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Generation of molecules with desired chemical and biological properties such as high drug-likeness, high binding affinity to target proteins, is critical for drug discovery. In this paper, we propose a probabilistic generative model to…

Biomolecules · Quantitative Biology 2023-07-12 Deqian Kong , Bo Pang , Tian Han , Ying Nian Wu

Autoregressive models (ARMs) currently constitute the dominant paradigm for large language models (LLMs). Energy-based models (EBMs) represent another class of models, which have historically been less prevalent in LLM development, yet…

Machine Learning · Computer Science 2026-05-26 Mathieu Blondel , Michael E. Sander , Germain Vivier-Ardisson , Tianlin Liu , Vincent Roulet

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

In this manuscript, we consider the problem of learning a flow or diffusion-based generative model parametrized by a two-layer auto-encoder, trained with online stochastic gradient descent, on a high-dimensional target density with an…

Machine Learning · Computer Science 2025-11-11 Hugo Cui , Cengiz Pehlevan , Yue M. Lu

Social networks as a representation of relational data, often possess multiple types of dependency structures at the same time. There could be clustering (beyond homophily) at a macro level as well as transitivity (a friend's friend is more…

Methodology · Statistics 2017-04-04 Ming Cao

Understanding the structure of real data is paramount in advancing modern deep-learning methodologies. Natural data such as images are believed to be composed of features organized in a hierarchical and combinatorial manner, which neural…

Machine Learning · Statistics 2024-12-25 Antonio Sclocchi , Alessandro Favero , Matthieu Wyart

Inference-time computation techniques, analogous to human System 2 Thinking, have recently become popular for improving model performances. However, most existing approaches suffer from several limitations: they are modality-specific (e.g.,…

This paper investigates energy guidance in generative modeling, where the target distribution is defined as $q(\mathbf x) \propto p(\mathbf x)\exp(-\beta \mathcal E(\mathbf x))$, with $p(\mathbf x)$ being the data distribution and $\mathcal…

Machine Learning · Computer Science 2025-03-10 Shiyuan Zhang , Weitong Zhang , Quanquan Gu

Neural language models can be successfully trained on source code, leading to applications such as code completion. However, their versatile autoregressive self-supervision objective overlooks important global sequence-level features that…

Machine Learning · Computer Science 2021-06-10 Tomasz Korbak , Hady Elsahar , Marc Dymetman , Germán Kruszewski

Maximum likelihood estimation is widely used in training Energy-based models (EBMs). Training requires samples from an unnormalized distribution, which is usually intractable, and in practice, these are obtained by MCMC algorithms such as…

Machine Learning · Computer Science 2021-04-23 Zhisheng Xiao , Qing Yan , Yali Amit

Since their introduction, diffusion models have quickly become the prevailing approach to generative modeling in many domains. They can be interpreted as learning the gradients of a time-varying sequence of log-probability density…

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

Despite the growing interest in diffusion models, gaining a deep understanding of the model class remains an elusive endeavour, particularly for the uninitiated in non-equilibrium statistical physics. Thanks to the rapid rate of progress in…

Machine Learning · Computer Science 2025-05-23 Fabio De Sousa Ribeiro , Ben Glocker

The use of Variational Autoencoders in different Machine Learning tasks has drastically increased in the last years. They have been developed as denoising, clustering and generative tools, highlighting a large potential in a wide range of…

Machine Learning · Computer Science 2019-07-12 Helena Andrés-Terré , Pietro Lió

A conditional latent-diffusion based framework for solving the electromagnetic inverse scattering problem associated with microwave imaging is introduced. This generative machine-learning model explicitly mirrors the non-uniqueness of the…

Image and Video Processing · Electrical Eng. & Systems 2025-10-30 Shirin Chehelgami , Joe LoVetri , Vahab Khoshdel

Latent diffusion models (LDMs) power state-of-the-art high-resolution generative image models. LDMs learn the data distribution in the latent space of an autoencoder (AE) and produce images by mapping the generated latents into RGB image…

Computer Vision and Pattern Recognition · Computer Science 2025-01-22 Tariq Berrada , Pietro Astolfi , Melissa Hall , Marton Havasi , Yohann Benchetrit , Adriana Romero-Soriano , Karteek Alahari , Michal Drozdzal , Jakob Verbeek

Conventional diffusion models typically relies on a fixed forward process, which implicitly defines complex marginal distributions over latent variables. This can often complicate the reverse process' task in learning generative…

Machine Learning · Statistics 2025-06-10 Grigory Bartosh , Dmitry Vetrov , Christian A. Naesseth

Among likelihood-based approaches for deep generative modelling, variational autoencoders (VAEs) offer scalable amortized posterior inference and fast sampling. However, VAEs are also more and more outperformed by competing models such as…

Machine Learning · Computer Science 2021-07-01 Antoine Wehenkel , Gilles Louppe

Energy-based language models (ELMs) parameterize an unnormalized distribution for natural sentences and are radically different from popular autoregressive language models (ALMs). As an important application, ELMs have been successfully…

Computation and Language · Computer Science 2023-05-30 Hong Liu , Zhaobiao Lv , Zhijian Ou , Wenbo Zhao , Qing Xiao

Deep generative models have become ubiquitous due to their ability to learn and sample from complex distributions. Despite the proliferation of various frameworks, the relationships among these models remain largely unexplored, a gap that…

Machine Learning · Computer Science 2025-10-24 J. Quetzalcóatl Toledo-Marin , Anindita Maiti , Geoffrey C. Fox , Roger G. Melko