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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 sequence recognition (DSR) models receive increasing attention due to their superior application to various applications. Most DSR models use merely the target sequences as supervision without considering other related sequences,…

计算机视觉与模式识别 · 计算机科学 2023-06-01 Zhenghua Peng , Yu Luo , Tianshui Chen , Keke Xu , Shuangping Huang

Intelligent biological systems are characterized by their embodiment in a complex environment and the intimate interplay between their nervous systems and the nonlinear mechanical properties of their bodies. This coordination, in which the…

机器学习 · 计算机科学 2023-02-02 Deniz Oktay , Mehran Mirramezani , Eder Medina , Ryan P. Adams

We present a multimodal deep learning (MDL) framework for predicting physical properties of a 10-dimensional acrylic polymer composite material by merging physical attributes and chemical data. Our MDL model comprises four modules,…

软凝聚态物质 · 物理学 2023-11-28 Shun Muroga , Yasuaki Miki , Kenji Hata

Despite an artificial intelligence-assisted modeling of disordered crystals is a widely used and well-tried method of new materials design, the issues of its robustness, reliability, and stability are still not resolved and even not…

计算物理 · 物理学 2024-11-08 Fedor S. Avilov , Roman A. Eremin , Semen A. Budennyy , Innokentiy S. Humonen

In this research, we introduce an innovative three-network architecture that comprises an encoder-decoder framework with an attention mechanism. The architecture comprises a 1st-order-pre-trainer, a 2nd-order-improver, and a discriminator…

计算物理 · 物理学 2023-11-28 Jian-Nan Chen , Jun-Jie Zhang

The neural network techniques are developed for artificial sequences based on approximate models of proteins. We only encode the hydrophobicity of the amino acid side chains without attempting to model the secondary structure. We use our…

软凝聚态物质 · 物理学 2024-07-17 R. G. Reilly , M. -T. Kechadi , Yu. A. Kuznetsov , E. G. Timoshenko , K. A. Dawson

We present a learning-based planner that aims to robustly drive a vehicle by mimicking human drivers' driving behavior. We leverage a mid-to-mid approach that allows us to manipulate the input to our imitation learning network freely. With…

机器人学 · 计算机科学 2021-08-04 Jinyun Zhou , Rui Wang , Xu Liu , Yifei Jiang , Shu Jiang , Jiaming Tao , Jinghao Miao , Shiyu Song

Deep learning models have proven to be exceptionally useful in performing many machine learning tasks. However, for each new dataset, choosing an effective size and structure of the model can be a time-consuming process of trial and error.…

机器学习 · 计算机科学 2019-08-08 Roozbeh Yousefzadeh , Dianne P O'Leary

Machine learning has made important headway in helping to improve the treatment of quantum many-body systems. A domain of particular relevance are correlated inhomogeneous systems. What has been missing so far is a general, scalable…

量子物理 · 物理学 2026-02-10 Alex Blania , Sandro Herbig , Fabian Dechent , Evert van Nieuwenburg , Florian Marquardt

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

DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…

新兴技术 · 计算机科学 2022-05-12 Jasmine Quah , Omer Sella , Thomas Heinis

Meta-learning aims to develop algorithms that can learn from other learning algorithms to adapt to new and changing environments. This requires a model of how other learning algorithms operate and perform in different contexts, which is…

机器学习 · 计算机科学 2023-05-23 Yuwei Sun

We present a new method for scaling automatic configuration of computer networks. The key idea is to relax the computationally hard search problem of finding a configuration that satisfies a given specification into an approximate objective…

网络与互联网体系结构 · 计算机科学 2022-11-04 Luca Beurer-Kellner , Martin Vechev , Laurent Vanbever , Petar Veličković

Neural networks are being increasingly applied to control and decision-making for learning-enabled cyber-physical systems (LE-CPSs). They have shown promising performance without requiring the development of complex physical models;…

系统与控制 · 电气工程与系统科学 2021-03-10 Yixuan Wang , Chao Huang , Zhilu Wang , Shichao Xu , Zhaoran Wang , Qi Zhu

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet,…

定量方法 · 定量生物学 2023-04-10 Mingchen Li , Liqi Kang , Yi Xiong , Yu Guang Wang , Guisheng Fan , Pan Tan , Liang Hong

High-fidelity full-field micro-mechanical modeling of the non-linear path-dependent materials demands a substantial computational effort. Recent trends in the field incorporates data-driven Artificial Neural Networks (ANNs) as surrogate…

材料科学 · 物理学 2023-11-27 Hon Lam Cheung , Petter Uvdal , Mohsen Mirkhalaf

Dense embedding models have become critical for modern information retrieval, particularly in RAG pipelines, but their performance often degrades when applied to specialized corpora outside their pre-training distribution. To address thi we…

信息检索 · 计算机科学 2025-10-29 Nathan Paull

Polymer matrix composites exhibit remarkable lightweight and high strength properties that make them attractive for aerospace applications. Constituents' materials such as advanced polymers and fibers or fillers with their hierarchical…

材料科学 · 物理学 2021-12-03 Satyajit Mojumder , Lei Tao , Ying Li , Wing Kam Liu

For protein sequence datasets, unlabeled data has greatly outpaced labeled data due to the high cost of wet-lab characterization. Recent deep-learning approaches to protein prediction have shown that pre-training on unlabeled data can yield…

机器学习 · 计算机科学 2020-12-02 Pascal Sturmfels , Jesse Vig , Ali Madani , Nazneen Fatema Rajani