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Neural-guided equation discovery systems use a data set as prompt and predict an equation that describes the data set without extensive search. However, if the equation does not meet the user's expectations, there are few options for getting other equation suggestions without intensive work with the system. To fill this gap, we propose Residuals for Equation Discovery (RED), a post-processing method that improves a given equation in a targeted manner, based on its residuals. By parsing the initial equation to a syntax tree, we can use node-based calculation rules to compute the residual for each subequation of the initial equation. It is then possible to use this residual as new target variable in the original data set and generate a new prompt. If, with the new prompt, the equation discovery system suggests a subequation better than the old subequation on a validation set, we replace the latter by the former. RED is usable with any equation discovery system, is fast to calculate, and is easy to extend for new mathematical operations. In experiments on 53 equations from the Feynman benchmark, we show that it not only helps to improve all tested neural-guided systems, but also all t

The continuous expansion of open data platforms and research repositories has led to a fragmented dataset ecosystem, posing significant challenges for cross-source data discovery and interpretation. To address these challenges, we introduce SeDa--a unified framework for dataset discovery, semantic annotation, and multi-entity augmented navigation. SeDa integrates more than 7.6 million datasets from over 200 platforms, spanning governmental, academic, and industrial domains. The framework first performs semantic extraction and standardization to harmonize heterogeneous metadata representations. On this basis, a topic-tagging mechanism constructs an extensible tag graph that supports thematic retrieval and cross-domain association, while a provenance assurance module embedded within the annotation process continuously validates dataset sources and monitors link availability to ensure reliability and traceability. Furthermore, SeDa employs a multi-entity augmented navigation strategy that organizes datasets within a knowledge space of sites, institutions, and enterprises, enabling contextual and provenance-aware exploration beyond traditional search paradigms. Comparative experiments

High throughput experimentation tools, machine learning (ML) methods, and open material databases are radically changing the way new materials are discovered. From the experimentally driven approach in the past, we are moving quickly towards the artificial intelligence (AI) driven approach, realizing the 'inverse design' capabilities that allow the discovery of new materials given the desired properties. This review aims to discuss different principles of AI-driven generative models that are applicable for materials discovery, including different materials representations available for this purpose. We will also highlight specific applications of generative models in designing new catalysts, semiconductors, polymers, or crystals while addressing challenges such as data scarcity, computational cost, interpretability, synthesizability, and dataset biases. Emerging approaches to overcome limitations and integrate AI with experimental workflows will be discussed, including multimodal models, physics informed architectures, and closed-loop discovery systems. This review aims to provide insights for researchers aiming to harness AI's transformative potential in accelerating materials dis

Recent advances in large language models (LLMs) have shown great potential to accelerate drug discovery. However, the specialized nature of biochemical data often necessitates costly domain-specific fine-tuning, posing major challenges. First, it hinders the application of more flexible general-purpose LLMs for cutting-edge drug discovery tasks. More importantly, it limits the rapid integration of the vast amounts of scientific data continuously generated through experiments and research. Compounding these challenges is the fact that real-world scientific questions are typically complex and open-ended, requiring reasoning beyond pattern matching or static knowledge retrieval.To address these challenges, we propose CLADD, a retrieval-augmented generation (RAG)-empowered agentic system tailored to drug discovery tasks. Through the collaboration of multiple LLM agents, CLADD dynamically retrieves information from biomedical knowledge bases, contextualizes query molecules, and integrates relevant evidence to generate responses - all without the need for domain-specific fine-tuning. Crucially, we tackle key obstacles in applying RAG workflows to biochemical data, including data heteroge

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We introduce Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), an active learning framework where large language models autonomously design, execute, and interpret atomistic simulations. In MASTER, a multimodal system translates natural language into density functional theory workflows, while higher-level reasoning agents guide discovery through a hierarchy of strategies, including a single agent baseline and three multi-agent approaches: peer review, triage-ranking, and triage-forms. Across two chemical applications, CO adsorption on Cu-surface transition metal (M) adatoms and on M-N-C catalysts, reasoning-driven exploration reduces required atomistic simulations by up to 90% relative to trial-and-error selection. Reasoning trajectories reveal chemically grounded decisions that cannot be explained by stochastic sampling or semantic bias. Altogether, multi-agent collaboration accelerates materials discovery and marks a new paradigm for autonomous scientific exploration.

Agent-Based Model (ABM) validation is crucial as it helps ensuring the reliability of simulations, and causal discovery has become a powerful tool in this context. However, current causal discovery methods often face accuracy and robustness challenges when applied to complex and noisy time series data, which is typical in ABM scenarios. This study addresses these issues by proposing a Robust Cross-Validation (RCV) approach to enhance causal structure learning for ABM validation. We develop RCV-VarLiNGAM and RCV-PCMCI, novel extensions of two prominent causal discovery algorithms. These aim to reduce the impact of noise better and give more reliable causal relation results, even with high-dimensional, time-dependent data. The proposed approach is then integrated into an enhanced ABM validation framework, which is designed to handle diverse data and model structures. The approach is evaluated using synthetic datasets and a complex simulated fMRI dataset. The results demonstrate greater reliability in causal structure identification. The study examines how various characteristics of datasets affect the performance of established causal discovery methods. These characteristics include

The role of Artificial Intelligence (AI) is growing in every stage of drug development. Nevertheless, a major challenge in drug discovery AI remains: Drug pharmacokinetic (PK) and Drug-Target Interaction (DTI) datasets collected in different studies often exhibit limited overlap, creating data overlap sparsity. Thus, data curation becomes difficult, negatively impacting downstream research investigations in high-throughput screening, polypharmacy, and drug combination. We propose xImagand-DKI, a novel SMILES/Protein-to-Pharmacokinetic/DTI (SP2PKDTI) diffusion model capable of generating an array of PK and DTI target properties conditioned on SMILES and protein inputs that exhibit data overlap sparsity. We infuse additional molecular and genomic domain knowledge from the Gene Ontology (GO) and molecular fingerprints to further improve our model performance. We show that xImagand-DKI-generated synthetic PK data closely resemble real data univariate and bivariate distributions, and can adequately fill in gaps among PK and DTI datasets. As such, xImagand-DKI is a promising solution for data overlap sparsity and may improve performance for downstream drug discovery research tasks. Code

Ancient manuscripts are the primary source of ancient linguistic corpora. However, many ancient manuscripts exhibit duplications due to unintentional repeated publication or deliberate forgery. The Dead Sea Scrolls, for example, include counterfeit fragments, whereas Oracle Bones (OB) contain both republished materials and fabricated specimens. Identifying ancient manuscript duplicates is of great significance for both archaeological curation and ancient history study. In this work, we design a progressive OB duplicate discovery framework that combines unsupervised low-level keypoints matching with high-level text-centric content-based matching to refine and rank the candidate OB duplicates with semantic awareness and interpretability. We compare our model with state-of-the-art content-based image retrieval and image matching methods, showing that our model yields comparable recall performance and the highest simplified mean reciprocal rank scores for both Top-5 and Top-15 retrieval results, and with significantly accelerated computation efficiency. We have discovered over 60 pairs of new OB duplicates in real-world deployment, which were missed by domain experts for decades. Code,

Correlation does not imply causation, but patterns of statistical association between variables can be exploited to infer a causal structure (even with purely observational data) with the burgeoning field of causal discovery. As a purely observational science, astrophysics has much to gain by exploiting these new methods. The supermassive black hole (SMBH)--galaxy interaction has long been constrained by observed scaling relations, that is low-scatter correlations between variables such as SMBH mass and the central velocity dispersion of stars in a host galaxy's bulge. This study, using advanced causal discovery techniques and an up-to-date dataset, reveals a causal link between galaxy properties and dynamically-measured SMBH masses. We apply a score-based Bayesian framework to compute the exact conditional probabilities of every causal structure that could possibly describe our galaxy sample. With the exact posterior distribution, we determine the most likely causal structures and notice a probable causal reversal when separating galaxies by morphology. In elliptical galaxies, bulge properties (built from major mergers) tend to influence SMBH growth, while in spiral galaxies, SMBH

Biomarkers play a central role in medicine's gradual progress towards proactive, personalized precision diagnostics and interventions. However, finding biomarkers that provide very early indicators of a change in health status, for example for multi-factorial diseases, has been challenging. Discovery of such biomarkers stands to benefit significantly from advanced information processing and means to detect complex correlations, which quantum computing offers. In this perspective paper, quantum algorithms, particularly in machine learning, are mapped to key applications in biomarker discovery. The opportunities and challenges associated with the algorithms and applications are discussed. The analysis is structured according to different data types - multi-dimensional, time series, and erroneous data - and covers key data modalities in healthcare - electronic health records (EHRs), omics, and medical images. An outlook is provided concerning open research challenges.

We present a long-horizon, hierarchical deep research (DR) agent designed for complex materials and device discovery problems that exceed the scope of existing Machine Learning (ML) surrogates and closed-source commercial agents. Our framework instantiates a locally deployable DR instance that integrates local retrieval-augmented generation with large language model reasoners, enhanced by a Deep Tree of Research (DToR) mechanism that adaptively expands and prunes research branches to maximize coverage, depth, and coherence. We systematically evaluate across 27 nanomaterials/device topics using a large language model (LLM)-as-judge rubric with five web-enabled state-of-the-art models as jurors. In addition, we conduct dry-lab validations on five representative tasks, where human experts use domain simulations (e.g., density functional theory, DFT) to verify whether DR-agent proposals are actionable. Results show that our DR agent produces reports with quality comparable to--and often exceeding--those of commercial systems (ChatGPT-5-thinking/o3/o4-mini-high Deep Research) at a substantially lower cost, while enabling on-prem integration with local data and tools.

Uncovering cause-effect relationships from observational time series is fundamental to understanding complex systems. While many methods infer static causal graphs, real-world systems often exhibit dynamic causality-where relationships evolve over time. Accurately capturing these temporal dynamics requires time-resolved causal graphs. We propose UnCLe, a novel deep learning method for scalable dynamic causal discovery. UnCLe employs a pair of Uncoupler and Recoupler networks to disentangle input time series into semantic representations and learns inter-variable dependencies via auto-regressive Dependency Matrices. It estimates dynamic causal influences by analyzing datapoint-wise prediction errors induced by temporal perturbations. Extensive experiments demonstrate that UnCLe not only outperforms state-of-the-art baselines on static causal discovery benchmarks but, more importantly, exhibits a unique capability to accurately capture and represent evolving temporal causality in both synthetic and real-world dynamic systems (e.g., human motion). UnCLe offers a promising approach for revealing the underlying, time-varying mechanisms of complex phenomena.

Charmonium is a bound state of a charmed quark and a charmed antiquark, and a charmoniumlike state is a resonant structure that contains at least a charmed quark-antiquark pair but has properties that are incompatible with a conventional charmonium state. The charmoniumlike states are also called XYZ particles to indicate their underlying nature is still unclear. The BESIII experiment has contributed significantly in the study of the XYZ particles, and here we review the discoveries of the Zc(3900), Zc(4020), and Zcs(3985) tetraquark states and the observations of several new vector charmoniumlike states at the BESIII experiment.

Recommender systems (RS) commonly retrieve potential candidate items for users from a massive number of items by modeling user interests based on historical interactions. However, historical interaction data is highly sparse, and most items are long-tail items, which limits the representation learning for item discovery. This problem is further augmented by the discovery of novel or cold-start items. For example, after a user displays interest in bitcoin financial investment shows in the podcast space, a recommender system may want to suggest, e.g., a newly released blockchain episode from a more technical show. Episode correlations help the discovery, especially when interaction data of episodes is limited. Accordingly, we build upon the classical Two-Tower model and introduce the novel Multi-Source Augmentations using a Contrastive Learning framework (MSACL) to enhance episode embedding learning by incorporating positive episodes from numerous correlated semantics. Extensive experiments on a real-world podcast recommendation dataset from a large audio streaming platform demonstrate the effectiveness of the proposed framework for user podcast exploration and cold-start episode rec

This is a review and statistical analysis of the evidence supporting the existence of a cosmological constant in the early 1990s, before its discovery made with distant supernovae in 1998. The earlier evidence was derived from newly precise measurements of the Universe, including its mass density, the Hubble constant, the age of the oldest stars, the filamentary large-scale structure, and the anisotropy of the cosmic microwave background. These measurements created tension for models assuming the cosmological constant was zero. This tension was alleviated by several insightful papers published before 1996, which proposed a cosmological constant that increased the expansion rate. Statistical analysis here shows that the probability of the cosmological constant being zero was demonstrably less than a few percent. Some models identified a best-fit value close to the modern estimate of Omega_Lambda ~ 0.7.

This paper presents an overview of the Volvo Discovery Challenge, held during the ECML-PKDD 2024 conference. The challenge's goal was to predict the failure risk of an anonymized component in Volvo trucks using a newly published dataset. The test data included observations from two generations (gen1 and gen2) of the component, while the training data was provided only for gen1. The challenge attracted 52 data scientists from around the world who submitted a total of 791 entries. We provide a brief description of the problem definition, challenge setup, and statistics about the submissions. In the section on winning methodologies, the first, second, and third-place winners of the competition briefly describe their proposed methods and provide GitHub links to their implemented code. The shared code can be interesting as an advanced methodology for researchers in the predictive maintenance domain. The competition was hosted on the Codabench platform.

This paper presents the second-place methodology in the Volvo Discovery Challenge at ECML-PKDD 2024, where we used Long Short-Term Memory networks and pseudo-labeling to predict maintenance needs for a component of Volvo trucks. We processed the training data to mirror the test set structure and applied a base LSTM model to label the test data iteratively. This approach refined our model's predictive capabilities and culminated in a macro-average F1-score of 0.879, demonstrating robust performance in predictive maintenance. This work provides valuable insights for applying machine learning techniques effectively in industrial settings.

"How to evaluate the de novo designs proposed by a generative model?" Despite the transformative potential of generative deep learning in drug discovery, this seemingly simple question has no clear answer. The absence of standardized guidelines challenges both the benchmarking of generative approaches and the selection of molecules for prospective studies. In this work, we take a fresh - critical and constructive - perspective on de novo design evaluation. By training chemical language models, we analyze approximately 1 billion molecule designs and discover principles consistent across different neural networks and datasets. We uncover a key confounder: the size of the generated molecular library significantly impacts evaluation outcomes, often leading to misleading model comparisons. We find increasing the number of designs as a remedy and propose new and compute-efficient metrics to compute at large-scale. We also identify critical pitfalls in commonly used metrics - such as uniqueness and distributional similarity - that can distort assessments of generative performance. To address these issues, we propose new and refined strategies for reliable model comparison and design evalu

Optical Music Recognition (OMR) automates the transcription of musical notation from images into machine-readable formats like MusicXML, MEI, or MIDI, significantly reducing the costs and time of manual transcription. This study explores knowledge discovery in OMR by applying instance segmentation using Mask R-CNN to enhance the detection and delineation of musical symbols in sheet music. Unlike Optical Character Recognition (OCR), OMR must handle the intricate semantics of Common Western Music Notation (CWMN), where symbol meanings depend on shape, position, and context. Our approach leverages instance segmentation to manage the density and overlap of musical symbols, facilitating more precise information retrieval from music scores. Evaluations on the DoReMi and MUSCIMA++ datasets demonstrate substantial improvements, with our method achieving a mean Average Precision (mAP) of up to 59.70\% in dense symbol environments, achieving comparable results to object detection. Furthermore, using traditional computer vision techniques, we add a parallel step for staff detection to infer the pitch for the recognised symbols. This study emphasises the role of pixel-wise segmentation in adva