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Globally interpretable models are a promising approach for trustworthy AI in safety-critical domains. Alongside global explanations, detailed local explanations are a crucial complement to effectively support human experts during inference.…

Machine Learning · Computer Science 2026-04-09 Thomas Norrenbrock , Timo Kaiser , Sovan Biswas , Neslihan Kose , Ramesh Manuvinakurike , Bodo Rosenhahn

Finely-tuned enzymatic pathways control cellular processes, and their dysregulation can lead to disease. Creating predictive and interpretable models for these pathways is challenging because of the complexity of the pathways and of the…

Molecular Networks · Quantitative Biology 2023-10-02 Zijun Zhang , Adam R. Lamson , Michael Shelley , Olga Troyanskaya

Raman spectroscopy is an effective, low-cost, non-intrusive technique often used for chemical identification. Typical approaches are based on matching observations to a reference database, which requires careful preprocessing, or supervised…

Machine Learning · Computer Science 2022-10-12 Bo Li , Mikkel N. Schmidt , Tommy S. Alstrøm

Deep learning models for anticipating the products of organic reactions have found many use cases, including validating retrosynthetic pathways and constraining synthesis-based molecular design tools. Despite compelling performance on…

Machine Learning · Computer Science 2025-01-14 John Bradshaw , Anji Zhang , Babak Mahjour , David E. Graff , Marwin H. S. Segler , Connor W. Coley

Identifying reaction coordinates(RCs) is an active area of research, given the crucial role RCs play in determining the progress of a chemical reaction. The choice of the reaction coordinate is often based on heuristic knowledge. However,…

Chemical Physics · Physics 2024-01-17 Abhijit Gupta

Reaction prediction remains one of the major challenges for organic chemistry, and is a pre-requisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, "learn" from being exposed to examples of the…

Chemical Physics · Physics 2017-06-01 Jennifer N. Wei , David Duvenaud , Alán Aspuru-Guzik

Artificial intelligence (AI) has demonstrated significant promise in advancing organic chemistry research; however, its effectiveness depends on the availability of high-quality chemical reaction data. Currently, most published chemical…

Computer Vision and Pattern Recognition · Computer Science 2025-03-12 Yufan Chen , Ching Ting Leung , Jianwei Sun , Yong Huang , Linyan Li , Hao Chen , Hanyu Gao

Graph based molecular representation learning is essential for accurately predicting molecular properties in drug discovery and materials science; however, it faces significant challenges due to the intricate relationships among molecules…

Computational Engineering, Finance, and Science · Computer Science 2025-05-28 Zhengyang Zhou , Yunrui Li , Pengyu Hong , Hao Xu

Dense retrieval (DR) has shown promising results in information retrieval. In essence, DR requires high-quality text representations to support effective search in the representation space. Recent studies have shown that pre-trained…

Information Retrieval · Computer Science 2022-08-23 Xinyu Ma , Ruqing Zhang , Jiafeng Guo , Yixing Fan , Xueqi Cheng

The integration of Multimodal Large Language Models (MLLMs) into chemistry promises to revolutionize scientific discovery, yet their ability to comprehend the dense, graphical language of reactions within authentic literature remains…

Computer Vision and Pattern Recognition · Computer Science 2026-01-29 Hanzheng Li , Xi Fang , Yixuan Li , Chaozheng Huang , Junjie Wang , Xi Wang , Hongzhe Bai , Bojun Hao , Shenyu Lin , Huiqi Liang , Linfeng Zhang , Guolin Ke

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional…

Machine Learning · Computer Science 2025-10-20 Jiaxi Zhuang , Yaorui Shi , Jue Hou , Yunong He , Mingwei Ye , Mingjun Xu , Yuming Su , Linfeng Zhang , Ying Qian , Linfeng Zhang , Guolin Ke , Hengxing Cai

The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic…

With the mass construction of Gen III nuclear reactors, it is a popular trend to use deep learning (DL) techniques for fast and effective diagnosis of possible accidents. To overcome the common problems of previous work in diagnosing…

Signal Processing · Electrical Eng. & Systems 2022-09-26 Chengyuan Li , Zhifang Qiu , Zhangrui Yan , Meifu Li

With the rise of data-driven reaction prediction models, effective reaction descriptors are crucial for bridging the gap between real-world chemistry and digital representations. However, general-purpose, reaction-wise descriptors remain…

Machine Learning · Computer Science 2026-01-08 Weiqi Liu , Fenglei Cao , Yuan Qi , Li-Cheng Xu

Advanced machine learning models have recently achieved high predictive accuracy for weather and climate prediction. However, these complex models often lack inherent transparency and interpretability, acting as "black boxes" that impede…

Atmospheric and Oceanic Physics · Physics 2024-03-29 Ruyi Yang , Jingyu Hu , Zihao Li , Jianli Mu , Tingzhao Yu , Jiangjiang Xia , Xuhong Li , Aritra Dasgupta , Haoyi Xiong

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for…

Quantitative Methods · Quantitative Biology 2026-04-09 Jueon Park , Wonjune Jang , Chanhwi Kim , Yein Park , Jaewoo Kang

Despite the superior performance in modeling complex patterns to address challenging problems, the black-box nature of Deep Learning (DL) methods impose limitations to their application in real-world critical domains. The lack of a smooth…

Reward models (RMs) are a crucial component in the alignment of large language models' (LLMs) outputs with human values. RMs approximate human preferences over possible LLM responses to the same prompt by predicting and comparing reward…

Machine Learning · Computer Science 2025-02-27 Junqi Jiang , Tom Bewley , Saumitra Mishra , Freddy Lecue , Manuela Veloso

While the uptake of data-driven approaches for materials science and chemistry is at an exciting, early stage, to realise the true potential of machine learning models for successful scientific discovery, they must have qualities beyond…

Materials Science · Physics 2022-06-28 Felipe Oviedo , Juan Lavista Ferres , Tonio Buonassisi , Keith Butler

Research Replication Prediction (RRP) is the task of predicting whether a published research result can be replicated or not. Building an interpretable neural text classifier for RRP promotes the understanding of why a research paper is…

Computation and Language · Computer Science 2022-03-29 Tianyi Luo , Rui Meng , Xin Eric Wang , Yang Liu