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Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…

Genomics · Quantitative Biology 2024-10-10 Alex M. Tseng , Gokcen Eraslan , Tommaso Biancalani , Gabriele Scalia

Neural networks are one of the most popularly used methods in machine learning and artificial intelligence nowadays. Due to the universal approximation theorem (Hornik et al. (1989)), a neural network with one hidden layer can approximate…

Statistics Theory · Mathematics 2019-09-18 Xiaoxi Shen , Chang Jiang , Lyudmila Sakhanenko , Qing Lu

Recent years have witnessed strong empirical performance of over-parameterized neural networks on various tasks and many advances in the theory, e.g. the universal approximation and provable convergence to global minimum. In this paper, we…

Machine Learning · Statistics 2021-01-26 Shiyun Xu , Zhiqi Bu

Link prediction plays an important role in network analysis and applications. Recently, approaches for link prediction have evolved from traditional similarity-based algorithms into embedding-based algorithms. However, most existing…

Social and Information Networks · Computer Science 2020-08-11 Lei Wang , Jing Ren , Bo Xu , Jianxin Li , Wei Luo , Feng Xia

Network neuroscience is the emerging discipline concerned with investigating the complex patterns of interconnections found in neural systems, and to identify principles with which to understand them. Within this discipline, one…

Neurons and Cognition · Quantitative Biology 2017-08-29 Richard F. Betzel , Danielle S. Bassett

We introduce a pruning algorithm that provably sparsifies the parameters of a trained model in a way that approximately preserves the model's predictive accuracy. Our algorithm uses a small batch of input points to construct a data-informed…

Machine Learning · Computer Science 2021-03-16 Cenk Baykal , Lucas Liebenwein , Igor Gilitschenski , Dan Feldman , Daniela Rus

Prototype-based interpretability methods provide intuitive explanations of model prediction by comparing samples to a reference set of memorized exemplars or typical representatives in terms of similarity. In the field of sequential data…

Machine Learning · Computer Science 2023-03-20 Yifei Zhang , Neng Gao , Cunqing Ma

The willingness to trust predictions formulated by automatic algorithms is key in a vast number of domains. However, a vast number of deep architectures are only able to formulate predictions without an associated uncertainty. In this…

Image and Video Processing · Electrical Eng. & Systems 2022-09-28 Matteo Ferrante , Tommaso Boccato , Nicola Toschi

Neural networks trained on biased datasets tend to inadvertently learn spurious correlations, hindering generalization. We formally prove that (1) samples that exhibit spurious correlations lie on a lower rank manifold relative to the ones…

Machine Learning · Computer Science 2024-11-07 Silpa Vadakkeeveetil Sreelatha , Adarsh Kappiyath , Abhra Chaudhuri , Anjan Dutta

Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…

Molecular Networks · Quantitative Biology 2007-05-23 Manuel Middendorf , Etay Ziv , Carter Adams , Jen Hom , Robin Koytcheff , Chaya Levovitz , Gregory Woods , Linda Chen , Chris Wiggins

Machine Learning algorithms are increasingly being used in recent years due to their flexibility in model fitting and increased predictive performance. However, the complexity of the models makes them hard for the data analyst to interpret…

Machine Learning · Statistics 2018-06-07 Joel Vaughan , Agus Sudjianto , Erind Brahimi , Jie Chen , Vijayan N. Nair

We consider the problem of selective prediction (also known as reject option) in deep neural networks, and introduce SelectiveNet, a deep neural architecture with an integrated reject option. Existing rejection mechanisms are based mostly…

Machine Learning · Computer Science 2019-06-28 Yonatan Geifman , Ran El-Yaniv

The predictive power of neural networks often costs model interpretability. Several techniques have been developed for explaining model outputs in terms of input features; however, it is difficult to translate such interpretations into…

Machine Learning · Computer Science 2017-08-17 Benjamin J. Lengerich , Sandeep Konam , Eric P. Xing , Stephanie Rosenthal , Manuela Veloso

Neural networks are becoming an increasingly important tool in applications. However, neural networks are not widely used in statistical genetics. In this paper, we propose a new neural networks method called expectile neural networks. When…

Statistics Theory · Mathematics 2020-11-04 Jinghang Lin , Xiaoxi Shen , Qing Lu

When artificial neural networks have demonstrated exceptional practical success in a variety of domains, investigations into their theoretical characteristics, such as their approximation power, statistical properties, and generalization…

Machine Learning · Statistics 2023-10-06 Shijin Gong , Xinyu Zhang

Ensembling a neural network is a widely recognized approach to enhance model performance, estimate uncertainty, and improve robustness in deep supervised learning. However, deep ensembles often come with high computational costs and memory…

Deep learning and convolutional neural networks in particular are powerful and promising tools for cosmological analysis of large-scale structure surveys. They are already providing similar performance to classical analysis methods using…

Cosmology and Nongalactic Astrophysics · Physics 2026-05-06 Gaspard Aymerich , Tomasz Kacprzak , Alexandre Refregier

Physical and functional constraints on biological networks lead to complex topological patterns across multiple scales in their organization. A particular type of higher-order network feature that has received considerable interest is…

Quantitative Methods · Quantitative Biology 2024-10-15 Alexis Bénichou , Jean-Baptiste Masson , Christian L. Vestergaard

Modeling uncertainty in deep neural networks, despite recent important advances, is still an open problem. Bayesian neural networks are a powerful solution, where the prior over network weights is a design choice, often a normal…

Machine Learning · Statistics 2019-10-29 Raanan Y. Rohekar , Yaniv Gurwicz , Shami Nisimov , Gal Novik

In this work, we build a generic architecture of Convolutional Neural Networks to discover empirical properties of neural networks. Our first contribution is to introduce a state-of-the-art framework that depends upon few hyper parameters…

Computer Vision and Pattern Recognition · Computer Science 2017-03-07 Edouard Oyallon
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