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Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited…

Machine Learning · Computer Science 2026-02-02 Hao Li , He Cao , Shenyao Peng , Zijing Liu , Bin Feng , Yu Wang , Zhiyuan Yan , Yonghong Tian , Yu Li , Li Yuan

Simulation models of critical systems often have parameters that need to be calibrated using observed data. For expensive simulation models, calibration is done using an emulator of the simulation model built on simulation output at…

Methodology · Statistics 2023-08-24 Özge Sürer , Matthew Plumlee , Stefan M. Wild

Chemical process optimization maximizes production efficiency and economic performance, but optimization algorithms, including gradient-based solvers, numerical methods, and parameter grid searches, become impractical when operating…

Machine Learning · Computer Science 2025-10-17 Tong Zeng , Srivathsan Badrinarayanan , Janghoon Ock , Cheng-Kai Lai , Amir Barati Farimani

Chemists need to perform many laborious and time-consuming experiments in the lab to discover and understand the properties of new materials. To support and accelerate this process, we propose a robot framework for manipulation that…

Rapid developments of AI tools are expected to offer unprecedented assistance to the research of natural science including chemistry. However, neither existing unimodal task-specific specialist models nor emerging general large multimodal…

Machine Learning · Computer Science 2025-01-03 Zihan Zhao , Bo Chen , Jingpiao Li , Lu Chen , Liyang Wen , Pengyu Wang , Zichen Zhu , Danyang Zhang , Ziping Wan , Yansi Li , Zhongyang Dai , Xin Chen , Kai Yu

Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall properties, could…

Computational Engineering, Finance, and Science · Computer Science 2020-10-08 David Medina-Ortiz , Sebastian Contreras , Juan Amado-Hinojosa , Jorge Torres-Almonacid , Juan A. Asenjo , Marcelo Navarrete , Álvaro Olivera-Nappa

Optimal operation of chemical processes is vital for energy, resource, and cost savings in chemical engineering. The problem of optimal operation can be tackled with reinforcement learning, but traditional reinforcement learning methods…

Machine Learning · Computer Science 2025-11-21 Dean Brandner , Sergio Lucia

Understanding and predicting the behavior of liquid matter across length scales, using only the microscopic interactions encoded in the Schr\"odinger equation, remains a central challenge in the physical sciences. Achieving this goal…

Chemical Physics · Physics 2026-03-24 Anna T. Bui , Stephen J. Cox

The calibration of CALPHAD (CALculation of PHAse Diagrams) models involves the solution of a very challenging high-dimensional multiobjective optimization problem. Traditional approaches to parameter fitting predominantly rely on…

Materials Science · Physics 2025-05-06 Courtney Kunselman , Brandon Bocklund , Richard Otis , Raymundo Arroyave

Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…

Medical Physics · Physics 2022-08-31 Patrick Vogel , Martin A. Rückert , Thomas Kampf , Volker C. Behr

Many systems require optimisation over multiple objectives, where objectives are characteristics of the system such as energy consumed or increase in time to perform the work. Optimisation is performed by selecting the `best' set of input…

Performance · Computer Science 2019-10-08 Alexander J. M. Kell , Matthew Forshaw , A. Stephen McGough

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling…

Computation and Language · Computer Science 2025-01-14 Xiangru Tang , Tianyu Hu , Muyang Ye , Yanjun Shao , Xunjian Yin , Siru Ouyang , Wangchunshu Zhou , Pan Lu , Zhuosheng Zhang , Yilun Zhao , Arman Cohan , Mark Gerstein

Multiscale modeling is an effective approach for investigating multiphysics systems with largely disparate size features, where models with different resolutions or heterogeneous descriptions are coupled together for predicting the system's…

Computational Engineering, Finance, and Science · Computer Science 2022-12-07 Minglang Yin , Enrui Zhang , Yue Yu , George Em Karniadakis

The advancement and extensive application of large language models (LLMs) have been remarkable, including their use in scientific research assistance. However, these models often generate scientifically incorrect or unsafe responses, and in…

Computation and Language · Computer Science 2024-11-28 Haochen Zhao , Xiangru Tang , Ziran Yang , Xiao Han , Xuanzhi Feng , Yueqing Fan , Senhao Cheng , Di Jin , Yilun Zhao , Arman Cohan , Mark Gerstein

Feature modeling is a widely used formalism to characterize a set of products (also called configurations). As a manual elaboration is a long and arduous task, numerous techniques have been proposed to reverse engineer feature models from…

Software Engineering · Computer Science 2015-02-17 Guillaume Bécan , Razieh Behjati , Arnaud Gotlieb , Mathieu Acher

Reliable predictions of the behaviour of chemical systems are essential across many industries, from nanoscale engineering over validation of advanced materials to nanotoxicity assessment in health and medicine. For the future we therefore…

Chemical Physics · Physics 2021-03-05 Judith B. Rommel

The goal of chemmodlab is to streamline the fitting and assessment pipeline for many machine learning models in R, making it easy for researchers to compare the utility of new models. While focused on implementing methods for model fitting…

Machine Learning · Statistics 2018-07-13 Jeremy R. Ash Jacqueline M. Hughes-Oliver

Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…

Quantitative Methods · Quantitative Biology 2025-12-23 Mamoru Saita , Yutaka Hori

Recent advances in machine learning force fields (MLFF) have significantly extended the reach of atomistic simulations. Continuous progress in this field requires reliable reference datasets, accurate MLFF architectures, and efficient…

Chemical Physics · Physics 2025-10-24 Tobias Henkes , Shubham Sharma , Alexandre Tkatchenko , Mariana Rossi , Igor Poltavskyi

The rise in internet usage has led to the generation of massive amounts of data, resulting in the adoption of various supervised and semi-supervised machine learning algorithms, which can effectively utilize the colossal amount of data to…

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