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Restricted Boltzmann Machines (RBMs) are a class of generative neural network that are typically trained to maximize a log-likelihood objective function. We argue that likelihood-based training strategies may fail because the objective does…

Machine Learning · Statistics 2018-04-25 Charles K. Fisher , Aaron M. Smith , Jonathan R. Walsh

Retrosynthesis -- the process of identifying a set of reactants to synthesize a target molecule -- is of vital importance to material design and drug discovery. Existing machine learning approaches based on language models and graph neural…

Chemical Physics · Physics 2021-12-10 Ruoxi Sun , Hanjun Dai , Li Li , Steven Kearnes , Bo Dai

Learning probabilistic models that can estimate the density of a given set of samples, and generate samples from that density, is one of the fundamental challenges in unsupervised machine learning. We introduce a new generative model based…

Machine Learning · Computer Science 2020-06-11 Siavash A. Bigdeli , Geng Lin , Tiziano Portenier , L. Andrea Dunbar , Matthias Zwicker

Latent-variable energy-based models (LVEBMs) assign a single normalized energy to joint pairs of observed data and latent variables, offering expressive generative modeling while capturing hidden structure. We recast maximum-likelihood…

Machine Learning · Computer Science 2025-10-20 Shiqin Tang , Shuxin Zhuang , Rong Feng , Runsheng Yu , Hongzong Li , Youzhi Zhang

Efficient sampling from the Boltzmann distribution given its energy function is a key challenge for modeling complex physical systems such as molecules. Boltzmann Generators address this problem by leveraging continuous normalizing flows to…

Machine Learning · Computer Science 2025-10-17 Rishal Aggarwal , Jacky Chen , Nicholas M. Boffi , David Ryan Koes

We focus on the problem of efficient sampling and learning of probability densities by incorporating symmetries in probabilistic models. We first introduce Equivariant Stein Variational Gradient Descent algorithm -- an equivariant sampling…

Machine Learning · Computer Science 2021-07-30 Priyank Jaini , Lars Holdijk , Max Welling

Probabilistic graphical models (PGMs) are widely used to discover latent structure in data, but their success hinges on selecting an appropriate model design. In practice, model specification is difficult and often requires iterative…

Machine Learning · Computer Science 2026-04-08 Kevin Zhang , Yixin Wang

Markov chains are simple yet powerful mathematical structures to model temporally dependent processes. They generally assume stationary data, i.e., fixed transition probabilities between observations/states. However, live, real-world…

Machine Learning · Computer Science 2024-11-27 Kutalmış Coşkun , Borahan Tümer , Bjarne C. Hiller , Martin Becker

Score matching (SM) provides a compelling approach to learn energy-based models (EBMs) by avoiding the calculation of partition function. However, it remains largely open to learn energy-based latent variable models (EBLVMs), except some…

Machine Learning · Computer Science 2020-10-19 Fan Bao , Chongxuan Li , Kun Xu , Hang Su , Jun Zhu , Bo Zhang

The ensemble average of physical properties of molecules is closely related to the distribution of molecular conformations, and sampling such distributions is a fundamental challenge in physics and chemistry. Traditional methods like…

Machine Learning · Computer Science 2025-08-06 Liya Guo , Zun Wang , Chang Liu , Junzhe Li , Pipi Hu , Yi Zhu

Bayesian Neural Networks (BNNs) offer a principled and natural framework for proper uncertainty quantification in the context of deep learning. They address the typical challenges associated with conventional deep learning methods, such as…

Computation · Statistics 2024-11-13 Zahra Moslemi , Yang Meng , Shiwei Lan , Babak Shahbaba

Extreme learning machine (ELM) is an extremely fast learning method and has a powerful performance for pattern recognition tasks proven by enormous researches and engineers. However, its good generalization ability is built on large numbers…

Machine Learning · Computer Science 2015-02-05 Wentao Zhu , Jun Miao , Laiyun Qing

Ensemble methods are known for enhancing the accuracy and robustness of machine learning models by combining multiple base learners. However, standard approaches like greedy or random ensembling often fall short, as they assume a constant…

Machine Learning · Computer Science 2025-06-24 Sebastian Pineda Arango , Maciej Janowski , Lennart Purucker , Arber Zela , Frank Hutter , Josif Grabocka

Latent space Energy-Based Models (EBMs), also known as energy-based priors, have drawn growing interests in the field of generative modeling due to its flexibility in the formulation and strong modeling power of the latent space. However,…

Machine Learning · Computer Science 2023-10-06 Peiyu Yu , Yaxuan Zhu , Sirui Xie , Xiaojian Ma , Ruiqi Gao , Song-Chun Zhu , Ying Nian Wu

Expectation-Maximization (EM) algorithm is a widely used iterative algorithm for computing (local) maximum likelihood estimate (MLE). It can be used in an extensive range of problems, including the clustering of data based on the Gaussian…

Machine Learning · Statistics 2023-03-28 Pierre Houdouin , Esa Ollila , Frederic Pascal

Spectral learning recently generated lots of excitement in machine learning, largely because it is the first known method to produce consistent estimates (under suitable conditions) for several latent variable models. In contrast, maximum…

Machine Learning · Computer Science 2014-06-19 Han Zhao , Pascal Poupart

Semi-supervised learning aims to learn prediction models from both labeled and unlabeled samples. There has been extensive research in this area. Among existing work, generative mixture models with Expectation-Maximization (EM) is a popular…

Machine Learning · Computer Science 2020-08-31 Wenchong He , Zhe Jiang

Unnormalized (or energy-based) models provide a flexible framework for capturing the characteristics of data with complex dependency structures. However, the application of standard Bayesian inference methods has been severely limited…

Methodology · Statistics 2026-03-11 Naruki Sonobe , Shonosuke Sugasawa , Daichi Mochihashi , Takeru Matsuda

Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…

Biomolecules · Quantitative Biology 2015-09-01 Giovanni Pinamonti , Sandro Bottaro , Cristian Micheletti , Giovanni Bussi

Global Autoregressive Models (GAMs) are a recent proposal [Parshakova et al., CoNLL 2019] for exploiting global properties of sequences for data-efficient learning of seq2seq models. In the first phase of training, an Energy-Based model…

Machine Learning · Computer Science 2019-12-19 Tetiana Parshakova , Jean-Marc Andreoli , Marc Dymetman