Related papers: PepEVOLVE: Position-Aware Dynamic Peptide Optimiza…

The development of Multimodal Large Language Models (MLLMs) has seen significant advancements with increasing demands in various fields (e.g., multimodal agents, embodied intelligence). While model-driven approaches attempt to enhance MLLMs…

A key advance in learning generative models is the use of amortized inference distributions that are jointly trained with the models. We find that existing training objectives for variational autoencoders can lead to inaccurate amortized…

Functional peptides have the potential to treat a variety of diseases. Their good therapeutic efficacy and low toxicity make them ideal therapeutic agents. Artificial intelligence-based computational strategies can help quickly identify new…

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely…

We study the learning dynamics of self-predictive learning for reinforcement learning, a family of algorithms that learn representations by minimizing the prediction error of their own future latent representations. Despite its recent…

Therapeutic peptides show promise in targeting previously undruggable binding sites, with recent advancements in deep generative models enabling full-atom peptide co-design for specific protein receptors. However, the critical role of…

Biologists frequently desire protein inhibitors for a variety of reasons, including use as research tools for understanding biological processes and application to societal problems in agriculture, healthcare, etc. Immunotherapy, for…

Practical networks for edge devices adopt shallow depth and small convolutional kernels to save memory and computational cost, which leads to a restricted receptive field. Conventional efficient learning methods focus on lightweight…

Deep learning has significantly advanced and accelerated de novo molecular generation. Generative networks, namely Variational Autoencoders (VAEs) can not only randomly generate new molecules, but also alter molecular structures to optimize…

Drug optimization has become increasingly crucial in light of fast-mutating virus strains and drug-resistant cancer cells. Nevertheless, it remains challenging as it necessitates retaining the beneficial properties of the original drug…

We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a…

In modular robotics, modules can be reconfigured to change the morphology of the robot, making it able to adapt for specific tasks. However, optimizing both the body and control is a difficult challenge due to the intricate relationship…

Auto-encoding Variational Bayes (AEVB) is a powerful and general algorithm for fitting latent variable models (a promising direction for unsupervised learning), and is well-known for training the Variational Auto-Encoder (VAE). In this…

A new adaptive hybrid optimization strategy, entitled squads, is proposed for complex inverse analysis of computationally intensive physical models. The new strategy is designed to be computationally efficient and robust in identification…

Training and inference efficiency of deep neural networks highly rely on the performance of tensor operators on hardware platforms. Manually optimizing tensor operators has limitations in terms of supporting new operators or hardware…

Prior work in multi-objective reinforcement learning typically uses linear reward scalarization with fixed weights, which provably fails to capture non-convex Pareto fronts and thus yields suboptimal results. This limitation becomes…

Probabilistic Manifold Decomposition (PMD)\cite{doi:10.1137/25M1738863}, developed in our earlier work, provides a nonlinear model reduction by embedding high-dimensional dynamics onto low-dimensional probabilistic manifolds. The PMD has…

Optimizing scientific computing algorithms for modern GPUs is a labor-intensive and iterative process involving repeated code modification, benchmarking, and tuning across complex hardware and software stacks. Recent work has explored large…

Deep Learning Reduced Order Models (ROMs) are becoming increasingly popular as surrogate models for parametric partial differential equations (PDEs) due to their ability to handle high-dimensional data, approximate highly nonlinear…

Large language models (LLMs) frequently refuse to respond to pseudo-malicious instructions: semantically harmless input queries triggering unnecessary LLM refusals due to conservative safety alignment, significantly impairing user…