Accurate protein function prediction requires integrating heterogeneous intrinsic signals (e.g., sequence and structure) with noisy extrinsic contexts (e.g., protein-protein interactions and GO term annotations). However, two key challenges hinder effective fusion: (i) cross-modal distributional mismatch among embeddings produced by pre-trained intrinsic encoders, and (ii) noisy relational graphs of extrinsic data that degrade GNN-based information aggregation. We propose Diffused and Aligned Multi-modal Protein Embedding (DAMPE), a unified framework that addresses these through two core mechanisms. First, we propose Optimal Transport (OT)-based representation alignment that establishes correspondence between intrinsic embedding spaces of different modalities, effectively mitigating cross-modal heterogeneity. Second, we develop a Conditional Graph Generation (CGG)-based information fusion method, where a condition encoder fuses the aligned intrinsic embeddings to provide informative cues for graph reconstruction. Meanwhile, our theoretical analysis implies that the CGG objective drives this condition encoder to absorb graph-aware knowledge into its produced protein representations. Empirically, DAMPE outperforms or matches state-of-the-art methods such as DPFunc on standard GO benchmarks, achieving AUPR gains of 0.002-0.013 pp and Fmax gains 0.004-0.007 pp. Ablation studies further show that OT-based alignment contributes 0.043-0.064 pp AUPR, while CGG-based fusion adds 0.005-0.111 pp Fmax. Overall, DAMPE offers a scalable and theoretically grounded approach for robust multi-modal protein representation learning, substantially enhancing protein function prediction.

Time series segmentation is a fundamental task in analyzing temporal data across various domains, from human activity recognition to energy monitoring. While numerous state-of-the-art methods have been developed to tackle this problem, the evaluation of their performance remains critically limited. Existing measures predominantly focus on change point accuracy or rely on point-based measures such as Adjusted Rand Index (ARI), which fail to capture the quality of the detected segments, ignore the nature of errors, and offer limited interpretability. In this paper, we address these shortcomings by introducing two novel evaluation measures: WARI (Weighted Adjusted Rand Index), that accounts for the position of segmentation errors, and SMS (State Matching Score), a fine-grained measure that identifies and scores four fundamental types of segmentation errors while allowing error-specific weighting. We empirically validate WARI and SMS on synthetic and real-world benchmarks, showing that they not only provide a more accurate assessment of segmentation quality but also uncover insights, such as error provenance and type, that are inaccessible with traditional measures.

The performance of machine learning and pattern recognition algorithms generally depends on data representation. That is why, much of the current effort in performing machine learning algorithms goes into the design of preprocessing frameworks and data transformations able to support effective machine learning. The method proposed in this work consists of a hybrid linear feature extraction scheme to be used in supervised multi-class classification problems. Inspired by two recent linear discriminant methods: robust sparse linear discriminant analysis (RSLDA) and inter-class sparsitybased discriminative least square regression (ICS_DLSR), we propose a unifying criterion that is able to retain the advantages of these two powerful methods. The resulting transformation relies on sparsity-promoting techniques both to select the features that most accurately represent the data and to preserve the row-sparsity consistency property of samples from the same class. The linear transformation and the orthogonal matrix are estimated using an iterative alternating minimization scheme based on steepest descent gradient method and different initialization schemes. The proposed framework is generic in the sense that it allows the combination and tuning of other linear discriminant embedding methods. According to the experiments conducted on several datasets including faces, objects, and digits, the proposed method was able to outperform competing methods in most cases.

This work applies Generative Flow Networks (GFlowNets) to three graph optimization problems: the Traveling Salesperson Problem, Minimum Spanning Tree, and Shortest Path. GFlowNets are generative models that learn to sample solutions proportionally to a reward function. The models are trained using the Trajectory Balance loss to build solutions sequentially, selecting edges for spanning trees, nodes for paths, and cities for tours. Experiments on benchmark instances of varying sizes show that GFlowNets learn to find optimal solutions. For each problem type, multiple graph configurations with different numbers of nodes were tested. The generated solutions match those from classical algorithms (Dijkstra for shortest path, Kruskal for spanning trees, and exact solvers for TSP). Training convergence depends on problem complexity, with the number of episodes required for loss stabilization increasing as graph size grows. Once training converges, the generated solutions match known optima from classical algorithms across the tested instances. This work demonstrates that generative models can solve combinatorial optimization problems through learned policies. The main advantage of this learning-based approach is computational scalability: while classical algorithms have fixed complexity per instance, GFlowNets amortize computation through training. With sufficient computational resources, the framework could potentially scale to larger problem instances where classical exact methods become infeasible.

Novel Markov Chain Monte Carlo (MCMC) methods have enabled the generation of large ensembles of redistricting plans through graph partitioning. However, existing algorithms such as Reversible Recombination (RevReCom) and Metropolized Forest Recombination (MFR) are constrained to sampling from distributions related to spanning trees. We introduce the marked edge walk (MEW), a novel MCMC algorithm for sampling from the space of graph partitions under a tunable distribution. The walk operates on the space of spanning trees with marked edges, allowing for calculable transition probabilities for use in the Metropolis-Hastings algorithm. Empirical results on real-world dual graphs show convergence under target distributions unrelated to spanning trees. For this reason, MEW represents an advancement in flexible ensemble generation. Introduction Recent advances in computational capabilities have greatly increased legislators' abilities to optimize political redistricting plans.

While attention has been empirically shown to improve model performance, it lacks a rigorous mathematical justification. This short paper establishes a novel connection between attention mechanisms and multinomial regression. Specifically, we show that in a fixed multinomial regression setting, optimizing over latent features yields solutions that align with the dynamics induced on features by attention blocks. In other words, the evolution of representations through a transformer can be interpreted as a trajectory that recovers the optimal features for classification.

Personal use of this material is permitted. Abstract-- The ability to operate safely in increasingly complex traffic scenarios is a fundamental requirement for Automated Driving Systems (ADS). T o support this objective, this work introduces a pipeline for traffic scenario clustering and the analysis of scenario category completeness. The Clustering V ector Quantized - V ariational Autoencoder (CVQ-V AE) is employed for the clustering of highway traffic scenarios and utilized to create various catalogs with differing numbers of traffic scenario categories. Subsequently, the impact of the number of categories on the completeness considerations of the traffic scenario categories is analyzed. The results show an outperforming clustering performance compared to previous work. The trade-off between cluster quality and the amount of required data to maintain completeness is discussed based on the publicly available highD dataset. A key challenge for the safe release of automated driving is equipping Automated Driving System (ADS) functions with the ability to accurately interpret and respond to the wide range of driving conditions they encounter. To ensure the safety of the system and maintain compliance with legal and regulatory requirements, this challenge is typically addressed through the concept of an Operational Design Domain (ODD).

Large language models are able to exploit in-context learning to access external knowledge beyond their training data through retrieval-augmentation. While promising, its inner workings remain unclear. In this work, we shed light on the mechanism of in-context retrieval augmentation for question answering by viewing a prompt as a composition of informational components. We propose an attribution-based method to identify specialized attention heads, revealing in-context heads that comprehend instructions and retrieve relevant contextual information, and parametric heads that store entities' relational knowledge. To better understand their roles, we extract function vectors and modify their attention weights to show how they can influence the answer generation process. Finally, we leverage the gained insights to trace the sources of knowledge used during inference, paving the way towards more safe and transparent language models.

Buildings account for a significant share of global energy consumption and emissions, making it critical to operate them efficiently. As electricity grids become more volatile with renewable penetration, buildings must provide flexibility to support grid stability. Building automation plays a key role in enhancing efficiency and flexibility via centralized operations, but it must prioritize occupant-centric strategies to balance energy and comfort targets. However, incorporating occupant information into large-scale, centralized building operations remains challenging due to data limitations. We investigate the potential of using whole-building smart meter data to infer both occupancy and system operations. Integrating these insights into data-driven building energy analysis allows more occupant-centric energy-saving and flexibility at scale. Specifically, we propose OccuEMBED, a unified framework for occupancy inference and system-level load analysis. It combines two key components: a probabilistic occupancy profile generator, and a controllable and interpretable load disaggregator supported by Kolmogorov-Arnold Networks (KAN). This design embeds knowledge of occupancy patterns and load-occupancy-weather relationships into deep learning models. We conducted comprehensive evaluations to demonstrate its effectiveness across synthetic and real-world datasets compared to various occupancy inference baselines. OccuEMBED always achieved average F1 scores above 0.8 in discrete occupancy inference and RMSE within 0.1-0.2 for continuous occupancy ratios. We further demonstrate how OccuEMBED integrates with building load monitoring platforms to display occupancy profiles, analyze system-level operations, and inform occupant-responsive strategies. Our model lays a robust foundation in scaling occupant-centric building management systems to meet the challenges of an evolving energy system.

Simulation-based inference (SBI) offers a flexible and general approach to performing Bayesian inference: In SBI, a neural network is trained on synthetic data simulated from a model and used to rapidly infer posterior distributions for observed data. A key goal for SBI is to achieve accurate inference with as few simulations as possible, especially for expensive simulators. In this work, we address this challenge by repurposing recent probabilistic foundation models for tabular data: We show how tabular foundation models -- specifically TabPFN -- can be used as pre-trained autoregressive conditional density estimators for SBI. We propose Neural Posterior Estimation with Prior-data Fitted Networks (NPE-PFN) and show that it is competitive with current SBI approaches in terms of accuracy for both benchmark tasks and two complex scientific inverse problems. Crucially, it often substantially outperforms them in terms of simulation efficiency, sometimes requiring orders of magnitude fewer simulations. NPE-PFN eliminates the need for inference network selection, training, and hyperparameter tuning. We also show that it exhibits superior robustness to model misspecification and can be scaled to simulation budgets that exceed the context size limit of TabPFN. NPE-PFN provides a new direction for SBI, where training-free, general-purpose inference models offer efficient, easy-to-use, and flexible solutions for a wide range of stochastic inverse problems.