Related papers: BindEnergyCraft: Casting Protein Structure Predict…

Energy-based models (EBMs) are a simple yet powerful framework for generative modeling. They are based on a trainable energy function which defines an associated Gibbs measure, and they can be trained and sampled from via well-established…

Development of scoring functions (SFs) used to predict protein-ligand binding energies requires high-quality 3D structures and binding assay data for training and testing their parameters. In this work, we show that one of the widely-used…

Motivated by the fact that forward and backward passes of a deep network naturally form symmetric mappings between input and output representations, we introduce a simple yet effective self-supervised vision model pretraining framework…

Existing methods, such as concept bottleneck models (CBMs), have been successful in providing concept-based interpretations for black-box deep learning models. They typically work by predicting concepts given the input and then predicting…

Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…

While deep learning-based classification is generally tackled using standardized approaches, a wide variety of techniques are employed for regression. In computer vision, one particularly popular such technique is that of confidence-based…

Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…

Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains to be challenging. We articulate a statistical inference…

Energy-based models (EBMs) have experienced a resurgence within machine learning in recent years, including as a promising alternative for probabilistic regression. However, energy-based regression requires a proposal distribution to be…

Latent space Energy-Based Models (EBMs), also known as energy-based priors, have drawn growing interests in generative modeling. Fueled by its flexibility in the formulation and strong modeling power of the latent space, recent works built…

Many applications of machine learning methods involve an iterative protocol in which data are collected, a model is trained, and then outputs of that model are used to choose what data to consider next. For example, one data-driven approach…

Purpose: Although recent deep energy-based generative models (EBMs) have shown encouraging results in many image generation tasks, how to take advantage of the self-adversarial cogitation in deep EBMs to boost the performance of Magnetic…

Recent advancements in machine learning techniques for protein folding motivate better results in its inverse problem -- protein design. In this work we introduce a new graph mimetic neural network, MimNet, and show that it is possible to…

Protein structure prediction remains to be an open problem in bioinformatics. There are two main categories of methods for protein structure prediction: Free Modeling (FM) and Template Based Modeling (TBM). Protein threading, belonging to…

Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests. There are two primary types of modeling algorithms, template-free modeling and template-based modeling. The…

Energy-based models (EBMs) provide a powerful and flexible way of learning a joint probability distribution over data by constructing an energy surface. This energy surface enables insight extraction and conditional sampling. We apply EBMs…

Predicting changes in binding free energy ($\Delta\Delta G$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $\Delta\Delta…

Learning embedding table plays a fundamental role in Click-through rate(CTR) prediction from the view of the model performance and memory usage. The embedding table is a two-dimensional tensor, with its axes indicating the number of feature…

Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to…

AlphaFold has transformed protein structure prediction, but emerging applications such as virtual ligand screening, proteome-wide folding, and de novo binder design demand predictions at a massive scale, where runtime and memory costs…