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A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
Effective trajectory stitching for long-horizon planning is a significant challenge in robotic decision-making. While diffusion models have shown promise in planning, they are limited to solving tasks similar to those seen in their training…
Recent inverse problem solvers that leverage generative diffusion priors have garnered significant attention due to their exceptional quality. However, adaptation of the prior is necessary when there exists a discrepancy between the…
The de novo design of ligand-binding proteins with tailored functions is essential for advancing biotechnology and molecular medicine, yet existing AI approaches are limited by scarce protein-ligand complex data. To circumvent this data…
Training-free conditional diffusion provides a flexible alternative to task-specific conditional model training, but existing samplers often allocate computation inefficiently: independent guided trajectories can vary widely in quality, and…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
Diversity control is an important task to alleviate bias amplification and filter bubble problems. The desired degree of diversity may fluctuate based on users' daily moods or business strategies. However, existing methods for controlling…
Discrete diffusion models (DMs) have achieved strong performance in language and other discrete domains, offering a compelling alternative to autoregressive modeling. Yet this performance typically depends on large training datasets,…
Large Language Models increasingly rely on distributed techniques for their training and inference. These techniques require communication across devices which can reduce scaling efficiency as the number of devices increases. While some…
Deep neural networks (DNNs) offer significant promise for improving breast cancer diagnosis in medical imaging. However, these models are highly susceptible to adversarial attacks--small, imperceptible changes that can mislead…
Trajectory generation for mobile robots in unstructured environments faces a critical dilemma: balancing kinematic smoothness for safe execution with terminal precision for fine-grained tasks. Existing generative planners often struggle…
Accurate identification of drug-target interactions (DTI) remains a central challenge in computational pharmacology, where sequence-based methods offer scalability. This work introduces a sequence-based drug-target interaction framework…
This paper introduces a diffusion-based planner for leader--follower formation control in cluttered environments. The diffusion policy is used to generate the trajectory of the midpoint of two leaders as a rigid bar in the plane, thereby…
Predicting drug-target affinity is fundamental to virtual screening and lead optimization. However, existing deep models often suffer from representation collapse in stringent cold-start regimes, where the scarcity of labels and domain…
Structure-based drug design (SBDD) focuses on designing small-molecule ligands that bind to specific protein pockets. Computational methods are integral in modern SBDD workflows and often make use of virtual screening methods via docking or…
We present TerraBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26-fold faster inference than state-of-the-art methods while improving affinity prediction accuracy by $\sim$20\%. Current…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
3D structure modeling is essential across scales, enabling applications from fluid simulation and 3D reconstruction to protein folding and molecular docking. Yet, despite shared 3D spatial patterns, current approaches remain fragmented,…
Unlike discriminative approaches in autonomous driving that predict a fixed set of candidate trajectories of the ego vehicle, generative methods, such as diffusion models, learn the underlying distribution of future motion, enabling more…
Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. However, most AI-driven approaches neglect the importance of…