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Biological systems in nature have evolved for millions of years to adapt and survive the environment. Many features they developed can be inspirational and beneficial for solving technical problems in modern industries. This leads to a…

计算与语言 · 计算机科学 2022-12-27 Qihao Zhu , Xinyu Zhang , Jianxi Luo

We present a diffusion-based, generative model for conformer generation. Our model is focused on the reproduction of bonded structure and is constructed from the associated terms traditionally found in classical force fields to ensure a…

生物大分子 · 定量生物学 2024-03-18 David C. Williams , Neil Inala

Most of the existing deep learning-based sequential recommendation approaches utilize the recurrent neural network architecture or self-attention to model the sequential patterns and temporal influence among a user's historical behavior and…

信息检索 · 计算机科学 2022-01-17 Liwei Huang , Yutao Ma , Yanbo Liu , Bohong , Du , Shuliang Wang , Deyi Li

Large language models (LLMs) have shown promise in various natural language processing tasks, including their application to proteomics data to classify protein fragments. In this study, we curated a limited mass spectrometry dataset with…

We propose a new class of physics-informed neural networks, called Physics-Informed Generator-Encoder Adversarial Networks, to effectively address the challenges posed by forward, inverse, and mixed problems in stochastic differential…

机器学习 · 计算机科学 2023-11-06 Ruisong Gao , Min Yang , Jin Zhang

In computed tomography (CT), reducing the number of projection views is an effective strategy to lower radiation exposure and/or improve temporal resolution. However, this often results in severe aliasing artifacts and loss of structural…

图像与视频处理 · 电气工程与系统科学 2025-11-19 Changsheng Fang , Yongtong Liu , Bahareh Morovati , Shuo Han , Li Zhou , Hengyong Yu

Synthetic data generation in histopathology faces unique challenges: preserving tissue heterogeneity, capturing subtle morphological features, and scaling to unannotated datasets. We present a latent diffusion model that generates realistic…

计算机视觉与模式识别 · 计算机科学 2025-10-03 Saghir Alfasly , Wataru Uegami , MD Enamul Hoq , Ghazal Alabtah , H. R. Tizhoosh

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them…

Generative models have the potential to accelerate key steps in the discovery of novel molecular therapeutics and materials. Diffusion models have recently emerged as a powerful approach, excelling at unconditional sample generation and,…

生物大分子 · 定量生物学 2024-07-17 Leo Klarner , Tim G. J. Rudner , Garrett M. Morris , Charlotte M. Deane , Yee Whye Teh

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…

机器学习 · 计算机科学 2025-03-04 Mufan Qiu , Xinyu Hu , Fengwei Zhan , Sukwon Yun , Jie Peng , Ruichen Zhang , Bhavya Kailkhura , Jiekun Yang , Tianlong Chen

Temporal sentence grounding is a challenging task that aims to localize the moment spans relevant to a language description. Although recent DETR-based models have achieved notable progress by leveraging multiple learnable moment queries,…

计算机视觉与模式识别 · 计算机科学 2024-12-20 Xiaolong Sun , Liushuai Shi , Le Wang , Sanping Zhou , Kun Xia , Yabing Wang , Gang Hua

Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…

定量方法 · 定量生物学 2025-10-13 Berker Demirel , Marco Fumero , Theofanis Karaletsos , Francesco Locatello

Generative models hold great promise for accelerating material discovery but are often limited by their inflexible single-stage generative process in designing valid and diverse materials. To address this, we propose a two-stage generative…

机器学习 · 计算机科学 2026-03-05 Cong Liu , Chengyue Gong , Zhenyu Liu , Jiale Zhao , Yuxuan Zhang

Protein sequence generation via stochastic attention produces plausible family members from small alignments without training, but treats all stored sequences equally and cannot direct generation toward a functional subset of interest. We…

机器学习 · 计算机科学 2026-03-23 Jeffrey D. Varner

We propose a novel framework that combines deep generative time series models with decision theory for generating personalized treatment strategies. It leverages historical patient trajectory data to jointly learn the generation of…

Electronic health records (EHRs) are rich clinical data sources but complex repositories of patient data, spanning structured elements (demographics, vitals, lab results, codes), unstructured clinical notes and other modalities of data.…

Production forecast based on historical data provides essential value for developing hydrocarbon resources. Classic history matching workflow is often computationally intense and geometry-dependent. Analytical data-driven models like…

机器学习 · 计算机科学 2022-09-27 Wendi Liu , Michael J. Pyrcz

Positron Emission Tomography (PET) image reconstruction is inherently challenged by Poisson noise and physical degradation factors, which are further exacerbated in limited-angle acquisitions. While deep learning methods demonstrate…

计算机视觉与模式识别 · 计算机科学 2026-05-11 Rüveyda Yilmaz , Yuli Wu , Johannes Stegmaier , Volkmar Schulz

The increasing availability of unstructured clinical narratives in electronic health records (EHRs) has created new opportunities for automated disease characterization, cohort identification, and clinical decision support. However,…

计算与语言 · 计算机科学 2026-03-03 Fariba Afrin Irany , Sampson Akwafuo

Organic photovoltaic (OPV) materials offer a promising avenue toward cost-effective solar energy utilization. However, optimizing donor-acceptor (D-A) combinations to achieve high power conversion efficiency (PCE) remains a significant…

机器学习 · 计算机科学 2025-04-01 Jiangjie Qiu , Hou Hei Lam , Xiuyuan Hu , Wentao Li , Siwei Fu , Fankun Zeng , Hao Zhang , Xiaonan Wang
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