Related papers: Protein Counterfactuals via Diffusion-Guided Laten…

Predicting counterfactual distributions in complex dynamical systems is essential for scientific modeling and decision-making in domains such as public health and medicine. However, existing methods often rely on point estimates or purely…

We present a novel way to predict molecular conformers through a simple formulation that sidesteps many of the heuristics of prior works and achieves state of the art results by using the advantages of scale. By training a diffusion…

Counterfactual explanations is one of the post-hoc methods used to provide explainability to machine learning models that have been attracting attention in recent years. Most examples in the literature, address the problem of generating…

Ensuring fairness in machine learning predictions is a critical challenge, especially when models are deployed in sensitive domains such as credit scoring, healthcare, and criminal justice. While many fairness interventions rely on data…

The goal of machine learning is to develop predictors that generalize well to test data. Ideally, this is achieved by training on an almost infinitely large training data set that captures all variations in the data distribution. In…

Controllable diffusion generation often relies on various heuristics that are seemingly disconnected without a unified understanding. We bridge this gap with Diffusion Controller (DiffCon), a unified control-theoretic view that casts…

We develop DeepOPF as a Deep Neural Network (DNN) approach for solving security-constrained direct current optimal power flow (SC-DCOPF) problems, which are critical for reliable and cost-effective power system operation.DeepOPF is inspired…

Predicting the fitness impact of mutations is central to protein engineering but constrained by limited assays relative to the size of sequence space. Protein language models (pLMs) trained with masked language modeling (MLM) exhibit strong…

Effective protein representation learning is crucial for predicting protein functions. Traditional methods often pretrain protein language models on large, unlabeled amino acid sequences, followed by finetuning on labeled data. While…

Protein representation learning has primarily benefited from the remarkable development of language models (LMs). Accordingly, pre-trained protein models also suffer from a problem in LMs: a lack of factual knowledge. The recent solution…

Diffusion probabilistic models (DPMs) have become the state-of-the-art in high-quality image generation. However, DPMs have an arbitrary noisy latent space with no interpretable or controllable semantics. Although there has been significant…

Diffusion probabilistic models have generated high quality image synthesis recently. However, one pain point is the notorious inference to gradually obtain clear images with thousands of steps, which is time consuming compared to other…

The paradigm shift toward structure-driven molecule generation has been propelled by advances in deep generative models, such as variational auto-encoders and diffusion models. However, these generative models for molecular design remain…

In distributed model predictive control (MPC), the control input at each sampling time is computed by solving a large-scale optimal control problem (OCP) over a finite horizon using distributed algorithms. Typically, such algorithms require…

The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…

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…

Directed evolution of proteins has been the most effective method for protein engineering. However, a new paradigm is emerging, fusing the library generation and screening approaches of traditional directed evolution with computation…

Various machine-learning models, including deep neural network models, have already been developed to predict deleteriousness of missense (non-synonymous) mutations. Potential improvements to the current state of the art, however, may still…

MultiPUFFIN is a domain-informed multimodal foundation model for predicting thermophysical properties of small molecules, addressing a critical gap in chemical engineering, drug discovery, and materials science. Existing molecular…

Counterfactual explanations can be obtained by identifying the smallest change made to a feature vector to qualitatively influence a prediction; for example, from 'loan rejected' to 'awarded' or from 'high risk of cardiovascular disease' to…