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We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…

Quantitative Methods · Quantitative Biology 2007-05-23 Christopher R. Myers , Ryan N. Gutenkunst , James. P. Sethna

Federated Learning (FL) has emerged as a promising technique for edge devices to collaboratively learn a shared machine learning model while keeping training data locally on the device, thereby removing the need to store and access the full…

Machine Learning · Computer Science 2022-07-19 Konstantin Burlachenko , Samuel Horváth , Peter Richtárik

While deep learning (DL)-based methods have achieved remarkable success in continuous wireless resource allocation, efficient solutions for problems involving discrete variables remain challenging. This is primarily due to the zero-gradient…

Machine Learning · Computer Science 2026-03-23 Yikun Wang , Yang Li , Yik-Chung Wu , Rui Zhang

In this work, we present a general purpose deep neural network package for representing energies, forces, dipole moments, and polarizabilities of atomistic systems. This so-called recursively embedded atom neural network model takes both…

Chemical Physics · Physics 2022-04-06 Yaolong Zhang , Junfan Xia , Bin Jiang

Microstructure plays a critical role in determining the macroscopic properties of materials, with applications spanning alloy design, MEMS devices, and tissue engineering, among many others. Computational frameworks have been developed to…

Computational Engineering, Finance, and Science · Computer Science 2024-09-24 Nikita Kartashov , Nikolaos N. Vlassis

Large language models (LLMs) are useful in many NLP tasks and become more capable with size, with the best open-source models having over 50 billion parameters. However, using these 50B+ models requires high-end hardware, making them…

Speculative decoding (SD) has become a standard technique for accelerating LLM inference without sacrificing output quality. Recent advances in speculative decoding have shifted from sequential chain-based drafting to tree-structured…

Computation and Language · Computer Science 2026-01-13 Tianyu Liu , Qitan Lv , Yuhao Shen , Xiao Sun , Xiaoyan Sun

Over the past decade, machine learning model complexity has grown at an extraordinary rate, as has the scale of the systems training such large models. However there is an alarmingly low hardware utilization (5-20%) in large scale AI…

Hardware Architecture · Computer Science 2022-11-14 Newsha Ardalani , Saptadeep Pal , Puneet Gupta

Developing, scaling, and deploying modern Machine Learning solutions remains challenging for small- and middle-sized enterprises (SMEs). This is due to a high entry barrier of building and maintaining a dedicated IT team as well as the…

Software Engineering · Computer Science 2021-05-11 Johannes Otterbach , Thomas Wollmann

Diffusion models have emerged as a prominent technique in generative modeling with neural networks, making their mark in tasks like text-to-image translation and super-resolution. In this tutorial, we provide a comprehensive guide to build…

Image and Video Processing · Electrical Eng. & Systems 2025-01-24 Harshith Bachimanchi , Giovanni Volpe

The yaglm package aims to make the broader ecosystem of modern generalized linear models accessible to data analysts and researchers. This ecosystem encompasses a range of loss functions (e.g. linear, logistic, quantile regression),…

Computation · Statistics 2021-10-13 Iain Carmichael , Thomas Keefe , Naomi Giertych , Jonathan P Williams

Modern software engineering deals with demanding problems that yield large and complex software. The area of Model-Driven Software Engineering tackles this issue by using models during the development process, but it does not address some…

Software Engineering · Computer Science 2020-04-27 Fernando Macías

Deep learning (DL) allows computer models to learn, visualize, optimize, refine, and predict data. To understand its present state, examining the most recent advancements and applications of deep learning across various domains is…

Deep learning frameworks such as TensorFlow and PyTorch provide a productive interface for expressing and training a deep neural network (DNN) model on a single device or using data parallelism. Still, they may not be flexible or efficient…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-04-20 Jinhui Yuan , Xinqi Li , Cheng Cheng , Juncheng Liu , Ran Guo , Shenghang Cai , Chi Yao , Fei Yang , Xiaodong Yi , Chuan Wu , Haoran Zhang , Jie Zhao

The rapid expansion of citizen science initiatives has led to a significant growth of biodiversity databases, and particularly presence-only (PO) observations. PO data are invaluable for understanding species distributions and their…

Machine Learning · Computer Science 2026-01-14 Maxime Ryckewaert , Diego Marcos , Christophe Botella , Maximilien Servajean , Pierre Bonnet , Alexis Joly

This paper focuses on a core task in computational sustainability and statistical ecology: species distribution modeling (SDM). In SDM, the occurrence pattern of a species on a landscape is predicted by environmental features based on…

Machine Learning · Computer Science 2021-02-19 Eugene Seo , Rebecca A. Hutchinson , Xiao Fu , Chelsea Li , Tyler A. Hallman , John Kilbride , W. Douglas Robinson

PiML (read $\pi$-ML, /`pai`em`el/) is an integrated and open-access Python toolbox for interpretable machine learning model development and model diagnostics. It is designed with machine learning workflows in both low-code and high-code…

Machine Learning · Computer Science 2023-12-21 Agus Sudjianto , Aijun Zhang , Zebin Yang , Yu Su , Ningzhou Zeng

FrOoDo is an easy-to-use and flexible framework for Out-of-Distribution detection tasks in digital pathology. It can be used with PyTorch classification and segmentation models, and its modular design allows for easy extension. The goal is…

Computer Vision and Pattern Recognition · Computer Science 2024-02-16 Jonathan Stieber , Moritz Fuchs , Anirban Mukhopadhyay

We present MADLens a python package for producing non-Gaussian lensing convergence maps at arbitrary source redshifts with unprecedented precision. MADLens is designed to achieve high accuracy while keeping computational costs as low as…

Cosmology and Nongalactic Astrophysics · Physics 2020-12-18 Vanessa Böhm , Yu Feng , Max E. Lee , Biwei Dai

Three-dimensional (3D) point cloud analysis has become central to applications ranging from autonomous driving and robotics to forestry and ecological monitoring. Although numerous deep learning methods have been proposed for point cloud…

Computer Vision and Pattern Recognition · Computer Science 2026-04-14 Said Ohamouddou , Hanaa El Afia , Abdellatif El Afia , Raddouane Chiheb