Decafs: Disentangled Conditional adversarial Flows

Flow-based models have established state-of-the-art performance in generative modeling across domains, but are hard to interpret due to their complex latent embeddings. In particular, the entanglement of generative factors in the latent space hinders controlled generation. We circumvent this issue by appealing to a novel conditional generator based on Lie groups that disentangles an alternative latent space, which is aligned closely with the latent flow space using an adversarial loss. Our approach facilitates interpretable conditional generation while obviating the need to expand the dimensionality of the flow space (owing to its invertibility requirements). The proposed model demonstrates strong performance across conditional image (including, outperforming StyleGAN on MNIST, dSprites) and molecule (using standard QM9, ZINC and MOSES) generation tasks

Collapsed Effective Operators for Higher-order Structures

Higher-order structures are powerful relational modeling tools, yet existing spectral operators decompose the topology into separate ranks, leaving practitioners to fuse the information back to vertices through ad hoc choices. We introduce Collapsed Effective Operators, which condense higher-order degrees of freedom into a single vertex-level operator via Schur complementation of a graded Laplacian. This yields a (generally dense) operator that encodes long-range interactions mediated by topology and is applicable to arbitrary higher-order constructs. We show it preserves positive semi-definiteness with a spectral upper bound relative to the rank-0 Hodge Laplacian, effectively lowering system energy under higher-order connectivity. Empirically, our operator improves spectral clustering, signal smoothing, and enables the inclusion of topological features in neural network architectures via positional encoding. The project page can be found http://circle-group.github.io/research/CollapsedEffectiveOperators

Learning Context-Aware Neural ODE Dynamics for Adaptive Robotic Control

Robotic systems deployed in uncertain and dynamically changing environments often face variations in contact conditions, aerodynamic effects, and external disturbances that challenge reliable control. To remain effective under model-based control, these systems require dynamics models that can adapt to such changes, especially when direct access to complete environmental information is limited. To enable adaptability and facilitate integration with model predictive control, we propose a context-aware dynamics model based on neural ordinary differential equations, which infers environmental factors from state-action histories using a two-phase training procedure. We validate the approach across diverse robotic platforms, including a quadrotor in simulation, as well as a Sphero BOLT robot and a Fanuc manipulator in real-world experiments. The results demonstrate that our method effectively adapts to temporally and spatially varying environmental changes across different tasks. Videos are available at https://youtu.be/PY0sNyF2rqE , and the source code is available at https://github.com/syyu410-yu/context-aware-neural-ode-control.git .

Flexible Flows for Biological Sequence Design

Designing functional biological sequences requires navigating vast discrete spaces under strict evolutionary and biophysical constraints. Discrete Flow Matching (DFM) offers a generative framework over such spaces, but existing approaches rely on biologically uninformative couplings and offer limited flexibility for variable-length sequence generation and fine-grained control. We propose a structured coupling that encodes domain-specific preferences among sequence elements, biasing the source distribution toward plausible regions without modifying the flow objective or training procedure. Building on this, we introduce a latent edit-based rate parameterization that models variable-length generation via edit operations conditioned on a shared global latent, akin to a latent variable model, while remaining tractable. We further introduce a latent classifier-free guidance mechanism that steers generation coherently in continuous latent space, along with Dirichlet-prior temperature scaling for test-time control over edit operations. Our method achieves state-of-the-art performance across diverse biological sequence tasks, including density estimation, unconditional and conditional DNA sequence generation, and peptide sequence generation.

Divide-and-Denoise: A Game-Theoretic Method for Fairly Composing Diffusion Models

The abundance of pre-trained diffusion models provides an opportunity for composition. Combining several models, however, runs the risk of one model dominating or models disagreeing with each other. Here, we propose Divide-and-Denoise, a method for coordinating multiple pre-trained diffusion models during sampling. Much like managing a specialized workforce, our method creates a fair but efficient division of labor across models. Central to our method is the notion of an allocation which defines the responsibility of each model to every region of the noisy sample. At every timestep, we then denoise by (i) updating the allocation by solving a fair division game, where we divide the sample into regions that maximize total utility under fairness constraints, and (ii) aligning the models with this allocation, where we guide each model to denoise within its assigned region. This leads to a new composite denoising process that evolves in tandem with a division process. We evaluate Divide-and-Denoise on conditional image generation. Across several quality metrics, including the GenEval benchmark, our method outperforms baselines and resolves common failures including missing objects and mismatched attributes. Experiments show that Divide-and-Denoise utilizes each model's expertise without neglecting any other model.

Margin-calibrated Classifier Guidance for Property-driven Synthesis Planning

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.

The Logical Expressiveness of Topological Neural Networks

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)\, \varphi(x_i,x_j), $ which explicitly quantifies pairs $(x_i, x_j)$ satisfying property $\varphi$. 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.

Contraction and Hourglass Persistence for Learning on Graphs, Simplices, and Cells

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}.

Canonicalizing Multimodal Contrastive Representation Learning

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/

On topological descriptors for graph products

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.