Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

We propose a new self-explainable Graph Neural Network (GNN) model: GraphChef. GraphChef integrates decision trees into the GNN message passing framework. Given a dataset, GraphChef returns a set of rules (a recipe) that explains each class in the dataset unlike existing GNNs and explanation methods that reason on individual graphs. Thanks to the decision trees, GraphChef recipes are human understandable. We also present a new pruning method to produce small and easy to digest trees. Experiments demonstrate that GraphChef reaches comparable accuracy to not self-explainable GNNs and produced decision trees are indeed small. We further validate the correctness of the discovered recipes on datasets where explanation ground truth is available: Reddit-Binary, MUTAG, BA-2Motifs, BA-Shapes, Tree-Cycle, and Tree-Grid.

Rigid origami has shown potential in large diversity of practical applications. However, current rigid origami crease pattern design mostly relies on known tessellations. This strongly limits the diversity and novelty of patterns that can be created. In this work, we build upon the recently developed principle of three units method to formulate rigid origami design as a discrete optimization problem, the rigid origami game. Our implementation allows for a simple definition of diverse objectives and thereby expands the potential of rigid origami further to optimized, application-specific crease patterns. We showcase the flexibility of our formulation through use of a diverse set of search methods in several illustrative case studies. We are not only able to construct various patterns that approximate given target shapes, but to also specify abstract, function-based rewards which result in novel, foldable and functional designs for everyday objects.

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel architecture for aligned proteins, and utilizes strong diffusion priors to improve the denoising process. Our approach improves protein diffusion by taking advantage of domain knowledge and physics-based constraints; handles sequence-length changes; and reduces memory complexity by an order of magnitude, enabling backbone and side chain generation. We validate AbDiffuser in silico and in vitro. Numerical experiments showcase the ability of AbDiffuser to generate antibodies that closely track the sequence and structural properties of a reference set. Laboratory experiments confirm that all 16 HER2 antibodies discovered were expressed at high levels and that 57.1% of the selected designs were tight binders.

We approach the graph generation problem from a spectral perspective by first generating the dominant parts of the graph Laplacian spectrum and then building a graph matching these eigenvalues and eigenvectors. Spectral conditioning allows for direct modeling of the global and local graph structure and helps to overcome the expressivity and mode collapse issues of one-shot graph generators. Our novel GAN, called SPECTRE, enables the one-shot generation of much larger graphs than previously possible with one-shot models. SPECTRE outperforms state-of-the-art deep autoregressive generators in terms of modeling fidelity, while also avoiding expensive sequential generation and dependence on node ordering. A case in point, in sizable synthetic and real-world graphs SPECTRE achieves a 4-to-170 fold improvement over the best competitor that does not overfit and is 23-to-30 times faster than autoregressive generators.

Learning system dynamics directly from observations is a promising direction in machine learning due to its potential to significantly enhance our ability to understand physical systems. However, the dynamics of many real-world systems are challenging to learn due to the presence of nonlinear potentials and a number of interactions that scales quadratically with the number of particles N, as in the case of the N-body problem. In this work we introduce an approach that transforms a fully-connected interaction graph into a hierarchical one which reduces the number of edges to O(N). This results in a linear time and space complexity while the pre-computation of the hierarchical graph requires O(N log (N)) time and O(N) space. Using our approach, we are able to train models on much larger particle counts, even on a single GPU. We evaluate how the phase space position accuracy and energy conservation depend on the number of simulated particles. Our approach retains high accuracy and efficiency even on large-scale gravitational N-body simulations which are impossible to run on a single machine if a fully-connected graph is used. Similar results are also observed when simulating Coulomb interactions. Furthermore, we make several important observations regarding the performance of this new hierarchical model, including: i) its accuracy tends to improve with the number of particles in the simulation and ii) its generalisation to unseen particle counts is also much better than for models that use all O(N^2) interactions.

This paper studies Dropout Graph Neural Networks (DropGNNs), a new approach that aims to overcome the limitations of standard GNN frameworks. In DropGNNs, we execute multiple runs of a GNN on the input graph, with some of the nodes randomly and independently dropped in each of these runs. Then, we combine the results of these runs to obtain the final result. We prove that DropGNNs can distinguish various graph neighborhoods that cannot be separated by message passing GNNs. We derive theoretical bounds for the number of runs required to ensure a reliable distribution of dropouts, and we prove several properties regarding the expressive capabilities and limits of DropGNNs. We experimentally validate our theoretical findings on expressiveness. Furthermore, we show that DropGNNs perform competitively on established GNN benchmarks.