30 accepted papers
With the widespread availability of pre-trained diffusion models, there are many options for which models to use and how to use them together. Making these decisions depends highly on both the user's goals and the expertise of each model. Taking this into account, we propose coordinating models as o…
Higher-order structures are powerful relational modeling tools, yet existing spectral operators decompose topology into separate ranks, leaving practitioners to fuse information back to vertices through ad-hoc choices. We introduce _Collapsed Effective Operators_, which marginalize higher-order stru…
Naive application of token-wise temperature scaling alters the maximum a posteriori (MAP) estimate at the sequence level, degrading model performance. This issue is exacerbated in MDMs, which estimate sequence-level likelihoods with high variance under different unmasking orders. In this paper, we a…
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 l…
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 prov…
Graph diffusion models, dominant in graph generative modeling, remain underexplored for graph-to-graph translation tasks like chemical reaction prediction. We demonstrate that standard permutation equivariant denoisers face fundamental limitations in these tasks due to their inability to break symme…
Conventional wisdom attributes the success of Generative Flow Networks (GFlowNets) to their ability to exploit the compositional structure of the sample space for learning generalizable flow functions (Bengio et al., 2021). Despite the abundance of empirical evidence, formalizing this belief with ve…
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…
Generative Flow Networks (GFlowNets) are an emerging class of sampling methods for distributions over discrete and compositional objects, e.g., graphs. In spite of their remarkable success in problems such as drug discovery and phylogenetic inference, the question of when and whether GFlowNets learn…
We introduce a novel positional encoding strategy for Transformer-style models, addressing the shortcomings of existing, often ad hoc, approaches. Our framework implements a flexible mapping from the algebraic specification of a domain to a positional encoding scheme where positions are interpreted…
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 n…
Heterogeneity, e.g., due to different types of layers or multiple sub-models, poses key challenges in analyzing the generalization behavior of several modern architectures. For instance, descriptors based on Persistent Homology (PH) are being increasingly integrated into Graph Neural Networks (GNNs)…
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 ste…
$E(n)$-Equivariant Graph Neural Networks (EGNNs) are among the most widely used and successful models for representation learning on geometric graphs (e.g., 3D molecules). However, while the expressivity of EGNNs has been explored in terms of geometric variants of the Weisfeiler-Leman isomorphism te…
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 G…
Graph neural networks (GNNs) have been analyzed from multiple perspectives, including the WL-hierarchy, which exposes limits on their expressivity to distinguish graphs. However, characterizing the class of functions that they learn has remained unresolved. We address this fundamental question for m…
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 structur…
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 distrib…
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…
Learning disentangled representations is important for unraveling the underlying complex interactions between latent generative factors. Disentanglement has been formalized using a symmetry-centric notion for unstructured spaces, however, graphs have eluded a similarly rigorous treatment. We fill th…
Domain generalization is the problem of machine learning when the training data and the test data come from different “domains” (data distributions). We propose an elementary theoretical model of the domain generalization problem, introducing the concept of a meta-distribution over domains. In our m…
We address two fundamental questions about graph neural networks (GNNs). First, we prove that several important graph properties, e.g., shortest/longest cycle, diameter, or certain motifs, cannot be computed by GNNs that rely entirely on local information. Such GNNs include the standard message pass…
We extend structured prediction to deliberative outcomes. Specifically, we learn parameterized games that can map any inputs to equilibria as the outcomes. Standard structured prediction models rely heavily on global scoring functions and are therefore unable to model individual player preferences o…
Engineered proteins offer the potential to solve many problems in biomedicine, energy, and materials science, but creating designs that succeed is difficult in practice. A significant aspect of this challenge is the complex coupling between protein sequence and 3D structure, with the task of finding…
We resolve the fundamental problem of online decoding with general nth order ergodic Markov chain models. Specifically, we provide deterministic and randomized algorithms whose performance is close to that of the optimal offline algorithm even when latency is small. Our algorithms admit efficient im…
We propose a new approach to graph compression by appeal to optimal transport. The transport problem is seeded with prior information about node importance, attributes, and edges in the graph. The transport formulation can be setup for either directed or undirected graphs, and its dual characterizat…
We introduce a new framework for learning in severely resource-constrained settings. Our technique delicately amalgamates the representational richness of multiple linear predictors with the sparsity of Boolean relaxations, and thereby yields classifiers that are compact, interpretable, and accurate…
We introduce a framework to transfer knowledge acquired from a repository of (heterogeneous) supervised datasets to new unsupervised datasets. Our perspective avoids the subjectivity inherent in unsupervised learning by reducing it to supervised learning, and provides a principled way to evaluate u…
Aggregative games provide a rich abstraction to model strategic multi-agent interactions. We focus on learning local aggregative games, where the payoff of each player is a function of its own action and the aggregate behavior of its neighbors in a connected digraph. We show the existence of a pure…
Many real phenomena, including behaviors, involve strategic interactions that can be learned from data. We focus on learning tree structured potential games where equilibria are represented by local maxima of an underlying potential function. We cast the learning problem within a max margin setting…