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The introduction of computational techniques to analyze chemical data has given rise to the analytical study of biological systems, known as "bioinformatics". One facet of bioinformatics is using machine learning (ML) technology to detect…

定量方法 · 定量生物学 2022-08-23 Tanish Jain , Praveen Kumar Pandian Shanmuganathan

Current pharmaceutical formulation development still strongly relies on the traditional trial-and-error approach by individual experiences of pharmaceutical scientists, which is laborious, time-consuming and costly. Recently, deep learning…

机器学习 · 计算机科学 2018-12-05 Yilong Yang , Zhuyifan Ye , Yan Su , Qianqian Zhao , Xiaoshan Li , Defang Ouyang

Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico…

定量方法 · 定量生物学 2022-04-07 Yan Ding , Xiaoqian Jiang , Yejin Kim

Accurate prediction of blood-brain barrier permeability (BBBP) is essential for central nervous system (CNS) drug development. While graph neural networks (GNNs) have advanced molecular property prediction, they often rely on molecular…

机器学习 · 计算机科学 2025-12-09 Trung Nguyen , Md Masud Rana , Farjana Tasnim Mukta , Chang-Guo Zhan , Duc Duy Nguyen

The blood-brain barrier (BBB) serves as a protective barrier that separates the brain from the circulatory system, regulating the passage of substances into the central nervous system. Assessing the BBB permeability of potential drugs is…

定量方法 · 定量生物学 2024-09-10 Shivesh Prakash

Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…

机器学习 · 计算机科学 2026-01-01 Pascal Passigan , Kevin Zhu , Angelina Ning

The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without…

机器学习 · 计算机科学 2020-12-22 QHwan Kim , Joon-Hyuk Ko , Sunghoon Kim , Nojun Park , Wonho Jhe

Machine learning accelerates molecular property prediction, yet state-of-the-art Large Language Models and Graph Neural Networks operate as black boxes. In drug discovery, where safety is critical, this opacity risks masking false…

机器学习 · 计算机科学 2026-03-03 Oscar Rivera , Ziqing Wang , Matthieu Dagommer , Abhishek Pandey , Kaize Ding

The rapid evolution of machine learning (ML) has led to the widespread adoption of complex "black box" models, such as deep neural networks and ensemble methods. These models exhibit exceptional predictive performance, making them…

机器学习 · 计算机科学 2025-03-28 Moncef Garouani , Josiane Mothe , Ayah Barhrhouj , Julien Aligon

Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vision and natural language processing, its development in…

计算物理 · 物理学 2021-03-19 Jun Zhang , Yao-Kun Lei , Zhen Zhang , Junhan Chang , Maodong Li , Xu Han , Lijiang Yang , Yi Isaac Yang , Yi Qin Gao

Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields including protein structural modeling. Protein structural modeling, such as predicting…

生物大分子 · 定量生物学 2020-07-17 Wenhao Gao , Sai Pooja Mahajan , Jeremias Sulam , Jeffrey J. Gray

Deep learning (DL) models have been popular due to their ability to learn directly from the raw data in an end-to-end paradigm, alleviating the concern of a separate error-prone feature extraction phase. Recent DL-based neuroimaging studies…

机器学习 · 计算机科学 2023-07-20 Md. Mahfuzur Rahman , Vince D. Calhoun , Sergey M. Plis

We present a perspective on molecular machine learning (ML) in the field of chemical process engineering. Recently, molecular ML has demonstrated great potential in (i) providing highly accurate predictions for properties of pure components…

化学物理 · 物理学 2025-09-01 Jan G. Rittig , Manuel Dahmen , Martin Grohe , Philippe Schwaller , Alexander Mitsos

Deep learning models are favored in many research and industry areas and have reached the accuracy of approximating or even surpassing human level. However they've long been considered by researchers as black-box models for their…

机器学习 · 计算机科学 2020-10-16 Xiaojian Wang , Jingyuan Wang , Ke Tang

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…

机器学习 · 计算机科学 2020-02-10 Paul Maragakis , Hunter Nisonoff , Brian Cole , David E. Shaw

In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…

生物大分子 · 定量生物学 2020-03-31 Marta M. Stepniewska-Dziubinska , Piotr Zielenkiewicz , Pawel Siedlecki

Magnetic Resonance Imaging (MRI) of the brain has benefited from deep learning (DL) to alleviate the burden on radiologists and MR technologists, and improve throughput. The easy accessibility of DL tools have resulted in the rapid increase…

图像与视频处理 · 电气工程与系统科学 2023-01-04 Kunal Aggarwal , Marina Manso Jimeno , Keerthi Sravan Ravi , Gilberto Gonzalez , Sairam Geethanath

Branch prediction is an architectural feature that speeds up the execution of branch instruction on pipeline processors and reduces the cost of branching. Recent advancements of Deep Learning (DL) in the post Moore's Law era is accelerating…

硬件体系结构 · 计算机科学 2022-01-03 Rinu Joseph

Diagnosis prediction is a critical task in healthcare, where timely and accurate identification of medical conditions can significantly impact patient outcomes. Traditional machine learning and deep learning models have achieved notable…

机器学习 · 计算机科学 2025-01-09 Qiuhao Lu , Rui Li , Elham Sagheb , Andrew Wen , Jinlian Wang , Liwei Wang , Jungwei W. Fan , Hongfang Liu

Machine learning (ML) is a promising approach for predicting small molecule properties in drug discovery. Here, we provide a comprehensive overview of various ML methods introduced for this purpose in recent years. We review a wide range of…

生物大分子 · 定量生物学 2023-08-25 Nikolai Schapin , Maciej Majewski , Alejandro Varela , Carlos Arroniz , Gianni De Fabritiis
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