Jungyoon Lee

Majdi Hassan, Nikhil Shenoy, Jungyoon Lee et al.

Predicting low-energy molecular conformations given a molecular graph is an important but challenging task in computational drug discovery. Existing state-of-the-art approaches either resort to large scale transformer-based models that diffuse over conformer fields, or use computationally expensive methods to generate initial structures and diffuse over torsion angles. In this work, we introduce Equivariant Transformer Flow (ET-Flow). We showcase that a well-designed flow matching approach with equivariance and harmonic prior alleviates the need for complex internal geometry calculations and large architectures, contrary to the prevailing methods in the field. Our approach results in a straightforward and scalable method that directly operates on all-atom coordinates with minimal assumptions. With the advantages of equivariance and flow matching, ET-Flow significantly increases the precision and physical validity of the generated conformers, while being a lighter model and faster at inference. Code is available https://github.com/shenoynikhil/ETFlow.

Tara Akhound-Sadegh, Jungyoon Lee, Avishek Joey Bose et al.

Sampling efficiently from a target unnormalized probability density remains a core challenge, with relevance across countless high-impact scientific applications. A promising approach towards this challenge is the design of amortized samplers that borrow key ideas, such as probability path design, from state-of-the-art generative diffusion models. However, all existing diffusion-based samplers remain unable to draw samples from distributions at the scale of even simple molecular systems. In this paper, we propose Progressive Inference-Time Annealing (PITA), a novel framework to learn diffusion-based samplers that combines two complementary interpolation techniques: I.) Annealing of the Boltzmann distribution and II.) Diffusion smoothing. PITA trains a sequence of diffusion models from high to low temperatures by sequentially training each model at progressively higher temperatures, leveraging engineered easy access to samples of the temperature-annealed target density. In the subsequent step, PITA enables simulating the trained diffusion model to procure training samples at a lower temperature for the next diffusion model through inference-time annealing using a novel Feynman-Kac PDE combined with Sequential Monte Carlo. Empirically, PITA enables, for the first time, equilibrium sampling of N-body particle systems, Alanine Dipeptide, and tripeptides in Cartesian coordinates with dramatically lower energy function evaluations. Code available at: https://github.com/taraak/pita

Yipeng Zhang, Hafez Ghaemi, Jungyoon Lee et al.

Joint-embedding self-supervised learning (SSL), the key paradigm for unsupervised representation learning from visual data, learns from invariances between semantically-related data pairs. We study the one-to-many mapping problem in SSL, where each datum may be mapped to multiple valid targets. This arises when data pairs come from naturally occurring generative processes, e.g., successive video frames. We show that existing methods struggle to flexibly capture this conditional uncertainty. As a remedy, we introduce a latent variable to account for this uncertainty and derive a variational lower bound on the mutual information between paired embeddings. Our derivation yields a simple regularization term for standard SSL objectives. The resulting method, which we call AdaSSL, applies to both contrastive and distillation-based SSL objectives, and we empirically show its versatility in causal representation learning, fine-grained image understanding, and world modeling on videos.