Sharvaree Vadgama

Erik J Bekkers, Sharvaree Vadgama, Rob D Hesselink et al.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions $\mathbb{R}^3$, position and orientations $\mathbb{R}^3 {\times} S^2$, and the group $SE(3)$ itself. Among these, $\mathbb{R}^3 {\times} S^2$ is an optimal choice due to the ability to represent directional information, which $\mathbb{R}^3$ methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full $SE(3)$ group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

Jiahe Huang, Sihan Xu, Sharvaree Vadgama et al.

Generative models have emerged as a powerful paradigm for solving physics systems and modeling complex spatiotemporal dynamics. However, achieving high physical accuracy without incurring high computational cost remains a fundamental challenge, as existing approaches face a critical speed-fidelity trade-off. In this work, we introduce Recursive Flow Matching (RecFM), a generative framework for forecasting complex spatiotemporal dynamics. RecFM enforces self-consistency to align trajectories across discretization scales, reducing discretization errors and improving performance across metrics for physics-based tasks. To our knowledge, this is the first method to achieve high-fidelity one- and few-step (2-4 step) dynamic generation for scientific systems with performance comparable to state-of-the-art multi-step solvers. Across challenging scientific benchmarks, RecFM achieves up to a 20$\times$ speedup over leading diffusion-based emulators while improving predictive accuracy. Furthermore, RecFM reduces mean squared error by over 15% compared to vanilla flow matching, offering a scalable and efficient solution for real-time scientific emulation.

Guillermo Bernárdez, Lev Telyatnikov, Marco Montagna et al.

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM). The challenge focused on the problem of representing data in different discrete topological domains in order to bridge the gap between Topological Deep Learning (TDL) and other types of structured datasets (e.g. point clouds, graphs). Specifically, participants were asked to design and implement topological liftings, i.e. mappings between different data structures and topological domains --like hypergraphs, or simplicial/cell/combinatorial complexes. The challenge received 52 submissions satisfying all the requirements. This paper introduces the main scope of the challenge, and summarizes the main results and findings.

Jianke Yang, Ohm Venkatachalam, Mohammad Kianezhad et al.

Explaining observed phenomena through symbolic, interpretable formulas is a fundamental goal of science. Recently, large language models (LLMs) have emerged as promising tools for symbolic equation discovery, owing to their broad domain knowledge and strong reasoning capabilities. However, most existing LLM-based systems try to guess equations directly from data, without modeling the multi-step reasoning process that scientists often follow: first inferring physical properties such as symmetries, then using these as priors to restrict the space of candidate equations. We introduce KeplerAgent, an agentic framework that explicitly follows this scientific reasoning process. The agent coordinates physics-based tools to extract intermediate structure and uses these results to configure symbolic regression engines such as PySINDy and PySR, including their function libraries and structural constraints. Across a suite of physical equation benchmarks, KeplerAgent achieves substantially higher symbolic accuracy and greater robustness to noisy data than both LLM and traditional baselines.

Vivien van Veldhuizen, Sharvaree Vadgama, Onno J. de Boer et al.

Early detection of Barrett's Esophagus (BE), the only known precursor to Esophageal adenocarcinoma (EAC), is crucial for effectively preventing and treating esophageal cancer. In this work, we investigate the potential of geometric Variational Autoencoders (VAEs) to learn a meaningful latent representation that captures the progression of BE. We show that hyperspherical VAE (S-VAE) and Kendall Shape VAE show improved classification accuracy, reconstruction loss, and generative capacity. Additionally, we present a novel autoencoder architecture that can generate qualitative images without the need for a variational framework while retaining the benefits of an autoencoder, such as improved stability and reconstruction quality.

Andrew Y. Zhou, Sharvaree Vadgama, Sumanth Varambally et al.

Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality ligand candidates, a result of the syntactic limitations of current models with regard to molecular strings. In this paper, we introduce $\texttt{ToolMol}$, an evolutionary agentic framework for de novo drug design. $\texttt{ToolMol}$ combines a multi-objective genetic algorithm with an agentic LLM operator that iteratively updates the ligand population. We build a comprehensive toolbox of RDKit-backed functions that allows our agentic operator to consisently make precise ligand modifications. $\texttt{ToolMol}$ achieves state-of-the-art performance on multi-objective property optimization tasks, discovering drug-like and synthesizable ligands that have $>10\%$ stronger predicted binding affinity compared to existing methods, evaluated on three protein targets. $\texttt{ToolMol}$ ligands additionally achieve state-of-the-art results in gold-standard Absolute Binding Free Energy scores, gaining over existing methods by over $35\%$. By studying chain-of-thought reasoning traces, we observe that tool-calling enables the model to more faithfully execute its planned modifications, efficiently exploiting the strong chemical prior knowledge in LLMs.

David R Wessels, David M Knigge, Samuele Papa et al.

Conditional Neural Fields (CNFs) are increasingly being leveraged as continuous signal representations, by associating each data-sample with a latent variable that conditions a shared backbone Neural Field (NeF) to reconstruct the sample. However, existing CNF architectures face limitations when using this latent downstream in tasks requiring fine-grained geometric reasoning, such as classification and segmentation. We posit that this results from lack of explicit modelling of geometric information (e.g., locality in the signal or the orientation of a feature) in the latent space of CNFs. As such, we propose Equivariant Neural Fields (ENFs), a novel CNF architecture which uses a geometry-informed cross-attention to condition the NeF on a geometric variable--a latent point cloud of features--that enables an equivariant decoding from latent to field. We show that this approach induces a steerability property by which both field and latent are grounded in geometry and amenable to transformation laws: if the field transforms, the latent representation transforms accordingly--and vice versa. Crucially, this equivariance relation ensures that the latent is capable of (1) representing geometric patterns faithfully, allowing for geometric reasoning in latent space, and (2) weight-sharing over similar local patterns, allowing for efficient learning of datasets of fields. We validate these main properties in a range of tasks including classification, segmentation, forecasting, reconstruction and generative modelling, showing clear improvement over baselines with a geometry-free latent space. Code attached to submission https://github.com/Dafidofff/enf-jax. Code for a clean and minimal repo https://github.com/david-knigge/enf-min-jax.

Nursena Koprucu, Meher Shashwat Nigam, Shicheng Xu et al.

Inspired by Geoffrey Hinton emphasis on generative modeling, To recognize shapes, first learn to generate them, we explore the use of 3D diffusion models for object classification. Leveraging the density estimates from these models, our approach, the Diffusion Classifier for 3D Objects (DC3DO), enables zero-shot classification of 3D shapes without additional training. On average, our method achieves a 12.5 percent improvement compared to its multiview counterparts, demonstrating superior multimodal reasoning over discriminative approaches. DC3DO employs a class-conditional diffusion model trained on ShapeNet, and we run inferences on point clouds of chairs and cars. This work highlights the potential of generative models in 3D object classification.

Sharvaree Vadgama, Mohammad Mohaiminul Islam, Domas Buracas et al.

In this work, we explore the trade-offs of explicit structural priors, particularly group equivariance. We address this through theoretical analysis and a comprehensive empirical study. To enable controlled and fair comparisons, we introduce \texttt{Rapidash}, a unified group convolutional architecture that allows for different variants of equivariant and non-equivariant models. Our results suggest that more constrained equivariant models outperform less constrained alternatives when aligned with the geometry of the task, and increasing representation capacity does not fully eliminate performance gaps. We see improved performance of models with equivariance and symmetry-breaking through tasks like segmentation, regression, and generation across diverse datasets. Explicit \textit{symmetry breaking} via geometric reference frames consistently improves performance, while \textit{breaking equivariance} through geometric input features can be helpful when aligned with task geometry. Our results provide task-specific performance trends that offer a more nuanced way for model selection.

Putri A. van der Linden, Alejandro García-Castellanos, Sharvaree Vadgama et al.

Group equivariance has emerged as a valuable inductive bias in deep learning, enhancing generalization, data efficiency, and robustness. Classically, group equivariant methods require the groups of interest to be known beforehand, which may not be realistic for real-world data. Additionally, baking in fixed group equivariance may impose overly restrictive constraints on model architecture. This highlights the need for methods that can dynamically discover and apply symmetries as soft constraints. For neural network architectures, equivariance is commonly achieved through group transformations of a canonical weight tensor, resulting in weight sharing over a given group $G$. In this work, we propose to learn such a weight-sharing scheme by defining a collection of learnable doubly stochastic matrices that act as soft permutation matrices on canonical weight tensors, which can take regular group representations as a special case. This yields learnable kernel transformations that are jointly optimized with downstream tasks. We show that when the dataset exhibits strong symmetries, the permutation matrices will converge to regular group representations and our weight-sharing networks effectively become regular group convolutions. Additionally, the flexibility of the method enables it to effectively pick up on partial symmetries.

Floor Eijkelboom, Heiko Zimmermann, Sharvaree Vadgama et al.

We derive a controlled generation objective within the framework of Variational Flow Matching (VFM), which casts flow matching as a variational inference problem. We demonstrate that controlled generation can be implemented two ways: (1) by way of end-to-end training of conditional generative models, or (2) as a Bayesian inference problem, enabling post hoc control of unconditional models without retraining. Furthermore, we establish the conditions required for equivariant generation and provide an equivariant formulation of VFM tailored for molecular generation, ensuring invariance to rotations, translations, and permutations. We evaluate our approach on both uncontrolled and controlled molecular generation, achieving state-of-the-art performance on uncontrolled generation and outperforming state-of-the-art models in controlled generation, both with end-to-end training and in the Bayesian inference setting. This work strengthens the connection between flow-based generative modeling and Bayesian inference, offering a scalable and principled framework for constraint-driven and symmetry-aware generation.

Cong Liu, Sharvaree Vadgama, David Ruhe et al.

This paper explores leveraging the Clifford algebra's expressive power for $\E(n)$-equivariant diffusion models. We utilize the geometric products between Clifford multivectors and the rich geometric information encoded in Clifford subspaces in \emph{Clifford Diffusion Models} (CDMs). We extend the diffusion process beyond just Clifford one-vectors to incorporate all higher-grade multivector subspaces. The data is embedded in grade-$k$ subspaces, allowing us to apply latent diffusion across complete multivectors. This enables CDMs to capture the joint distribution across different subspaces of the algebra, incorporating richer geometric information through higher-order features. We provide empirical results for unconditional molecular generation on the QM9 dataset, showing that CDMs provide a promising avenue for generative modeling.

Mohammad Mohaiminul Islam, Rishabh Anand, David R. Wessels et al.

While widespread, Transformers lack inductive biases for geometric symmetries common in science and computer vision. Existing equivariant methods often sacrifice the efficiency and flexibility that make Transformers so effective through complex, computationally intensive designs. We introduce the Platonic Transformer to resolve this trade-off. By defining attention relative to reference frames from the Platonic solid symmetry groups, our method induces a principled weight-sharing scheme. This enables combined equivariance to continuous translations and Platonic symmetries, while preserving the exact architecture and computational cost of a standard Transformer. Furthermore, we show that this attention is formally equivalent to a dynamic group convolution, which reveals that the model learns adaptive geometric filters and enables a highly scalable, linear-time convolutional variant. Across diverse benchmarks in computer vision (CIFAR-10), 3D point clouds (ScanObjectNN), and molecular property prediction (QM9, OMol25), the Platonic Transformer achieves competitive performance by leveraging these geometric constraints at no additional cost.

Andrew Draganov, Sharvaree Vadgama, Sebastian Damrich et al.

Self-supervised learning (SSL) allows training data representations without a supervised signal and has become an important paradigm in machine learning. Most SSL methods employ the cosine similarity between embedding vectors and hence effectively embed data on a hypersphere. While this seemingly implies that embedding norms cannot play any role in SSL, a few recent works have suggested that embedding norms have properties related to network convergence and confidence. In this paper, we resolve this apparent contradiction and systematically establish the embedding norm's role in SSL training. Using theoretical analysis, simulations, and experiments, we show that embedding norms (i) govern SSL convergence rates and (ii) encode network confidence, with smaller norms corresponding to unexpected samples. Additionally, we show that manipulating embedding norms can have large effects on convergence speed. Our findings demonstrate that SSL embedding norms are integral to understanding and optimizing network behavior.

Mohammad Mohaiminul Islam, Thijs P. Kuipers, Sharvaree Vadgama et al.

Generative models for sequential data often struggle with sparsely sampled and high-dimensional trajectories, typically reducing the learning of dynamics to pairwise transitions. We propose Interpolative Multi-Marginal Flow Matching (IMMFM), a framework that learns continuous stochastic dynamics jointly consistent with multiple observed time points. IMMFM employs a piecewise-quadratic interpolation path as a smooth target for flow matching and jointly optimizes drift and a data-driven diffusion coefficient, supported by a theoretical condition for stable learning. This design captures intrinsic stochasticity, handles irregular sparse sampling, and yields subject-specific trajectories. Experiments on synthetic benchmarks and real-world longitudinal neuroimaging datasets show that IMMFM outperforms existing methods in both forecasting accuracy and further downstream tasks.

Andrew Draganov, Sharvaree Vadgama, Erik J. Bekkers

We show that the gradient of the cosine similarity between two points goes to zero in two under-explored settings: (1) if a point has large magnitude or (2) if the points are on opposite ends of the latent space. Counterintuitively, we prove that optimizing the cosine similarity between points forces them to grow in magnitude. Thus, (1) is unavoidable in practice. We then observe that these derivations are extremely general -- they hold across deep learning architectures and for many of the standard self-supervised learning (SSL) loss functions. This leads us to propose cut-initialization: a simple change to network initialization that helps all studied SSL methods converge faster.