Giosue Migliorini

Gavin Kerrigan, Giosue Migliorini, Padhraic Smyth

We study the geometry of conditional optimal transport (COT) and prove a dynamical formulation which generalizes the Benamou-Brenier Theorem. Equipped with these tools, we propose a simulation-free flow-based method for conditional generative modeling. Our method couples an arbitrary source distribution to a specified target distribution through a triangular COT plan, and a conditional generative model is obtained by approximating the geodesic path of measures induced by this COT plan. Our theory and methods are applicable in infinite-dimensional settings, making them well suited for a wide class of Bayesian inverse problems. Empirically, we demonstrate that our method is competitive on several challenging conditional generation tasks, including an infinite-dimensional inverse problem.

Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts et al.

Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules. Yet understanding which internal features drive their outputs remains challenging. Standard sparse autoencoders (SAEs), effective on transformer-style sequence embeddings, do not transfer cleanly to pairformer-like architectures: naively operating on pairwise representations yields a quadratic blow-up of features and obscures concepts distributed jointly across sequence and pair representations. We introduce PairSAE, which summarizes pairwise tensors via an N-mode SVD into token-wise interaction roles, then uses a sparse autoencoder to learn a shared set of token-level features that decode into both sequence and pair representations. Evaluated on Boltz-2 activations for PLINDER protein-ligand complexes, PairSAE yields interpretable features that align with UniProt annotations and predict Boltz-2 affinity values. These results indicate that PairSAE links the latent space of foundation models for structural biology to interpretable structural concepts, clarifying what the model "knows" while avoiding pairformer-induced pitfalls that limit conventional SAEs.

Giosue Migliorini, Padhraic Smyth

Systems of interacting continuous-time Markov chains are a powerful model class, but inference is typically intractable in high dimensional settings. Auxiliary information, such as noisy observations, is typically only available at discrete times, and incorporating it via a Doob's $h-$transform gives rise to an intractable posterior process that requires approximation. We introduce Latent Interacting Particle Systems, a model class parameterizing the generator of each Markov chain in the system. Our inference method involves estimating look-ahead functions (twist potentials) that anticipate future information, for which we introduce an efficient parameterization. We incorporate this approximation in a twisted Sequential Monte Carlo sampling scheme. We demonstrate the effectiveness of our approach on a challenging posterior inference task for a latent SIRS model on a graph, and on a neural model for wildfire spread dynamics trained on real data.

Gavin Kerrigan, Giosue Migliorini, Padhraic Smyth

We propose Functional Flow Matching (FFM), a function-space generative model that generalizes the recently-introduced Flow Matching model to operate in infinite-dimensional spaces. Our approach works by first defining a path of probability measures that interpolates between a fixed Gaussian measure and the data distribution, followed by learning a vector field on the underlying space of functions that generates this path of measures. Our method does not rely on likelihoods or simulations, making it well-suited to the function space setting. We provide both a theoretical framework for building such models and an empirical evaluation of our techniques. We demonstrate through experiments on several real-world benchmarks that our proposed FFM method outperforms several recently proposed function-space generative models.