However, autoregressive sampling generates tokens one at a time making it slow, and even prohibitive in certain tasks.

ARXIV PREPRINT 1 Attention-Based V ariational Framework for Joint and Individual Components Learning with Applications in Brain Network Analysis Yifei Zhang, Meimei Liu, and Zhengwu Zhang Abstract Brain organization is increasingly characterized through multiple imaging modalities, most notably structural connectivity (SC) and functional connectivity (FC). Integrating these inherently distinct yet complementary data sources is essential for uncovering the cross-modal patterns that drive behavioral phenotypes. However, effective integration is hindered by the high dimensionality and non-linearity of connectome data, complex non-linear SC-FC coupling, and the challenge of disentangling shared information from modality-specific variations. To address these issues, we propose the Cross-Modal Joint-Individual Variational Network (CM-JIVNet), a unified probabilistic framework designed to learn factorized latent representations from paired SC-FC datasets. Our model utilizes a multi-head attention fusion module to capture non-linear cross-modal dependencies while isolating independent, modality-specific signals. V alidated on Human Connectome Project Y oung Adult (HCP-Y A) data, CM-JIVNet demonstrates superior performance in cross-modal reconstruction and behavioral trait prediction. By effectively disentangling joint and individual feature spaces, CM-JIVNet provides a robust, interpretable, and scalable solution for large-scale multimodal brain analysis.

Rényi transfer entropy (RTE) is a generalization of classical transfer entropy that replaces Shannon's entropy with Rényi's information measure. This, in turn, introduces a new tunable parameter $α$, which accounts for sensitivity to low- or high-probability events. Although RTE shows strong potential for analyzing causal relations in complex, non-Gaussian systems, its practical use is limited, primarily due to challenges related to its accurate estimation and interpretation. These difficulties are especially pronounced when working with finite, high-dimensional, or heterogeneous datasets. In this paper, we systematically study the performance of a k-nearest neighbor estimator for both Rényi entropy (RE) and RTE using various synthetic data sets with clear cause-and-effect relationships inherent to their construction. We test the estimator across a broad range of parameters, including sample size, dimensionality, memory length, and Rényi order $α$. In particular, we apply the estimator to a set of simulated processes with increasing structural complexity, ranging from linear dynamics to nonlinear systems with multi-source couplings. To address interpretational challenges arising from potentially negative RE and RTE values, we introduce three reliability conditions and formulate practical guidelines for tuning the estimator parameters. We show that when the reliability conditions are met and the parameters are calibrated accordingly, the resulting effective RTE estimates accurately capture directional information flow across a broad range of scenarios. Results obtained show that the explanatory power of RTE depends sensitively on the choice of the Rényi parameter $α$. This highlights the usefulness of the RTE framework for identifying the drivers of extreme behavior in complex systems.

We propose a new framework for formulating optimal transport distances between Markov chains. Previously known formulations studied couplings between the entire joint distribution induced by the chains, and derived solutions via a reduction to dynamic programming (DP) in an appropriately defined Markov decision process. This formulation has, however, not led to particularly efficient algorithms so far, since computing the associated DP operators requires fully solving a static optimal transport problem, and these operators need to be applied numerous times during the overall optimization process. In this work, we develop an alternative perspective by considering couplings between a ``flattened'' version of the joint distributions that we call discounted occupancy couplings, and show that calculating optimal transport distances in the full space of joint distributions can be equivalently formulated as solving a linear program (LP) in this reduced space. This LP formulation formulation allows us to port several algorithmic ideas from other areas of optimal transport theory. In particular, our formulation makes it possible to introduce an appropriate notion of entropy regularization into the optimization problem, which in turn enables us to directly calculate optimal transport distances via a Sinkhorn-like method we call Sinkhorn Value Iteration (SVI). We show both theoretically and empirically that this method converges quickly to an optimal coupling, essentially at the same computational cost of running vanilla Sinkhorn in each pair of states. Along the way, we point out that our optimal transport distance exactly matches the common notion of bisimulation metrics between Markov chains, and thus our results also apply to computing such metrics, and in fact our algorithm turns out to be significantly more efficient than the best known methods developed so far for this purpose.

Optimal transport (OT) is a general framework for finding a minimum-cost transport plan, or coupling, between probability distributions, and has many applications in machine learning. A key challenge in applying OT to massive datasets is the quadratic scaling of the coupling matrix with the size of the dataset.

Inferring directional couplings from the spike data of networks is desired in various scientific fields such as neuroscience. Here, we apply a recently proposed objective procedure to the spike data obtained from the Hodgkin-Huxley type models and in vitro neuronal networks cultured in a circular structure. As a result, we succeed in reconstructing synaptic connections accurately from the evoked activity as well as the spontaneous one. To obtain the results, we invent an analytic formula approximately implementing a method of screening relevant couplings. This significantly reduces the computational cost of the screening method employed in the proposed objective procedure, making it possible to treat large-size systems as in this study.