, a benchmark of 57 expert-verified computational imaging tasks spanning six scientific domains, each grounded in a peer-reviewed paper and canonicalized into a standardized four-stage pipeline (preprocessing, forward physics modeling, inverse solver, and visualization) Three evaluation tracks (planning, function-level unit tests, and end-to-end reconstruction) probe distinct agent capabilities across the full pipeline. Evaluating seven frontier LLMs uncovers systematic challenges in applying coding agents to computational imaging that go beyond those exposed by general coding benchmarks, spanning algorithm selection, physical convention handling, and pipeline integration. These findings highlight concrete capability gaps and point toward skill-augmented, domain-specialized agents as a practical path to reliable computational imaging assistance.

Siyi Chen, Jiahe Ying, Yixuan Jia +9

Key Laboratory of Spacecraft Design Optimization and Dynamic Simulation Technologies, Ministry of Education, Beijing, 102206, China

Deterministic Reconstruction Coding Agents Model Discovery

Jul 10, 2026cs.NE

Evolutionary Intelligence for Scientific Discovery: From Evolutionary Computation to Cumulative Discovery Systems

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.

Chao Wang, Lingling Li, Fang Liu +1

1*School of Artificial Intelligence, Xidian University, No. 2 South Taibai Road, Xi’an, 710071, Shaanxi, China.

Scientific Discovery Model Discovery Evolutionary Search Artificial Intelligence Systems Recursive Self-Improvement

Jul 5, 2026cs.CV

Explainable Novel Category Discovery in Semantic Concept Space

Novel category discovery aims to identify unseen classes from unlabeled data by transferring knowledge from labeled categories, but most existing methods perform discovery in opaque latent feature spaces. As a result, they may separate novel categories accurately while providing little insight into what semantic evidence defines each discovered group. We propose xNCD, an explainable novel category discovery framework that performs both representation-based discovery and pseudo-label assignment directly in a structured semantic concept space. Instead of clustering arbitrary deep features, xNCD learns a label-free concept representation by aligning visual features with vision-language similarity priors from pretrained multimodal models, and then applies a unified labeled-and-unlabeled self-labeling objective over concept-space logits. This design makes each discovered category explainable by construction through stable concept signatures and instance-level concept evidence. Theoretically, we show that routing discovery through a semantic concept bottleneck induces a strict restriction of the feature-space hypothesis class, excluding a large family of unconstrained decision rules and biasing induced partitions toward semantically interpretable concept coordinates. Experiments on CIFAR-10, CIFAR-100, and CUB-200 demonstrate that xNCD preserves strong discovery performance while providing intrinsic explanations. Under task-agnostic evaluation, xNCD achieves 92.63% overall accuracy on CIFAR-10, close to UNO's 93.4%, and improves CIFAR-100 overall accuracy from 73.2% to 76.45%, while being the only compared method that provides human-readable cluster- and instance-level explanations.

Ifrat Ikhtear Uddin, Yang Zhou, KC Santosh +1

Department of Computer Science, University of South Dakota, USA · Department of Computer Science and Software Engineering, Auburn University, USA

Generalized Category Discovery Model Discovery Deep Semantic Representations

Jul 5, 2026cs.LG

Dictionaries, Not Darwin: Set-Level Selection Beats LLM Evolution in Scientific Equation Discovery

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.

Pan Li

Independent Researcher

Scientific Discovery Model Discovery Discovery Deepseek Robotwin

Jul 1, 2026cs.LG

LLM-Guided ODE Discovery and Parameter Inference from Small-Cohort Aggregate Data

Mechanistic modeling via ordinary differential equations (ODEs) provides interpretable descriptions of complex dynamics and enables inference of underlying mechanisms, which is particularly valuable in clinical settings. However, in rare diseases, both the structure and parameters of the model are typically unknown, while individual-level data is scarce, noisy, heterogeneous, and subject to privacy constraints. In such settings, population-level summary statistics provide a practical privacy-preserving data representation, while capturing heterogeneity further requires modeling parameters as distributions rather than fixed values. Yet no existing method jointly discovers ODE structure and refines parameter distributions solely from summary statistics. We present AgentODE, an end-to-end framework that addresses this gap. An LLM proposes candidate ODE structures, while a tool-augmented inference agent iteratively refines parameter distributions through a diagnosis--update loop, operating on population-level summary statistics alone. We evaluate AgentODE on three benchmark problems across different fields and two clinical datasets, including the rare disease recessive dystrophic epidermolysis bullosa (RDEB), with only 231 observations across 46 patients. AgentODE recovers functionally consistent ODE structures across all settings, and experiments on RDEB demonstrates that in sparse and noisy data settings reasoning from summary statistics promotes mechanistically principled structure discovery, whereas baselines with individual-level data access recover implausible structures despite better predictive performance. AgentODE opens new possibilities for mechanistic modeling of rare diseases directly from population-level summary statistics, where data scarcity and privacy constraints have traditionally limited such analyses.

Hanning Yang, Meropi Karakioulaki, Lennart Purucker +3

Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany · Department of Dermatology, Medical Faculty and Medical Center, University of Freiburg, Germany · Prior Labs, University of Freiburg, Germany

Rare Disease Model Discovery Ordinary Differential Equations Discovery

Jun 29, 2026cs.AI

How Can AI Find My Model? A Model-Finding Experimental Study Considering Data Formats, Embeddings, and Retrieval Strategies

Discovering simulation models for reuse remains a fundamental challenge in Modeling and Simulation (M&S). When many models coexist, identifying those that align with a given modeling intent remains difficult. Recent advances in Artificial Intelligence (AI), particularly retrieval-based approaches, offer a promising pathway to operate at this semantic layer. In this paper, we present an experimental study investigating the impact of data representation, transformer-based embedding models, and retrieval strategies on the discovery of simulation models using natural language queries. We evaluated performance across multiple query types using standard information retrieval metrics, including recall@5 and nDCG@5. Results show that data representation matters, open-source embedding models can achieve high performance, and reranking methods are important, especially as query complexity increases. This work provides a baseline for AI-driven model discovery and discusses its role in advancing toward AI-driven composability and interoperability.

Jhon G. Botello, Jose J. Padilla, Erika Frydenlund +2

Dept. of Computer Science, Old Dominion University, Norfolk, VA, USA · Virginia Modeling, Analysis, and Simulation Center, Old Dominion University, Norfolk, VA, USA · Virginia Digital Maritime Center, Old Dominion University, Norfolk, VA, USA +1

Artificial Intelligence Models Model Discovery Natural Language

Jun 28, 2026cs.LG

Sample Complexity of Scientific Discovery: PAC Learnability of Compositional Function Trees

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}

.

Şuayp Talha Kocabay, Talha Rüzgar Akkuş, Kerem Yalçın

Independent Researcher · TÜBİTAK Science High School

Symbolic Regression Sample Complexity Hypothesis Class Learnability Model Discovery Scientific Discovery

Jun 27, 2026cs.CL

AnTenA: Actionable and Explainable Tensor Analysis System with Large Language Models

Accurately explaining hidden patterns in multi-aspect data has typically been done by leveraging labels and/or accompanying auxiliary metadata. However, labels and auxiliary data may be inaccurate (e.g. nonstandard, inconsistent), insufficient (e.g. static tabular metadata for time-dependent recordings), or unavailable. % We propose \fullmethod (\method), which leverages the knowledge of large language models (LLMs) to explain the hidden patterns in human narratives. \method uses task-agnostic and task-specific prompts to explain extracted co-clustered latent patterns from tensor decomposition. To evaluate these explanations, we test the LLMs on forward and backward inference tasks. % Our demo system is available at https://github.com/dawonahn/ECML_PKDD_AnTenA.

Dawon Ahn, Auder Der, Evangelos E. Papalexakis

University of California, Riverside CA 92507, USA · Neuralix AI, Houston, TX, USA

Explainable AI Methods Model Discovery Reconfigurable Intelligent Surfaces

Jun 26, 2026cs.CL

Turn-Averaged SAEs for Feature Discovery and Long-Context Attribution

Sparse autoencoders (SAEs) have become a useful tool for extracting interpretable features in language models. However, standard SAE architectures operate on individual token activations, meaning that the number of active features scales linearly with context length, and studying long model transcripts becomes difficult. We introduce turn-averaged SAEs, which represent a single Human or Assistant turn with a fixed number of features by learning to reconstruct the average model activation across the turn. We find that turn-averaged features describe a single turn's high-level characteristics more completely than per-token features when judged by an LLM. We also demonstrate that turn-averaged SAEs greatly simplify common downstream uses of SAEs like attribution graphs. Broadly, turn-averaged SAEs make interpretability techniques practical at long context lengths.

Kevin Der, Harish Kamath, Ben Thompson

Anthropic Fellows Program · Anthropic

Sparse Autoencoder Features Improving Sparse Autoencoders Efficient Long-Context Inference Model Activations Model Discovery

Jun 25, 2026cs.AI

Scientific discovery as meta-optimization: a combinatorial optimization case study

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.

Yuan-Hang Zhang, Chesson Sipling, Massimiliano Di Ventra

Scientific Discovery Model Discovery Optimization Modeling Combinatorial Optimization

Jun 22, 2026physics.data-an

Where Is My Physics Wrong? Localized and Identifiable Discovery of Model Discrepancy

Hybrid models combine trusted physics with data-driven correction, but a physical model is rarely wrong everywhere or in the same way. The key diagnostic question is local: where does the model fail, what missing mechanism explains the failure, and is the evidence statistically real? Existing sparse-discovery and discrepancy-learning methods usually fit one global correction, which can spread a local error into clean regimes, bias trusted physical parameters, and provide no calibrated significance for selected terms. We introduce LISDD, Localized, Identifiable Sparse Discovery of Discrepancy, a framework that localizes model error to an operating regime, identifies a sparse symbolic form for the missing mechanism, and certifies the discovery with an exact finite-sample test. LISDD fits the known physics on an automatically detected clean regime, flags discrepant regions with a calibrated residual-energy statistic, selects the local missing term by exhaustive holdout over a candidate library, and confirms significance with a sample-split

F

-test. A false-discovery-rate extension handles multiple discrepant regions with different missing mechanisms. In controlled experiments, LISDD keeps physical-parameter bias at 0.002 versus 0.43 for global-discrepancy and black-box baselines, raises localization

F_1

from 0.44 to 0.80, recovers the correct symbolic form with probability one, attains exact detection, and controls the multi-region false-discovery rate while recovering every planted mechanism. The result is a calibrated diagnostic tool for grey-box building-energy models when a fixed physical law silently breaks in one operating regime.

Yifan Wang

Department of Mechanical Engineering, McGill University, QC, H3A 2T7, Canada

Discrepancy Model Discovery False Discovery Rate Evidence Conflict AI Trustworthiness

Jun 22, 2026cs.SE

DeepDiscovery: A Location-Inference Framework for Task-Level Repository Understanding

Large language models have shown strong performance on software engineering (SE) tasks, yet understanding large industrial repositories remains challenging. Existing methods often retrieve only local fragments and fail to recover the broader task-relevant context needed for complex repository-level tasks. We present DeepDiscovery, a task-level repository-understanding method for large industrial codebases. DeepDiscovery uses a two-stage \textit{Location--Inference} framework to localize high-confidence task anchors and recover broader task-relevant context over multi-relational repository structure under budget constraints. Across controlled method-level evaluation, organization-internal industrial repository-understanding scenarios, and end-to-end evaluation on SWE-bench Verified, DeepDiscovery consistently improves task-relevant file recovery and downstream SE performance. On 27 medium-scale tasks, DeepDiscovery achieves the best file recovery quality among five representative baselines without offline preprocessing. On organization-internal industrial tasks from a production-scale integrated codebase ecosystem, including 27 medium-scale tasks and 40 large-scale tasks, DeepDiscovery improves Full Recall Rate across multiple AI coding systems, with absolute gains ranging from 1.6 to 9.2 percentage points on large subprojects and from 2.5 to 7.4 percentage points on medium-scale subprojects. In a controlled end-to-end evaluation on SWE-bench Verified, a system equipped with DeepDiscovery achieves a 78.6% Solve Rate, outperforming the corresponding baseline by 8.2 percentage points. These results suggest that stronger task-level repository understanding can improve coding-agent performance on complex SE tasks.

Jiawei He, Weisong Sun, Mengyu Shi +4

AMAP, Alibaba Group · Nanyang Technological University · Nanjing University +1

Codebases Model Discovery Discovery Precision Recall Path

Jun 15, 2026cs.LG

Demystifying Variance in Circuit Discovery of LLMs

Circuit discovery is a key technique in mechanistic interpretability to pinpoint the model components that are crucial for performing a given task. Although the current state-of-the-art method (EAP-IG) performs well on the metric of (un)faithfulness, it suffers from substantial variability. This includes resampling variance, where the circuit changes when we probe with a new batch of data from the same distribution; rephrasing variance, where the discovered circuit shifts when the prompts are rephrased; and sample-wise variance, where a circuit with low population unfaithfulness exhibits large fluctuations in unfaithfulness across individual samples. This paper studies the roots of these variances. We demonstrate that CEAP, our new circuit discovery method that improves upon EAP-IG with a theoretical guarantee, can substantially lessen resampling variance. We further show that rephrasing variance arises because prompts with different templates tend to activate different circuits in the model. This leads us to argue that it may be challenging to find a comprehensive circuit that explains and controls the model's behavior on a task, which can be expressed in countless templates, suggesting that LLMs may be inherently hard to steer. We show that sparsity, which has been claimed to form more compact and interpretable task circuits, fails to solve this problem. Regarding sample-wise variance, we argue that it is largely benign: extremely poor unfaithfulness scores often stem from how unfaithfulness is defined, rather than from defects in the measured circuits. We show that the magnitude of unfaithfulness is affected by selective contribution scaling, a neural mechanism that accounts for the extremely poor scores sometimes observed.

Frank Zhengqing Wu, Francesco Tonin, Volkan Cevher

Laboratory for Information and Inference Systems (LIONS) École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland · Laboratory for Informationand Inference Systems (LIONS) École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

Mechanistic Interpretability Circuits Model Discovery Variance Faithful Explanation Discovery

Jun 12, 2026cs.LG

Discovery under Hypothesis Redundancy: A Geometric Theory of Discovery Bottlenecks

Scientific discovery saturates when new hypotheses cease to provide independent information, even if the nominal hypothesis space remains large. We study hybrid discovery systems that combine structured local search with LLM-generated non-local proposals and pose the Search Compression Hypothesis: non-local exploration helps only when three geometric conditions co-occur: spectral compression, orthogonal escape from the explored span, and residual signal alignment with the target. We formalize these conditions, derive necessary conditions for hybrid advantage, and test the mechanism in controlled synthetic environments, large-scale A-share factor discovery, and symbolic-regression benchmarks; a public tabular operational sanity check tests the associated budget-allocation implication. Signal-planting and directed-versus-random experiments show that novelty alone is insufficient: random orthogonal jumps expand coverage but do not improve yield without predictive alignment. Across compression sweeps, real factor archives, and LLM-SRBench tasks, hybrid gains concentrate in weakly represented but target-bearing directions and vanish as the hypothesis space approaches full rank. The framework turns LLM-guided discovery from generic novelty search into a diagnostic procedure for deciding when directed non-local exploration is warranted.

Li Xia, Baoxun Wang

School of Economics and Management, Tsinghua University · Platform & Content Group, Tencent

Model Discovery Discovery Hypothesis Class Stochastic Exploration Redundancy Theory+2

Jun 8, 2026cs.LG

Data-driven discovery of governing differential equations across physical systems

Differential equations play a critical role in scientific discovery because they provide a mathematical framework to describe the behaviour of physical phenomena. As a promising alternative to traditional first principles, data-driven differential equation discovery has attracted increasing attention for its ability to infer governing laws directly from experimental or simulated data, especially when the underlying physics is unclear. However, the field has expanded rapidly along diverse methodological directions, particularly with the emergence of AI-based approaches, and still lacks a clear organizing perspective. In this Review, we propose a problem-oriented perspective on data-driven differential equation discovery. We first introduce a two-dimensional phase diagram of equation discoverability, where discovery problems are organized according to structural complexity and coefficient complexity. This phase diagram shows how the field has moved from the discovery of sparse equations with simple coefficients toward more complex governing laws with richer structures and more flexible parameterizations. It also clarifies why different methodological families succeed or fail in different problem settings. We then present the representation-evaluation-optimization (REO) framework as a fundamental abstraction of the discovery process. By identifying the core problems of equation discovery that persist across algorithmic variations, REO shifts the discussion from individual algorithms to the fundamental principles that determine discoverability. We connect these perspectives to applications across physics and adjacent sciences, and argue that the next challenge is not merely recovering equations, but using them to revise existing theories, distil mechanisms and form new scientific concepts.

Siyu Lou, Hao Xu, Wenguan Wang +6

School of Computer Science, Shanghai Jiao Tong University, Shanghai, China · Ningbo Key Laboratory of Advanced Manufacturing Simulation, Eastern Institute of Technology, Ningbo, Ningbo, China · The State Key Lab of Brain-Machine Intelligence, Zhejiang University, Hangzhou, China. +5

Ordinary Differential Equations Model Discovery Discovery Scientific Discovery Phase Transitions Structural Complexity

Jun 7, 2026cs.PL

Compile Once, Differentiate Everywhere: A Differentiable Meta-Circular Interpreter

The boundary between program execution and gradient-based optimization has long limited the use of code itself as a learnable scientific model. We present a compiler that translates a self-hosting subset of Scheme into differentiable computation graphs for autograd backends. Because the subset can compile its own evaluator, this yields differentiable meta-circular interpretation (DMCI): a compiled Scheme interpreter executes programs supplied as data, while reverse-mode autodiff propagates gradients to continuous constants embedded in those programs. The interpreter is compiled once, so new programs inherit differentiability without recompilation or custom gradient machinery, while retaining closures, recursion, and data structures. We prove that gradients through the compiled interpreter are correct almost everywhere and show that they match direct compilation to numerical precision across 171 recursive and higher-order program-seed pairs. We then use DMCI for program-and-parameter co-search, where a large language model proposes Scheme programs and exact gradients calibrate their continuous parameters through a single frozen interpreter. This enables OpenEvolve-style program search in which an outer loop proposes discrete program structures and DMCI supplies exact gradient-based calibration of each candidate's continuous parameters. On battery capacity-fade data, the search recovers a knee-like degradation structure and improves held-out extrapolation over hand-crafted baselines on the harder early-extrapolation split, matching them on the later split. On a high-dimensional El Nino inverse problem, DMCI optimizes an interpreted Kalman-filter likelihood where gradient-free search fails. These results extend symbolic regression and neurosymbolic search from closed-form expressions to executable, stateful programs, making model-generated code directly optimizable against data.

Lucas Sheneman

Institute for Interdisciplinary Data Sciences University of Idaho

Differentiable Optimization Gradient-Based Optimization Symbolic Regression Model Discovery

Jun 6, 2026cs.LG

GPT-Micro: A large language paradigm for accelerated, inexpensive, and thermodynamics-consistent discovery of constitutive models in manufacturing

Constitutive modeling of the relationship between process-imposed material states and fundamental material properties is critical to control of material microstructure in manufacturing processes. The limited accuracy resulting from the typical reliance on fallible human expertise and intuition for postulation and revision of the models functional form results in incremental and time consuming model discovery. Conventional Machine Learning (ML) incurs significant cost and time of data generation. Model discovery using Large Language Models (LLMs) suffers from the above issues and/or ignores the inviolability of fundamental thermodynamics laws. This work creates a novel GPT-Micro paradigm for autonomous, data sparse, and thermodynamics-compliant discovery of de-novo constitutive models. This framework seamlessly integrates semantic knowledge extraction from literature, enforcement of thermodynamics-based conservation laws, and sparse datasets, with LLM-driven generation and refinement of model hypotheses. Validation is performed for a long-intractable constitutive modeling problem in a printed electronics process testbed. This reveals significant and simultaneous advantages over the state-of-the-art including: (a) More than 70 percent reduction in data burden relative to ML-based modeling without loss in accuracy; (b) 400X reduction in discovery time after data generation, from months to hours, relative to human-driven modeling; (c) Discovery of models with novel functional forms without subjective human choice of a starting hypothesis; (d) Enhanced physics-rooted trustworthiness, human interpretability, and mechanistic insight via synthesis of compact, conservation-compliant, and physically complete analytical models. The potential of GPT-Micro to realize rapid, low-cost, physically trustworthy, and interpretable microstructure modeling across the manufacturing landscape is discussed.

Soumik Dutta, Kiarash Naghavi Khanghah, Sania Shree +4

Department of Mechanical and Aerospace Engineering, Rutgers University, USA · Department of Mechanical, Aerospace & Manufacturing Engineering, University of Connecticut, USA · Edison Welding Institute, USA +2

Data-Driven Materials Discovery Materials Porous Media Model Discovery Manufacturing Thermodynamics+1

Jun 6, 2026cs.CL

Shared Semantics, Divergent Mechanisms: Unsupervised Feature Discovery by Aligning Semantics and Mechanisms

As large language models are increasingly deployed in high-stakes settings, there is a growing need for tools that audit not only model outputs but also the internal computations that produce them. Circuit analysis is a central approach in mechanistic interpretability, but it is typically target-conditioned, explaining a single prompt paired with a chosen completion. This target-conditioned setup can obscure heterogeneity across a model's continuation distribution. We introduce distribution-level unsupervised feature discovery, which clusters sampled continuations using both semantic content and sequence-level mechanistic attributions, without manually specifying target outputs. Our method represents each continuation with a semantic embedding and a prefix-to-continuation attribution signature, then optimizes a rate-distortion objective that trades off semantic coherence, mechanistic consistency, and cluster granularity. Across clustering and steering analyses, the discovered clusters expose continuation modes that single-view baselines miss and provide interventional evidence that cluster signatures correspond to actionable mechanistic factors. Overall, our approach complements circuit analysis and behavioral evaluation by providing a scalable audit of the mechanisms underlying a model's continuation distribution.

Hyunjin Cho, Youngji Roh, Jaehyung Kim

Yonsei University

Mechanistic Interpretability Interpretability Model Discovery Process-Level Supervision Circuits Shared Control

Jun 5, 2026cs.LG

Discovering Multiscale Deep Formulas in Complex Systems via Neural-Guided Lambda Calculus

A fundamental problem in science is identifying underlying patterns of complex systems in the form of concise mathematical formulas. Current Artificial Intelligence (AI)-based methods have shown strong performance in single-scale systems, yet remain limited in identifying scale-specific formulas in multiscale complex systems. We present Deflex, an end-to-end AI method to automatically extract multiscale formulas with potentially different forms, including invariants and distributions, from complex systems. Deflex consists of two subsystems named Deflexformer and Deflexpressor. Deflexpressor is a lambda-calculus symbolic regression model for higher-order formulas. Deflexformer is a decomposable deep energy model for learning unified representations across scales. Deflexpressor generates synthetic data to pre-train Deflexformer, which then guides formula discovery by decoupling multiscale latent relationships. Across six representative complex systems with diverse behaviors, Deflex achieves up to 7-fold higher efficiency than the state-of-the-art methods while enabling automated multiscale discovery. Our work could be a useful tool for scientific discovery across disciplines.

Hanqiao Yu, Shusen Yang, Xuebin Ren +1

National Engineering Laboratory for Big Data Analytics, Xi’an Jiaotong University, Xi’an, 710049, Shaanxi, China. · School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, 710049, Shaanxi, China. · School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049, Shaanxi, China.

Model Discovery Multiscale Symbolic Regression Expression

Jun 2, 2026cs.LG

CauTion: Knowing When to Trust LLMs for Ensemble Causal Discovery

Causal discovery from observational data remains challenging due to the fundamental limitations of purely statistical methods, such as statistical distinguishability within equivalence classes and sensitivity to finite sample sizes. While large language models (LLMs) offer a promising source of domain knowledge to complement statistical inference, existing LLM-augmented methods are vulnerable to LLM errors and incur high token costs. Moreover, reliance on a single data-centric algorithm can make results sensitive to algorithm-specific biases. To address these limitations, we propose CauTion, a framework that reliably integrates LLM domain knowledge into an ensemble of statistical causal discovery algorithms through consensus filtering and LLM reliability estimation. CauTion proceeds in three stages. First, an algorithm ensemble utilizes a consensus voting to resolve up to 96% of edges on which algorithms agree, achieving near-perfect accuracy on the filtered consensus edges. Second, a trust-calibrated arbitration mechanism estimates the relative reliability of the LLM and the algorithms via an annotation-free trust calibration procedure, which is then utilized to govern a trust-weighted voting process that restricts LLM arbitration exclusively to edges with unreliable algorithmic evidence. Third, a cycle repair step is applied to guarantee the final causal graph is validly acyclic. Experiments on six datasets demonstrate that CauTion consistently outperforms both data-centric and LLM-augmented baselines, with larger gains on larger graphs and strong robustness to LLM errors. Code is available at https://github.com/OpenCausaLab/CauTion.

Bo Peng, Kaiwen Wu, Sirui Chen +3

Shanghai AI Laboratory · Shanghai Innovation Institute · Shanghai Jiao Tong University +2

Causal Discovery Methods Model Discovery Ensemble Security Signals

May 29, 2026cs.LG

TabCausal: Pretraining Across Causal Environments for Tabular Causal Discovery

Causal discovery aims to recover directed causal relations from observational and interventional data, providing a basis for mechanistic understanding and reliable decision-making. Causal discovery foundation models (CDFMs) seek to amortize this problem by mapping a dataset directly to a causal graph in a single forward pass, avoiding per-dataset testing, search, or optimization. However, existing CDFMs remain limited, often failing to consistently match strong classical methods, and we find that a key bottleneck is how causal pretraining tasks are constructed. Based on this observation, we propose TabCausal, a data-driven CDFM trained with broad causal pretraining over diverse graph priors, structural mechanisms, noise models, dimensions, sample sizes, and intervention regimes. A dynamic task construction strategy composes these causal environments into varied discovery tasks, enabling more transferable structural learning from observational and mixed-interventional data. On large-scale synthetic benchmarks, TabCausal achieves better macro-averaged performance than a diverse set of causal discovery baselines. To further bridge abstract synthetic generators and realistic causal reasoning scenarios, we introduce a protocol-guided and LLM-audited semantic causal environment benchmark, where domain-grounded SCMs generate interpretable observational and interventional datasets for out-of-distribution analysis. Across both synthetic and semantic environments, TabCausal demonstrates robust structure recovery, especially under interventional evidence, highlighting broad causal pretraining as a key ingredient for transferable amortized causal discovery.

Zi-Rong Li, Si-Yang Liu, Tian-Zuo Wang +1

Nanjing University

Causal Discovery Methods Causal Model Discovery Causal Attention Data-Driven Environment

May 26, 2026cs.CV

Model discovery for dynamical systems with complex-valued product units

Discovering the governing equations of a dynamical system from observed trajectories provides deeper insight into its structure than mere prediction of future states. We present a data-driven approach to model discovery based on complex-valued product-unit networks, in which each unit represents a complex monomial and the network output is a sparse linear combination of such monomials. In contrast to established library-based methods such as SINDy, our approach does not require a predefined set of candidate functions: the relevant monomials, including those with fractional or negative exponents, are learned directly from data. Across four chaotic benchmark systems (Lorenz63, Lorenz84, the Four-Wing attractor, and a fractional variant of Lorenz63), we recover the exact governing equations in 90% of trials for the first three systems, and in 70-90% of trials for the fractional case, using at least 3000 training points. Applied to real-world human-gait accelerometer signals, the model produced stable trajectories with bounded prediction errors, corresponding to an RMSE of approximately 12-14% of the signal amplitude range over a test horizon three times longer than the training interval, demonstrating its potential for high-dimensional systems in which analytic equations are unavailable.

Martin Brückmann, Babette Dellen, Uwe Jaekel

Department of Mathematics, Informatics, and Technology, RheinAhrCampus Remagen University of Applied Sciences Koblenz Joseph-Rovan-Allee 2, 53424 Remagen, Germany

Dynamical Systems Chaos Model Discovery

May 23, 2026cs.AI

Summoning the Oracle to Slay It: Mitigating Look-Ahead Bias in Financial Backtesting with Large Language Models

Backtesting large language models (LLMs) on historical financial data is unreliable because pre-training cuts off after the events happened. An LLM trained in 2024 already "knows" which way 2018-2020 stocks moved. We name this failure parametric look-ahead bias and propose FinCAD, an inference-time adaptation of Context-Aware Decoding that suppresses an LLM's memory of historical outcomes without retraining. FinCAD pairs an adversarial bias-discovery pipeline that learns a model-specific memory-activating prior prompt with an entity- and date-adaptive rule that scales the CAD strength to per-(entity, date) memorisation, so the penalty fires on memorised in-sample dates and decays to zero out-of-sample. Across five 7-14B LLMs and five mega-cap equities, FinCAD cuts in-sample backtest returns by up to -67.1% on memorised dates while leaving 2025 out-of-sample returns within $8K and Sharpe within 0.10 of baseline, and preserves general-purpose reasoning within 1.7 pts. On an eleven-model leaderboard, it raises the in-sample / out-of-sample Spearman correlation from +0.779 to +0.846, recovering rankings that genuinely predict out-of-sample performance.

Weixian Waylon Li, Mengyu Wang, Tiejun Ma

University of Edinburgh

Financial Question Answering Lookahead Oracles Model Discovery

May 21, 2026cond-mat.str-el

Comment on "Spin-1/2 Kagome Heisenberg Antiferromagnet: Machine Learning Discovery of the Spinon Pair-Density-Wave Ground State"

A recent article [Phys. Rev. X 15, 011047 (2025)] utilizes group-equivariant convolutional neural networks to study the ground state of the kagome Heisenberg antiferromagnet. On the largest finite-size cluster studied to date (

N=108

), the authors report variational energies significantly lower than other numerical methods, including state-of-the-art density matrix renormalization group (DMRG) calculations. In contrast to previous results suggesting a possible spin-liquid ground state, the authors observe a spinon pair-density-wave ground state. We find that: (i) the reported low energies are artifacts of broken ergodicity in the Metropolis--Hastings sampling, since the single-spin-flip update rule utilized by the authors effectively freezes the Markov chains; and (ii) when ergodic sampling is enforced via spin-exchange updates, the neural network converges to energies significantly higher than existing DMRG results, calling the paper's claims into question.

Helia Kamal, Dominik Kufel, DinhDuy Vu +2

Department of Physics, Harvard University, Cambridge, MA 02138, USA · Harvard Quantum Initiative, Cambridge, MA 02138, USA · Department of Physics, Boston University, Boston, MA 02215, USA

Quantum Phases Model Discovery

May 20, 2026cs.LG

Beyond Scalar Objectives: Expert-Feedback-Driven Autonomous Experimentation for Scientific Discovery at the Nanoscale

Self-driving laboratories or autonomous experimentation are emerging as transformative platforms for accelerating scientific discovery. Bayesian optimization (BO) is among the most widely used machine learning frameworks for these purposes, but these BO-based frameworks rely on predefined scalar descriptors to guide experimentation. In many situations, the determination of an appropriate scalar descriptor can be challenging, and may fail to capture subtle yet scientifically important phenomena apparent to experts with interdisciplinary insight. To overcome this limitation, here we develop deep-kernel pairwise learning (DKPL), an approach for autonomous microscopy experiments which incorporates human expertise and interdisciplinary scientific knowledge into an active learning loop. Instead of relying on explicit scalar objectives, DKPL enables experts to directly evaluate which experimental output is more promising using interdisciplinary knowledge. DKPL then learns a latent utility function from these expert judgements to guide subsequent autonomous microscopy experiments. We demonstrate DKPL's performance in learning physically meaningful nanoscale structures while effectively prioritizing high-information measurement regions using an experimental model dataset with known ground truth. We further apply DKPL to analyze the character of ferroelectric domain walls, where we find DKPL capable of distinguishing between high and low characteristic domain-wall angles in bismuth ferrite, and able to discover both head-to-head and tail-to-tail domain-wall character in erbium manganite. This development establishes an approach to integrate expert knowledge into autonomous microscopy experiments and demonstrates a pathway toward expert-guided self-driving laboratories capable of addressing scientific problems beyond the limits of scalar-metrics-driven learning.

Ralph Bulanadi, Jefferey Baxter, Arpan Biswas +5

Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA · University of Tennessee-Oak Ridge Innovation Institute, University of Tennessee, Knoxville, TN 37996, USA · Department of Material Science and Engineering, School of Materials and Chemical Technology, Institute of Science Tokyo, Yokohama, 226-8502, Japan +3

Microscopy Model Discovery Bayesian Optimization Scientific Discovery Magnetic Tunnel Junction

May 20, 2026cs.LG

Learning First Integrals via Backward-Generated Data and Guided Reinforcement Learning

The discovery of first integrals is of fundamental scientific importance for understanding conservation laws in dynamical systems. However, existing symbolic computation tools and Large Language Models (LLMs) remain limited on this task because high-quality training data are scarce and successful solutions often depend on mathematical intuition. This paper presents FISolver, an LLM-based solver developed to address this challenge. First, we introduce a "Backward Generation" algorithm that systematically builds large-scale datasets of (differential equation, first integral) pairs by deriving differential equations from sampled integrals, thereby alleviating the data scarcity bottleneck. Second, we apply supervised fine-tuning to a compact mathematical model and further improve its performance through reinforcement learning with a Levenshtein Distance-based shaped reward. In addition, we design data synthesis and blending strategies that support effective adaptation to difficult problem families from sparse examples. Experiments show that FISolver, while requiring substantially lower computational cost, significantly outperforms larger mathematical LLMs and commercial solvers such as Mathematica on challenging benchmarks, indicating a new data-driven route for automated discovery of first integrals.

Jingfeng Zhong, Zhengxiang Liu, Zhijie Wang +1

Shanghai Jiao Tong University China

Integral Functional Code Solvers Math Problems Model Discovery Symbol-Offline Reinforcement Learning

May 19, 2026cs.IR

Beyond Text and Tables: Vision-Language Model Integration in ComProScanner for Extracting Materials Data from Scientific Figures with High Accuracy

Automated extraction of materials composition-property data from scientific literature has advanced considerably with the development of large language model-based pipelines; however, existing frameworks remain limited to textual and tabular content, overlooking the substantial proportion of quantitative property data reported exclusively in scientific figures. Here, we extend ComProScanner, a fully end-to-end multi-agent framework for automated composition-property database construction, with a native vision-language model (VLM) based figure extraction capability. The extension introduces a FigureExtractor utility for caption-keyword-based figure filtering across all supported publishers, and a GraphExtractorTool agent that passes extracted figures to a configurable VLM to recover composition-property pairs from scientific charts and plots. Four VLMs are selected for evaluation on the basis of the LMArena Diagram leaderboard with an input cost criterion of less than $1.50 per million tokens. Benchmarking on 50 piezoelectric ceramic articles from the established

d_{33}

test corpus demonstrates that Gemini-3-Flash-Preview achieves the highest performance with a composition accuracy of 0.97 and a normalised F1 score of 0.97, whilst remaining the most cost-effective model among the four evaluated. We additionally introduce a range-based value error threshold parameter into the evaluation framework, providing a more physically meaningful assessment of numeric property values extracted from figures than exact value matching. These contributions establish VLM-integrated ComProScanner as the first materials-specific, fully automated, multimodal literature mining platform capable of extracting structured composition-property data from text, tables, and figures within a single unified pipeline.

Aritra Roy, Enrico Grisan, Chiara Gattinoni +1

Energy, Materials and Environment Research Centre, London South Bank University, London SE1 0AA, UK. · School of Engineering and Design, London South Bank University, London SE1 0AA, UK. · Bioscience and Bioengineering Research Centre, London South Bank University, London SE1 0AA, UK. +1

Scientific Figure Extraction Model Discovery Vision-Language Foundation Models Recent Vision-Language Models

May 18, 2026physics.data-an

A Unified Framework for Structured Flow Modeling: From Representation to Verification and Model Discovery

Many dynamical systems can be described in terms of structured flows combining source/sink behavior, cyclic dynamics, and topology-constrained transport. These features arise across a wide range of physical, engineered, and data-driven systems. The objective of this work is to establish a unified perspective on such systems, to identify modeling approaches that balance expressivity, interpretability, computational complexity, and data requirements, and to investigate how highly expressive models can be used to uncover the dominant mechanisms underlying observed dynamics. Starting from the Helmholtz-Hodge decomposition of continuous vector fields, we review the recently proposed Graph Vector Field (GVF) framework and its discrete representation on simplicial complexes. We then introduce a hierarchy of alternative approaches, including parametric conditional models, linear graph dynamical systems, and reduced Hodge representations. Finally, we propose a verification and validation methodology based on benchmark datasets from well-understood physical systems and on systematic model-reduction and ablation studies. The resulting family of structured-flow models within a common framework, ranging from low-dimensional parametric representations to full GVF formulations, supports a diagnostic methodology in which gradient, curl, harmonic, and topological contributions are systematically assessed through ablation studies. This process enables the identification of dominant mechanisms underlying the observed dynamics and guides the construction of simplified models tailored to the available data and operational constraints. By separating structural verification, behavioral verification, and domain-specific validation, the proposed approach provides a foundation for scalable and interpretable analysis of complex dynamical systems across multiple application domains.

Diego Casadei

Fly High Engineering AG, Badenerstrasse 13, 5200 Brugg AG, Switzerland

Vector Fields Flow Models Model Discovery Unified Framework

May 18, 2026cs.LG

LEAP: A closed-loop framework for perovskite precursor additive discovery

Efficient discovery of precursor additives is essential for improving the performance of perovskite solar cells, yet the large chemical space makes conventional trial-and-error screening inefficient. We develop LEAP(LLM-driven Exploration via Active Learning for Perovskites), an expert-in-the-loop closed framework that couples a domain-specialized large language model(LLM) with active learning for iterative additive prioritization. The LLM is trained to extract mechanism-relevant knowledge from the perovskite additive literature and to represent candidate molecules through interpretable descriptors, which are further integrated into a Bayesian optimization workflow for uncertainty-aware prioritization under low-data conditions. Benchmark results on unseen literature show that the domain-specialized model outperforms general-purpose models in mechanism-consistent reasoning. Experimental validation in an expert-in-the-loop proof-of-concept study suggests improved additive prioritization across three screening rounds, leading to average device PCEs of 20.13% and 20.87% for the later-round 6-CDQ- and 2-CNA-treated devices, respectively, compared with 19.25% for the control, with a champion PCE of 21.32%. These results provide preliminary evidence that literature-grounded mechanistic descriptors, when coupled with Bayesian optimization and expert feasibility review, can support mechanism-aware additive prioritization in perovskite photovoltaics.

Xin-De Wang, Zhi-Rui Chen, Ze-Feng Gao +3

School of Physics, Renmin University of China, Beijing, China · School of Chemistry and Life Resource, Renmin University of China, Beijing, China

Photovoltaic Chemical Structures Model Discovery Closed Loop Active Learning

May 16, 2026cs.LG

ArtifactLinker: Linking Scientific Artifacts for Automatic State-of-the-Art Discovery

Scientific artifacts such as models and datasets are foundations for research. With the rapid growth of platforms like HuggingFace, researchers now have access to a large number of artifacts. Yet, a key challenge remains: how can we automatically discover the state-of-the-art (SOTA) model for a given dataset by fully leveraging existing artifacts? We formalize this task as automatic SOTA discovery by modeling HuggingFace as an artifact graph, where nodes are models/datasets and edges represent evaluations. We propose ArtifactLinker, a two-stage framework: (1) ranking promising unobserved model--dataset links using Graph Neural Networks (GNNs) or graph-augmented Large Language Models (LLMs), and (2) verifying top-ranked links via coding experiments with LLM-based agents. We further introduce a benchmark named ArtifactBench with 14,053 artifacts and 51,337 relations to evaluate the performance of both stages. Results show that (1) graph structures between existing artifacts are effective for missing link prediction; (2) end-to-end ranking and verification with ArtifactLinker help discover potential SOTA results and research insights.

Haofei Yu, Jiaxuan You, Peter Clark +2

University of Illinois Urbana-Champaign · Allen Institute for AI

Model Discovery Artifacts Artificial Intelligence Models Graph Neural Networks

May 14, 2026cs.AI

SMCEvolve: Principled Scientific Discovery via Sequential Monte Carlo Evolution

LLM-driven program evolution has emerged as a powerful tool for automated scientific discovery, yet existing frameworks offer no principled guide for designing their individual components and provide no guarantee that the search converges. We introduce SMCEvolve, which recasts program search as sampling from a reward-tilted target distribution and approximates it with a Sequential Monte Carlo (SMC) sampler. From this view, three core mechanisms emerge as principled components: adaptive parent resampling, mixture of mutation with acceptance, and automatic convergence control. We further provide a finite-sample complexity analysis that bounds the LLM-call budget required to reach a target approximation error. Across math, algorithm efficiency, symbolic regression, and end-to-end ML research benchmarks, SMCEvolve surpasses state-of-the-art evolving systems while using fewer LLM calls under self-determined termination. The code is available at https://github.com/kongwanbianjinyu/SMCEvolve.

Jiachen Jiang, Huminhao Zhu, Zhihui Zhu

Department of Computer Science and Engineering The Ohio State University

Evolutionary Search Alphaevolve Symbolic Regression Model Discovery Mle-Bench Lite Monte Carlo+1

May 14, 2026astro-ph.IM

Beyond AI as Assistants: Toward Autonomous Discovery in Cosmology

Recent advances in artificial intelligence (AI) agents are pushing AI beyond tools toward autonomous scientific discovery. We discuss two complementary agentic systems for cosmology: \texttt{CMBEvolve}, which targets tasks with explicit quantitative objectives through LLM-guided code evolution and tree search, and \texttt{CosmoEvolve}, which targets open-ended scientific workflows through a virtual multi-agent research laboratory. As preliminary demonstrations, we apply \texttt{CMBEvolve} to out-of-distribution detection in weak-lensing maps, where it iteratively improves the benchmark score through code evolution, and \texttt{CosmoEvolve} to autonomous ACT DR6 data analysis, where it identifies non-trivial pair- and scale-dependent behaviour and produces analysis-grade diagnostics. These examples show how cosmology can provide both controlled benchmark tasks and realistic open-ended research problems for the development of AI scientist systems.

Licong Xu, Thomas Borrett

Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA, UK · Kavli Institute for Cosmology, University of Cambridge, Madingley Road, Cambridge CB3 0HA, UK · Cavendish Astrophysics, University of Cambridge, Madingley Road, Cambridge CB3 0HA, UK

Artificial Intelligence Scientists Cosmology Agentic Discovery Astronomical Images Model Discovery Discovery+1