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This chapter describes gene expression analysis by Singular Value Decomposition (SVD), emphasizing initial characterization of the data. We describe SVD methods for visualization of gene expression data, representation of the data using a…

Biological Physics · Physics 2007-05-23 Michael E. Wall , Andreas Rechtsteiner , Luis M. Rocha

We present a thermodynamic interpretation of the stationary behavior of stochastic gradient descent (SGD) under fixed learning rates (LRs) in neural network training. We show that SGD implicitly minimizes a free energy function $F=U-TS$,…

Machine Learning · Computer Science 2025-05-30 Ildus Sadrtdinov , Ivan Klimov , Ekaterina Lobacheva , Dmitry Vetrov

Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…

Chemical Physics · Physics 2020-01-08 Ivan S. Novikov , Alexander V. Shapeev , Yury V. Suleimanov

In this paper, we propose a novel Convolutional Neural Network (CNN) approach for the classification of raw dry-EEG signals without any data pre-processing. To illustrate the effectiveness of our approach, we utilise the Steady State Visual…

Human-Computer Interaction · Computer Science 2019-01-23 Nik Khadijah Nik Aznan , Stephen Bonner , Jason D. Connolly , Noura Al Moubayed , Toby P. Breckon

We present a novel optimization-based decoding algorithm for LDPC codes that is suitable for hardware architectures specialized to feed-forward neural networks. The algorithm is based on the projected gradient descent algorithm with a…

Information Theory · Computer Science 2019-01-16 Tadashi Wadayama , Satoshi Takabe

In this paper we propose an efficient deep learning encoder-decoder network for performing Harmonic-Percussive Source Separation (HPSS). It is shown that we are able to greatly reduce the number of model trainable parameters by using a…

Sound · Computer Science 2019-07-31 Carlos Lordelo , Emmanouil Benetos , Simon Dixon , Sven Ahlbäck

We propose a scheme to perform the variational principle directly on the coherent pair condensate (VDPC). The result is equivalent to that of the so-called variation after particle-number projection, but now the particle number is always…

Nuclear Theory · Physics 2019-01-09 L. Y. Jia

Canonical Polyadic (CP) tensor decomposition is a fundamental technique for analyzing high-dimensional tensor data. While the Alternating Least Squares (ALS) algorithm is widely used for computing CP decomposition due to its simplicity and…

Methodology · Statistics 2025-05-30 Runshi Tang , Julien Chhor , Olga Klopp , Anru R. Zhang

Projected Gradient Descent (PGD) under the $L_\infty$ ball has become one of the defacto methods used in adversarial robustness evaluation for computer vision (CV) due to its reliability and efficacy, making a strong and easy-to-implement…

Computer Vision and Pattern Recognition · Computer Science 2025-03-26 Philip Doldo , Derek Everett , Amol Khanna , Andre T Nguyen , Edward Raff

We present a convolutional neural network (CNN) based solution for modeling physically plausible spatially varying surface reflectance functions (SVBRDF) from a single photograph of a planar material sample under unknown natural…

Graphics · Computer Science 2018-09-05 Xiao Li , Yue Dong , Pieter Peers , Xin Tong

In this paper, we propose a computationally efficient iterative algorithm for proper orthogonal decomposition (POD) using random sampling based techniques. In this algorithm, additional rows and columns are sampled and a merging technique…

Numerical Analysis · Mathematics 2020-11-23 Charumathi V , M. Ramakrishna , Vinita Vasudevan

In this paper, we propose a computationally efficient iterative algorithm for proper orthogonal decomposition (POD) using random sampling based techniques. In this algorithm, additional rows and columns are sampled and a merging technique…

Numerical Analysis · Computer Science 2021-07-07 V. Charumathi , M. Ramakrishna , Vinita Vasudevan

Physics-informed Neural Networks (PINNs) have been widely used to obtain accurate neural surrogates for a system of Partial Differential Equations (PDE). One of the major limitations of PINNs is that the neural solutions are challenging to…

Machine Learning · Computer Science 2023-03-14 Ritam Majumdar , Vishal Jadhav , Anirudh Deodhar , Shirish Karande , Lovekesh Vig , Venkataramana Runkana

In the present work, a method is proposed in order to compute a Canonical Polyadic (CP) approximation of a given tensor. It is based on a greedy method and an adaptation of the TT-SVD method. The proposed approach can be straightforwardly…

Numerical Analysis · Mathematics 2020-11-20 Virginie Ehrlacher , Maria Fuente Ruiz , Damiano Lombardi

This study proposes an acceleration technique for the computational challenges in extending the variational deterministic-particle-based scheme (VDS) [Bao et al., Journal of Computational Physics 522 (2025) 113589] to 3D complex fluid…

Computational Physics · Physics 2026-03-16 L. Fang , X. Bao , Z. Song , S. Xu , H. Huang

Singular value decomposition (SVD) is the mathematical basis of principal component analysis (PCA). Together, SVD and PCA are one of the most widely used mathematical formalism/decomposition in machine learning, data mining, pattern…

Machine Learning · Computer Science 2018-04-17 Shuai Zheng , Chris Ding , Feiping Nie

De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…

Machine Learning · Computer Science 2018-12-06 Yanjun Li , Hengtong Kang , Ketian Ye , Shuyu Yin , Xiaolin Li

This paper investigates the fundamental coupling between loads and locational marginal prices (LMPs) in security-constrained economic dispatch (SCED). Theoretical analysis based on multi-parametric programming theory points out the unique…

Systems and Control · Computer Science 2016-03-24 Xinbo Geng , Le Xie

In this paper, we present a simple and parameter-efficient drop-in module for one-stage object detectors like SSD when learning from scratch (i.e., without pre-trained models). We call our module GFR (Gated Feature Reuse), which exhibits…

Computer Vision and Pattern Recognition · Computer Science 2019-07-09 Zhiqiang Shen , Honghui Shi , Jiahui Yu , Hai Phan , Rogerio Feris , Liangliang Cao , Ding Liu , Xinchao Wang , Thomas Huang , Marios Savvides

This paper is the second in a two-part exposition on {\it surface-directed spinodal decomposition} (SDSD), i.e., the interplay of kinetics of wetting and phase separation at a surface which is wetted by one of the components of a binary…

Statistical Mechanics · Physics 2020-08-25 Prasenjit Das , Prabhat K. Jaiswal , Sanjay Puri
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