2 citations · 3 across the 14 of their papers we have counts for
14 papers
Contraction and Hourglass Persistence for Learning on Graphs, Simplices, and Cells
Mattie Ji, Indradyumna Roy, Vikas Garg
Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an…
Canonicalizing Multimodal Contrastive Representation Learning
Sharut Gupta, Sanyam Kansal, Stefanie Jegelka +2
As models and data scale, independently trained networks often induce analogous notions of similarity. But, matching similarities is weaker than establishing an explicit correspond…
Let Physics Guide Your Protein Flows: Topology-aware Unfolding and Generation
Yogesh Verma, Markus Heinonen, Vikas Garg
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have re…
Positional Encoding meets Persistent Homology on Graphs
Yogesh Verma, Amauri H. Souza, Vikas Garg
The local inductive bias of message-passing graph neural networks (GNNs) hampers their ability to exploit key structural information (e.g., connectivity and cycles). Positional enc…
The Spacetime of Diffusion Models: An Information Geometry Perspective
Rafał Karczewski, Markus Heinonen, Alison Pouplin +2
We present a novel geometric perspective on the latent space of diffusion models. We first show that the standard pullback approach, utilizing the deterministic probability flow OD…
Robust Simulation-Based Inference under Missing Data via Neural Processes
Yogesh Verma, Ayush Bharti, Vikas Garg
Simulation-based inference (SBI) methods typically require fully observed data to infer parameters of models with intractable likelihood functions. However, datasets often contain…
Devil is in the Details: Density Guidance for Detail-Aware Generation with Flow Models
Rafał Karczewski, Markus Heinonen, Vikas Garg
Diffusion models have emerged as a powerful class of generative models, capable of producing high-quality images by mapping noise to a data distribution. However, recent findings s…
Diffusion Models as Cartoonists: The Curious Case of High Density Regions
Rafał Karczewski, Markus Heinonen, Vikas Garg
We investigate what kind of images lie in the high-density regions of diffusion models. We introduce a theoretical mode-tracking process capable of pinpointing the exact mode of th…
Diffusion Twigs with Loop Guidance for Conditional Graph Generation
Giangiacomo Mercatali, Yogesh Verma, Andre Freitas +1
We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or…
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?
Rafał Karczewski, Samuel Kaski, Markus Heinonen +1
Several generative models with elaborate training and sampling procedures have been proposed to accelerate structure-based drug design (SBDD); however, their empirical performance…
Topological Neural Networks go Persistent, Equivariant, and Continuous
Yogesh Verma, Amauri H Souza, Vikas Garg
Topological Neural Networks (TNNs) incorporate higher-order relational information beyond pairwise interactions, enabling richer representations than Graph Neural Networks (GNNs).…
Equivariant Denoisers Cannot Copy Graphs: Align Your Graph Diffusion Models
Najwa Laabid, Severi Rissanen, Markus Heinonen +2
Graph diffusion models, dominant in graph generative modeling, remain underexplored for graph-to-graph translation tasks like chemical reaction prediction. We demonstrate that stan…
ClimODE: Climate and Weather Forecasting with Physics-informed Neural ODEs
Yogesh Verma, Markus Heinonen, Vikas Garg
Climate and weather prediction traditionally relies on complex numerical simulations of atmospheric physics. Deep learning approaches, such as transformers, have recently challenge…
E(3)-equivariant models cannot learn chirality: Field-based molecular generation
Alexandru Dumitrescu, Dani Korpela, Markus Heinonen +4
Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utili…