228 citations · 770 across the 19 of their papers we have counts for
19 papers
Multi-Scale Protein Structure Modelling with Geometric Graph U-Nets
Chang Liu, Vivian Li, Linus Leong +3
Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents th…
Towards Mechanistic Interpretability of Graph Transformers via Attention Graphs
Batu El, Deepro Choudhury, Pietro Liò +1
We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between mess…
RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design
Rishabh Anand, Chaitanya K. Joshi, Alex Morehead +7
We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for dat…
Understanding Biology in the Age of Artificial Intelligence
Elsa Lawrence, Adham El-Shazly, Srijit Seal +6
Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML)…
A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems
Alexandre Duval, Simon V. Mathis, Chaitanya K. Joshi +7
Recent advances in computational modelling of atomic systems, spanning molecules, proteins, and materials, represent them as geometric graphs with atoms embedded as nodes in 3D Euc…
Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?
Charles Harris, Kieran Didi, Arian R. Jamasb +4
Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years.…
Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems
Xuan Zhang, Limei Wang, Jacob Helwig +60
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating…
Group Invariant Global Pooling
Kamil Bujel, Yonatan Gideoni, Chaitanya K. Joshi +1
Much work has been devoted to devising architectures that build group-equivariant representations, while invariance is often induced using simple global pooling mechanisms. Little…
gRNAde: Geometric Deep Learning for 3D RNA inverse design
Chaitanya K. Joshi, Arian R. Jamasb, Ramon Viñas +5
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D confo…
On the Expressive Power of Geometric Graph Neural Networks
Chaitanya K. Joshi, Cristian Bodnar, Simon V. Mathis +2
The expressive power of Graph Neural Networks (GNNs) has been studied extensively through the Weisfeiler-Leman (WL) graph isomorphism test. However, standard GNNs and the WL framew…
On Representation Knowledge Distillation for Graph Neural Networks
Chaitanya K. Joshi, Fayao Liu, Xu Xun +2
Knowledge distillation is a learning paradigm for boosting resource-efficient graph neural networks (GNNs) using more expressive yet cumbersome teacher models. Past work on distill…
Point Discriminative Learning for Data-efficient 3D Point Cloud Analysis
Fayao Liu, Guosheng Lin, Chuan-Sheng Foo +2
3D point cloud analysis has drawn a lot of research attention due to its wide applications. However, collecting massive labelled 3D point cloud data is both time-consuming and labo…
Learning the Travelling Salesperson Problem Requires Rethinking Generalization
Chaitanya K. Joshi, Quentin Cappart, Louis-Martin Rousseau +1
End-to-end training of neural network solvers for graph combinatorial optimization problems such as the Travelling Salesperson Problem (TSP) have seen a surge of interest recently,…
Benchmarking Graph Neural Networks
Vijay Prakash Dwivedi, Chaitanya K. Joshi, Anh Tuan Luu +3
In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive…
Multi-Graph Transformer for Free-Hand Sketch Recognition
Peng Xu, Chaitanya K. Joshi, Xavier Bresson
Learning meaningful representations of free-hand sketches remains a challenging task given the signal sparsity and the high-level abstraction of sketches. Existing techniques have…
On Learning Paradigms for the Travelling Salesman Problem
Chaitanya K. Joshi, Thomas Laurent, Xavier Bresson
We explore the impact of learning paradigms on training deep neural networks for the Travelling Salesman Problem. We design controlled experiments to train supervised learning (SL)…
An Efficient Graph Convolutional Network Technique for the Travelling Salesman Problem
Chaitanya K. Joshi, Thomas Laurent, Xavier Bresson
This paper introduces a new learning-based approach for approximately solving the Travelling Salesman Problem on 2D Euclidean graphs. We use deep Graph Convolutional Networks to bu…
Working women and caste in India: A study of social disadvantage using feature attribution
Kuhu Joshi, Chaitanya K. Joshi
Women belonging to the socially disadvantaged caste-groups in India have historically been engaged in labour-intensive, blue-collar work. We study whether there has been any change…
Personalization in Goal-Oriented Dialog
Chaitanya K. Joshi, Fei Mi, Boi Faltings
The main goal of modeling human conversation is to create agents which can interact with people in both open-ended and goal-oriented scenarios. End-to-end trained neural dialog sys…