Vikas Garg

David Alvarez-Melis, Vikas Garg, Adam Tauman Kalai · harvard, microsoft-research

This work offers a novel theoretical perspective on why, despite numerous attempts, adversarial approaches to generative modeling (e.g., GANs) have not been as popular for certain generation tasks, particularly sequential tasks such as Natural Language Generation, as they have in others, such as Computer Vision. In particular, on sequential data such as text, maximum-likelihood approaches are significantly more utilized than GANs. We show that, while it may seem that maximizing likelihood is inherently different than minimizing distinguishability, this distinction is largely artificial and only holds for limited models. We argue that minimizing KL-divergence (i.e., maximizing likelihood) is a more efficient approach to effectively minimizing the same distinguishability criteria that adversarial models seek to optimize. Reductions show that minimizing distinguishability can be seen as simply boosting likelihood for certain families of models including n-gram models and neural networks with a softmax output layer. To achieve a full polynomial-time reduction, a novel next-token distinguishability model is considered.

Amauri H. Souza, Diego Mesquita, Samuel Kaski et al.

Temporal graph networks (TGNs) have gained prominence as models for embedding dynamic interactions, but little is known about their theoretical underpinnings. We establish fundamental results about the representational power and limits of the two main categories of TGNs: those that aggregate temporal walks (WA-TGNs), and those that augment local message passing with recurrent memory modules (MP-TGNs). Specifically, novel constructions reveal the inadequacy of MP-TGNs and WA-TGNs, proving that neither category subsumes the other. We extend the 1-WL (Weisfeiler-Leman) test to temporal graphs, and show that the most powerful MP-TGNs should use injective updates, as in this case they become as expressive as the temporal WL. Also, we show that sufficiently deep MP-TGNs cannot benefit from memory, and MP/WA-TGNs fail to compute graph properties such as girth. These theoretical insights lead us to PINT -- a novel architecture that leverages injective temporal message passing and relative positional features. Importantly, PINT is provably more expressive than both MP-TGNs and WA-TGNs. PINT significantly outperforms existing TGNs on several real-world benchmarks.

Timur Garipov, Sebastiaan De Peuter, Ge Yang et al.

High training costs of generative models and the need to fine-tune them for specific tasks have created a strong interest in model reuse and composition. A key challenge in composing iterative generative processes, such as GFlowNets and diffusion models, is that to realize the desired target distribution, all steps of the generative process need to be coordinated, and satisfy delicate balance conditions. In this work, we propose Compositional Sculpting: a general approach for defining compositions of iterative generative processes. We then introduce a method for sampling from these compositions built on classifier guidance. We showcase ways to accomplish compositional sculpting in both GFlowNets and diffusion models. We highlight two binary operations $\unicode{x2014}$ the harmonic mean ($p_1 \otimes p_2$) and the contrast ($p_1 \unicode{x25D1}\,p_2$) between pairs, and the generalization of these operations to multiple component distributions. We offer empirical results on image and molecular generation tasks.

Yogesh Verma, Samuel Kaski, Markus Heinonen et al.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

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 increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

Rafał Karczewski, Samuel Kaski, Markus Heinonen et al.

Several generative models with elaborate training and sampling procedures have been proposed to accelerate structure-based drug design (SBDD); however, their empirical performance turns out to be suboptimal. We seek to better understand this phenomenon from both theoretical and empirical perspectives. Since most of these models apply graph neural networks (GNNs), one may suspect that they inherit the representational limitations of GNNs. We analyze this aspect, establishing the first such results for protein-ligand complexes. A plausible counterview may attribute the underperformance of these models to their excessive parameterizations, inducing expressivity at the expense of generalization. We investigate this possibility with a simple metric-aware approach that learns an economical surrogate for affinity to infer an unlabelled molecular graph and optimizes for labels conditioned on this graph and molecular properties. The resulting model achieves state-of-the-art results using 100x fewer trainable parameters and affords up to 1000x speedup. Collectively, our findings underscore the need to reassess and redirect the existing paradigm and efforts for SBDD. Code is available at https://github.com/rafalkarczewski/SimpleSBDD.

Mattie Ji, Amauri H. Souza, Vikas Garg

Topological descriptors have been increasingly utilized for capturing multiscale structural information in relational data. In this work, we consider various filtrations on the (box) product of graphs and the effect on their outputs on the topological descriptors - the Euler characteristic (EC) and persistent homology (PH). In particular, we establish a complete characterization of the expressive power of EC on general color-based filtrations. We also show that the PH descriptors of (virtual) graph products contain strictly more information than the computation on individual graphs, whereas EC does not. Additionally, we provide algorithms to compute the PH diagrams of the product of vertex- and edge-level filtrations on the graph product. We also substantiate our theoretical analysis with empirical investigations on runtime analysis, expressivity, and graph classification performance. Overall, this work paves way for powerful graph persistent descriptors via product filtrations. Code is available at https://github.com/Aalto-QuML/tda_graph_product.

Amirreza Akbari, Amauri H. Souza, Vikas Garg

Graph neural networks (GNNs) are the standard for learning on graphs, yet they have limited expressive power, often expressed in terms of the Weisfeiler-Leman (WL) hierarchy or within the framework of first-order logic. In this context, topological neural networks (TNNs) have recently emerged as a promising alternative for graph representation learning. By incorporating higher-order relational structures into message-passing schemes, TNNs offer higher representational power than traditional GNNs. However, a fundamental question remains open: what is the logical expressiveness of TNNs? Answering this allows us to characterize precisely which binary classifiers TNNs can represent. In this paper, we address this question by analyzing isomorphism tests derived from the underlying mechanisms of general TNNs. We introduce and investigate the power of higher-order variants of WL-based tests for combinatorial complexes, called $k$-CCWL test. In addition, we introduce the topological counting logic (TC$_k$), an extension of standard counting logic featuring a novel pairwise counting quantifier $ \exists^{N}(x_i,x_j)\, φ(x_i,x_j), $ which explicitly quantifies pairs $(x_i, x_j)$ satisfying property $φ$. We rigorously prove the exact equivalence: $ \text{k-CCWL} \equiv \text{TC}_{k{+}2} \equiv \text{Topological }(k{+}2)\text{-pebble game}.$ These results establish a logical expressiveness theory for TNNs.

Johanna Immonen, Amauri H. Souza, Vikas Garg

Representational limits of message-passing graph neural networks (MP-GNNs), e.g., in terms of the Weisfeiler-Leman (WL) test for isomorphism, are well understood. Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem. Specifically, we establish the necessary and sufficient conditions for distinguishing graphs based on the persistence of their connected components, obtained from filter functions on vertex and edge colors. Our constructions expose the limits of vertex- and edge-level PH, proving that neither category subsumes the other. Leveraging these theoretical insights, we propose RePHINE for learning topological features on graphs. RePHINE efficiently combines vertex- and edge-level PH, achieving a scheme that is provably more powerful than both. Integrating RePHINE into MP-GNNs boosts their expressive power, resulting in gains over standard PH on several benchmarks for graph classification.

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 the denoising distribution, and we propose a practical high-density sampler that consistently generates images of higher likelihood than usual samplers. Our empirical findings reveal the existence of significantly higher likelihood samples that typical samplers do not produce, often manifesting as cartoon-like drawings or blurry images depending on the noise level. Curiously, these patterns emerge in datasets devoid of such examples. We also present a novel approach to track sample likelihoods in diffusion SDEs, which remarkably incurs no additional computational cost. Code is available at https://github.com/Aalto-QuML/high-density-diffusion.

Konstantinos Kogkalidis, Jean-Philippe Bernardy, Vikas Garg

We introduce a novel positional encoding strategy for Transformer-style models, addressing the shortcomings of existing, often ad hoc, approaches. Our framework provides a flexible mapping from the algebraic specification of a domain to an interpretation as orthogonal operators. This design preserves the algebraic characteristics of the source domain, ensuring that the model upholds its desired structural properties. Our scheme can accommodate various structures, ncluding sequences, grids and trees, as well as their compositions. We conduct a series of experiments to demonstrate the practical applicability of our approach. Results suggest performance on par with or surpassing the current state-of-the-art, without hyper-parameter optimizations or "task search" of any kind. Code is available at https://github.com/konstantinosKokos/ape.

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 missing values due to incomplete observations, data corruptions (common in astrophysics), or instrument limitations (e.g., in high-energy physics applications). In such scenarios, missing data must be imputed before applying any SBI method. We formalize the problem of missing data in SBI and demonstrate that naive imputation methods can introduce bias in the estimation of SBI posterior. We also introduce a novel amortized method that addresses this issue by jointly learning the imputation model and the inference network within a neural posterior estimation (NPE) framework. Extensive empirical results on SBI benchmarks show that our approach provides robust inference outcomes compared to standard baselines for varying levels of missing data. Moreover, we demonstrate the merits of our imputation model on two real-world bioactivity datasets (Adrenergic and Kinase assays). Code is available at https://github.com/Aalto-QuML/RISE.

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 suggest that image likelihood does not align with perceptual quality: high-likelihood samples tend to be smooth, while lower-likelihood ones are more detailed. Controlling sample density is thus crucial for balancing realism and detail. In this paper, we analyze an existing technique, Prior Guidance, which scales the latent code to influence image detail. We introduce score alignment, a condition that explains why this method works and show that it can be tractably checked for any continuous normalizing flow model. We then propose Density Guidance, a principled modification of the generative ODE that enables exact log-density control during sampling. Finally, we extend Density Guidance to stochastic sampling, ensuring precise log-density control while allowing controlled variation in structure or fine details. Our experiments demonstrate that these techniques provide fine-grained control over image detail without compromising sample quality. Code is available at https://github.com/Aalto-QuML/density-guidance.

Najwa Laabid, Vikas Garg

Synthesis planning seeks an efficient sequence of chemical reactions that produce a target molecule. Typically, a pretrained single-step (autoregressive) retrosynthesis model is repeatedly invoked to generate such a sequence. Classifier guidance can, in principle, help steer the output of single-step model toward reactions that satisfy specific constraints or accommodate chemist's preferences during inference without having to retrain the autoregressive generator. We expose the insufficiency of auxiliary classifiers trained with cross-entropy loss to override the unconditional token-level distributions learned from typical sparse single-disconnection reaction datasets. We overcome this issue with a novel method called Sequence Completion Ranking (SCR), which employs contrastive argumentation and a margin-based loss to calibrate the classifier so that it can meaningfully discriminate between continuations during decoding. We formally establish that margin-calibrated classifiers can expand the set of property-satisfying sequences reachable under guided beam search. Empirically, on USPTO-190, given chemist-specified guidance targets, SCR substantially improves multi-step solve rates from $16.8\%$ (unguided generator) to $78.4\%$ with reaction-type guidance and $95.3\%$ with Tanimoto guidance, unlocking valid routes for 33 targets ($17.4\%$) previously unsolvable with baselines. Our method also effectively closes the long-standing diversity gap between template-free and template-based methods.

Sharut Gupta, Sanyam Kansal, Stefanie Jegelka et al.

As models and data scale, independently trained networks often induce analogous notions of similarity. But, matching similarities is weaker than establishing an explicit correspondence between the representation spaces, especially for multimodal models, where consistency must hold not only within each modality, but also for the learned image-text coupling. We therefore ask: given two independently trained multimodal contrastive models (with encoders $(f, g)$ and $(\widetilde{f},\widetilde{g})$) -- trained on different distributions and with different architectures -- does a systematic geometric relationship exist between their embedding spaces? If so, what form does it take, and does it hold uniformly across modalities? In this work, we show that across model families such as CLIP, SigLIP, and FLAVA, this geometric relationship is well approximated by an orthogonal map (up to a global mean shift), i.e., there exists an orthogonal map $Q$ where $Q^\top Q = I$ such that $\widetilde{f}(x)\approx Q f(x)$ for paired images $x$. Strikingly, the same $Q$ simultaneously aligns the text encoders i.e., $\widetilde{g}(y)\approx Q g(y)$ for texts $y$. Theoretically, we prove that if the multimodal kernel agrees across models on a small anchor set i.e. $\langle f(x), g(y)\rangle \approx \langle \widetilde{f}(x), \widetilde{g}(y)\rangle$, then the two models must be related by a single orthogonal map $Q$ and the same $Q$ maps images and text across models. More broadly, this finding enables backward-compatible model upgrades, avoiding costly re-embedding, and has implications for the privacy of learned representations. Our project page: https://canonical-multimodal.github.io/

Rafał Karczewski, Markus Heinonen, Alison Pouplin et al.

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 ODE decoder, is fundamentally flawed. It provably forces geodesics to decode as straight segments in data space, effectively ignoring any intrinsic data geometry beyond the ambient Euclidean space. Complementing this view, diffusion also admits a stochastic decoder via the reverse SDE, which enables an information geometric treatment with the Fisher-Rao metric. However, a choice of $x_T$ as the latent representation collapses this metric due to memorylessness. We address this by introducing a latent spacetime $z=(x_t,t)$ that indexes the family of denoising distributions $p(x_0 | x_t)$ across all noise scales, yielding a nontrivial geometric structure. We prove these distributions form an exponential family and derive simulation-free estimators for curve lengths, enabling efficient geodesic computation. The resulting structure induces a principled Diffusion Edit Distance, where geodesics trace minimal sequences of noise and denoise edits between data. We also demonstrate benefits for transition path sampling in molecular systems, including constrained variants such as low-variance transitions and region avoidance. Code is available at: https://github.com/rafalkarczewski/spacetime-geometry

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 challenged the simulation paradigm with complex network forecasts. However, they often act as data-driven black-box models that neglect the underlying physics and lack uncertainty quantification. We address these limitations with ClimODE, a spatiotemporal continuous-time process that implements a key principle of advection from statistical mechanics, namely, weather changes due to a spatial movement of quantities over time. ClimODE models precise weather evolution with value-conserving dynamics, learning global weather transport as a neural flow, which also enables estimating the uncertainty in predictions. Our approach outperforms existing data-driven methods in global and regional forecasting with an order of magnitude smaller parameterization, establishing a new state of the art.

Yue Jiang, Changkong Zhou, Vikas Garg et al.

Present-day graphical user interfaces (GUIs) exhibit diverse arrangements of text, graphics, and interactive elements such as buttons and menus, but representations of GUIs have not kept up. They do not encapsulate both semantic and visuo-spatial relationships among elements. To seize machine learning's potential for GUIs more efficiently, Graph4GUI exploits graph neural networks to capture individual elements' properties and their semantic-visuo-spatial constraints in a layout. The learned representation demonstrated its effectiveness in multiple tasks, especially generating designs in a challenging GUI autocompletion task, which involved predicting the positions of remaining unplaced elements in a partially completed GUI. The new model's suggestions showed alignment and visual appeal superior to the baseline method and received higher subjective ratings for preference. Furthermore, we demonstrate the practical benefits and efficiency advantages designers perceive when utilizing our model as an autocompletion plug-in.

Giangiacomo Mercatali, Yogesh Verma, Andre Freitas et al.

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 trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Alexandru Dumitrescu, Dani Korpela, Markus Heinonen et al.

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, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

Fredrik Hagström, Vikas Garg, Fabricio Oliveira

Buildings account for 40% of global energy consumption. A considerable portion of building energy consumption stems from heating, ventilation, and air conditioning (HVAC), and thus implementing smart, energy-efficient HVAC systems has the potential to significantly impact the course of climate change. In recent years, model-free reinforcement learning algorithms have been increasingly assessed for this purpose due to their ability to learn and adapt purely from experience. They have been shown to outperform classical controllers in terms of energy cost and consumption, as well as thermal comfort. However, their weakness lies in their relatively poor data efficiency, requiring long periods of training to reach acceptable policies, making them inapplicable to real-world controllers directly. In this paper, we demonstrate that using federated learning to train the reinforcement learning controller of HVAC systems can improve the learning speed, as well as improve their ability to generalize, which in turn facilitates transfer learning to unseen building environments. In our setting, a global control policy is learned by aggregating local policies trained on multiple data centers located in different climate zones. The goal of the policy is to minimize energy consumption and maximize thermal comfort. We perform experiments evaluating three different optimizers for local policy training, as well as three different federated learning algorithms against two alternative baselines. Our experiments show that these effects lead to a faster learning speed, as well as greater generalization capabilities in the federated policy compared to any individually trained policy. Furthermore, the learning stability is significantly improved, with the learning process and performance of the federated policy being less sensitive to the choice of parameters and the inherent randomness of reinforcement learning.

Marshal Arijona Sinaga, Julien Martinelli, Vikas Garg et al.

Preferential Bayesian optimization (PBO) is a sample-efficient framework for learning human preferences between candidate designs. PBO classically relies on homoscedastic noise models to represent human aleatoric uncertainty. Yet, such noise fails to accurately capture the varying levels of human aleatoric uncertainty, particularly when the user possesses partial knowledge among different pairs of candidates. For instance, a chemist with solid expertise in glucose-related molecules may easily compare two compounds from that family while struggling to compare alcohol-related molecules. Currently, PBO overlooks this uncertainty during the search for a new candidate through the maximization of the acquisition function, consequently underestimating the risk associated with human uncertainty. To address this issue, we propose a heteroscedastic noise model to capture human aleatoric uncertainty. This model adaptively assigns noise levels based on the distance of a specific input to a predefined set of reliable inputs known as anchors provided by the human. Anchors encapsulate partial knowledge and offer insight into the comparative difficulty of evaluating different candidate pairs. Such a model can be seamlessly integrated into the acquisition function, thus leading to candidate design pairs that elegantly trade informativeness and ease of comparison for the human expert. We perform an extensive empirical evaluation of the proposed approach, demonstrating a consistent improvement over homoscedastic PBO.

Shao-Yi Yu, Jen-Wei Wang, Maya Horii et al.

Mobile robots, such as ground vehicles and quadrotors, are becoming increasingly important in various fields, from logistics to agriculture, where they automate processes in environments that are difficult to access for humans. However, to perform effectively in uncertain environments using model-based controllers, these systems require dynamics models capable of responding to environmental variations, especially when direct access to environmental information is limited. To enable such adaptivity and facilitate integration with model predictive control, we propose an adaptive dynamics model which bypasses the need for direct environmental knowledge by inferring operational environments from state-action history. The dynamics model is based on neural ordinary equations, and a two-phase training procedure is used to learn latent environment representations. We demonstrate the effectiveness of our approach through goal-reaching and path-tracking tasks on three robotic platforms of increasing complexity: a 2D differential wheeled robot with changing wheel contact conditions, a 3D quadrotor in variational wind fields, and the Sphero BOLT robot under two contact conditions for real-world deployment. Empirical results corroborate that our method can handle temporally and spatially varying environmental changes in both simulation and real-world systems.

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 revolutionized protein design, enabling the creation of novel proteins. However, these methods often neglect the intrinsic physical realism of proteins, driven by noising dynamics that lack grounding in physical principles. To address this, we first introduce a physically motivated non-linear noising process, grounded in classical physics, that unfolds proteins into secondary structures (e.g., alpha helices, linear beta sheets) while preserving topological integrity--maintaining bonds, and preventing collisions. We then integrate this process with the flow-matching paradigm on SE(3) to model the invariant distribution of protein backbones with high fidelity, incorporating sequence information to enable sequence-conditioned folding and expand the generative capabilities of our model. Experimental results demonstrate that the proposed method achieves state-of-the-art performance in unconditional protein generation, producing more designable and novel protein structures while accurately folding monomer sequences into precise protein conformations.

Maximilian Krahn, Vikas Garg

Topological neural networks have emerged as powerful successors of graph neural networks. However, they typically involve higher-order message passing, which incurs significant computational expense. We circumvent this issue with a novel topological framework that introduces a Laplacian operator on combinatorial complexes (CCs), enabling efficient computation of heat kernels that serve as node descriptors. Our approach captures multiscale information and enables permutation-equivariant representations, allowing easy integration into modern transformer-based architectures. Theoretically, the proposed method is maximally expressive because it can distinguish arbitrary non-isomorphic CCs. Empirically, it significantly outperforms existing topological methods in terms of computational efficiency. Besides demonstrating competitive performance with the state-of-the-art descriptors on standard molecular datasets, it exhibits superior capability in distinguishing complex topological structures and avoiding blind spots on topological benchmarks. Overall, this work advances topological deep learning by providing expressive yet scalable representations, thereby opening up exciting avenues for molecular classification and property prediction tasks.

Haishan Wang, Arno Solin, Vikas Garg

Graph neural networks (GNNs) are known to be vulnerable to oversmoothing due to their implicit homophily assumption. We mitigate this problem with a novel scheme that regulates the aggregation of messages, modulating the type and extent of message passing locally thereby preserving both the low and high-frequency components of information. Our approach relies solely on learnt embeddings, obviating the need for auxiliary labels, thus extending the benefits of heterophily-aware embeddings to broader applications, e.g., generative modelling. Our experiments, conducted across various data sets and GNN architectures, demonstrate performance enhancements and reveal heterophily patterns across standard classification benchmarks. Furthermore, application to molecular generation showcases notable performance improvements on chemoinformatics benchmarks.

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). Concurrently, topological descriptors based on persistent homology (PH) are being increasingly employed to augment the GNNs. We investigate the benefits of integrating these two paradigms. Specifically, we introduce TopNets as a broad framework that subsumes and unifies various methods in the intersection of GNNs/TNNs and PH such as (generalizations of) RePHINE and TOGL. TopNets can also be readily adapted to handle (symmetries in) geometric complexes, extending the scope of TNNs and PH to spatial settings. Theoretically, we show that PH descriptors can provably enhance the expressivity of simplicial message-passing networks. Empirically, (continuous and E(n)-equivariant extensions of) TopNets achieve strong performance across diverse tasks, including antibody design, molecular dynamics simulation, and drug property prediction.

Yogesh Verma, Markus Heinonen, Vikas Garg

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.