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The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…

Quantitative Methods · Quantitative Biology 2025-10-03 Ekaterina Podplutova , Anastasia Vepreva , Olga A. Konovalova , Vladimir Vinogradov , Dmitrii O. Shkil , Andrei Dmitrenko

Learning vectorized embeddings is fundamental to many recommender systems for user-item matching. To enable efficient online inference, representation binarization, which embeds latent features into compact binary sequences, has recently…

Information Retrieval · Computer Science 2025-06-04 Yankai Chen , Yue Que , Xinni Zhang , Chen Ma , Irwin King

AI-driven molecular generation is reshaping drug discovery and materials design, yet the lack of protection mechanisms leaves AI-generated molecules vulnerable to unauthorized reuse and provenance ambiguity. Such limitation undermines both…

Machine Learning · Computer Science 2025-12-22 Runwen Hu , Peilin Chen , Keyan Ding , Shiqi Wang

Representation learning is an important step in the machine learning pipeline. Given the current biological sequencing data volume, learning an explicit representation is prohibitive due to the dimensionality of the resulting feature…

Machine Learning · Computer Science 2023-04-04 Sarwan Ali , Usama Sardar , Murray Patterson , Imdad Ullah Khan

While previous AI Scientist systems can generate novel findings, they often lack the focus to produce scientifically valuable contributions that address pressing human-defined challenges. We introduce DeepScientist, a system designed to…

Computation and Language · Computer Science 2025-10-01 Yixuan Weng , Minjun Zhu , Qiujie Xie , Qiyao Sun , Zhen Lin , Sifan Liu , Yue Zhang

Precision medicine is a paradigm shift in healthcare relying heavily on genomics data. However, the complexity of biological interactions, the large number of genes as well as the lack of comparisons on the analysis of data, remain a…

Manual annotation of medical images is a labor-intensive and time-consuming process, posing a significant bottleneck in the development and deployment of robust medical imaging AI systems. This paper introduces a novel hands-free Human-AI…

Image and Video Processing · Electrical Eng. & Systems 2025-07-29 Yizhe Zhang

Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities…

Image and Video Processing · Electrical Eng. & Systems 2021-06-09 Leonardo Rundo

The assessment of imaging biomarkers is critical for advancing precision medicine and improving disease characterization. Despite the availability of methods to derive disease heterogeneity metrics in imaging studies, a robust framework for…

Dermatological conditions affect 1.9 billion people globally, yet accurate diagnosis remains challenging due to limited specialist availability and complex clinical presentations. Family history significantly influences skin disease…

Computer Vision and Pattern Recognition · Computer Science 2026-03-03 Satya Narayana Panda , Vaishnavi Kukkala , Spandana Iyer

Deep learning has shown its human-level performance in various applications. However, current deep learning models are characterised by catastrophic forgetting of old knowledge when learning new classes. This poses a challenge particularly…

Machine Learning · Computer Science 2022-04-29 Yang Yang , Zhiying Cui , Junjie Xu , Changhong Zhong , Wei-Shi Zheng , Ruixuan Wang

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

Computation and Language · Computer Science 2024-07-01 Chen Tang , Bohao Yang , Kun Zhao , Bo Lv , Chenghao Xiao , Frank Guerin , Chenghua Lin

Sparked by innovations in generative artificial intelligence (AI), the field of protein design has undergone a paradigm shift with an explosion of new models for optimizing existing enzymes or creating them from scratch. After more than one…

Biomolecules · Quantitative Biology 2026-02-04 Lasse Middendorf , Noelia Ferruz

A ubiquitous challenge in machine learning is the problem of domain generalisation. This can exacerbate bias against groups or labels that are underrepresented in the datasets used for model development. Model bias can lead to unintended…

The extraordinary ability of generative models to generate photographic images has intensified concerns about the spread of disinformation, thereby leading to the demand for detectors capable of distinguishing between AI-generated fake…

Computer Vision and Pattern Recognition · Computer Science 2023-06-27 Mingjian Zhu , Hanting Chen , Qiangyu Yan , Xudong Huang , Guanyu Lin , Wei Li , Zhijun Tu , Hailin Hu , Jie Hu , Yunhe Wang

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that…

Computation and Language · Computer Science 2024-06-19 Minbyul Jeong , Jiwoong Sohn , Mujeen Sung , Jaewoo Kang

Gene-regulatory enhancers have been identified by many lines of evidence, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. To integrate these different approaches, we…

Genomics · Quantitative Biology 2015-06-17 Genevieve D. Erwin , Rebecca M. Truty , Dennis Kostka , Katherine S. Pollard , John A. Capra

A key obstacle in automated analytics and meta-learning is the inability to recognize when different datasets contain measurements of the same variable. Because provided attribute labels are often uninformative in practice, this task may be…

Machine Learning · Computer Science 2019-09-12 Jonas Mueller , Alex Smola

Data-driven science is an emerging paradigm where scientific discoveries depend on the execution of computational AI models against rich, discipline-specific datasets. With modern machine learning frameworks, anyone can develop and execute…

Machine Learning · Computer Science 2022-08-09 Seth Ockerman , John Wu , Christopher Stewart

The accelerating advancement of generative models has introduced new challenges for detecting AI-generated images, especially in real-world scenarios where novel generation techniques emerge rapidly. Existing learning paradigms are likely…

Computer Vision and Pattern Recognition · Computer Science 2026-03-30 Qinghui He , Haifeng Zhang , Xiuli Bi , Bo Liu , Chi-Man Pun , Bin Xiao