Bayesian additive spanning tree (BAST) is an useful tool for interpretable, non-parametric regression on complex constrained domains. It improves upon the performance of Bayesian additive regression trees (BART) by replacing axis-aligned splits through binary tree components by cuts on a spanning tree components, enabling the formation of contiguous splits that respect the underlying complex structure. While BAST is effective for learning on constrained spaces, it still relies on hard partitions, albeit on spanning trees, which limits its ability to represent smoothly varying functions on constrained domains. We propose Probabilistically-routed Bayesian additive spanning trees (PR-BAST), a principled relaxation that replaces hard cuts on spanning tree components with probabilistic routing along spanning tree components. PR-BAST represents the regression surface as an additive ensemble of such spanning tree-aligned smooth components. Conditional on a fixed spanning tree, each component in PR-BAST induces a Gaussian random field with a sparse, tree-structured precision matrix, enabling scalable posterior computation via sparse linear algebra. We theoretically establish that PR-BAST yields strictly faster posterior contraction rates compared to BAST under graph-smooth truth. Experiments on synthetic and real datasets demonstrate that PR-BAST consistently improves accuracy over BAST and other baselines, while retaining the interpretability of tree-based models.
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Social Aspects · Accountability, Transparency, and Interpretability
Personalization underpins the modern digital economy. Today, personalization is largely implemented through provider-managed infrastructure that infers user preferences from behavioral data, with limited portability or user control. However, large language models (LLMs) are increasingly being used to perform tasks on users' behalf. The age of LLMs for the first time provides a path to a more controllable and interpretable personalization paradigm, grounded in user-expressed natural language preferences and context. In this position paper, we argue that to provide robust and user-centric personalization, we need a new Human Context Protocol (HCP) to represent and share personal preferences across AI systems. HCP treats preferences as a portable, user-governed layer in the personalization stack, enabling interoperability, scoped access, and revocation. Along with a working prototype to ground discussion, we consider counterarguments along adoption dynamics and market incentives, high-stakes use cases, and outline novel paths via the HCP towards trustworthy personalization in the human-AI economy.
Deep Learning · Large Language Models
Dictionary learning has recently emerged as a promising approach for mechanistic interpretability of large transformer models. Disentangling high-dimensional transformer embeddings requires algorithms that scale to high-dimensional data with large sample sizes. Recent work has explored sparse autoencoders (SAEs) for this problem. However, SAEs use a simple linear encoder to solve the sparse encoding subproblem, which is known to be NP-hard. It is therefore interesting to understand whether this approach is sufficient to find good solutions to the dictionary learning problem or if a more sophisticated algorithm could find better solutions. In this work, we propose Double-Batch KSVD (DB-KSVD), a scalable dictionary learning algorithm that adapts the classic KSVD algorithm. DB-KSVD is informed by the rich theoretical foundations of KSVD but scales to datasets with millions of samples and thousands of dimensions. We demonstrate the efficacy of DB-KSVD by disentangling text embeddings of the Gemma-2-2B and Pythia-160M models and evaluating on six metrics from the SAEBench benchmark, where we achieve competitive results when compared to established approaches based on SAEs. We further show similar results when disentangling image embeddings obtained from the DINOv2-S and DINOv2-B models, solidifying our findings. By matching SAE performance with an entirely different optimization approach, our results suggest that (i) SAEs do find strong solutions to the dictionary learning problem and (ii) traditional optimization approaches can be scaled to the required problem sizes, offering a promising avenue for further research. We make an implementation of DB-KSVD available.
Applications · Health / Medicine
Predicting high-dimensional transcriptional responses to genetic perturbations is challenging due to severe experimental noise and sparse gene-level effects. Existing methods often suffer from mean collapse, where high correlation is achieved by predicting global average expression rather than perturbation-specific responses, leading to many false positives and limited biological interpretability. Recent approaches incorporate biological knowledge graphs into perturbation models, but these graphs are typically treated as dense and static, which can propagate noise and obscure true perturbation signals. We propose AdaPert, a perturbation-conditioned framework that addresses mean collapse by explicitly modeling sparsity and biological structure. AdaPert learns perturbation-specific subgraphs from biological knowledge graphs and applies adaptive learning to separate true signals from noise. Across multiple genetic perturbation benchmarks, AdaPert consistently outperforms existing baselines and achieves substantial improvements on DEG-aware evaluation metrics, indicating more accurate recovery of perturbation-specific transcriptional changes.
Applications · Computer Vision
Recent multimodal large language models have demonstrated strong reasoning ability, yet their reliability as automated evaluators remains limited by a critical weakness: when visual evidence conflicts with textual cues, MLLM judges tend to reward plausible narratives over perceptually correct answers. We identify and systematically analyze this phenomenon, which we term \textit{Perceptual Judgment Bias}. Through controlled visual perturbations, existing multimodal judges frequently anchor on the response text instead of their own visual perception, leading to inconsistent and non-verifiable evaluations. To address this issue, we introduce the \textit{Perceptually Perturbed Judgment Dataset}, which constructs minimally edited counterfactual responses that isolate perceptual errors and enable verifiable supervision. Building on this dataset, we develop a unified training framework that combines a structured GRPO-based reward with a batch-ranking objective, achieving coherent global ordering without explicit pairwise labels. Experiments across diverse MLLM-as-a-Judge benchmarks show that our approach substantially improves perceptual fidelity, ranking coherence, and alignment with human evaluation. Our results establish a scalable and generalizable pathway for training multimodal judges that are perceptually grounded, interpretable, and robust to visual–reasoning conflicts.
Applications · Computer Vision
With the rapid development of Vision-Language Models (VLMs) and the growing demand for their applications, efficient compression of the image inputs has become increasingly important. Existing VLMs predominantly digest and understand high-bitrate compressed images, while their ability to interpret low-bitrate compressed images has yet to be explored by far. In this paper, we introduce the first comprehensive benchmark to evaluate the ability of VLM against compressed images, varying existing widely used image codecs and diverse set of tasks, encompassing over one million compressed images in our benchmark. Next, we analyse the source of performance gap, by categorising the gap from a) the information loss during compression and b) generalisation failure of VLM. We visualize these gaps with concrete examples and identify that for compressed images, only the generalization gap can be mitigated. Finally, we propose a universal VLM adaptor to enhance model performance on images compressed by existing codecs. Consequently, we demonstrate that a single adaptor can improve VLM performance across images with varying codecs and bitrates by 10%-30%. We believe that our benchmark and enhancement method provide valuable insights and contribute toward bridging the gap between VLMs and compressed images.
Social Aspects · Accountability, Transparency, and Interpretability
Pre-trained transformers have demonstrated remarkable generalization abilities, at times extending beyond the scope of their training data. Yet, real-world deployments often face unexpected or adversarial data that diverges from training data distributions. Without explicit mechanisms for handling such shifts, model reliability and safety degrade, urging more disciplined study of out-of-distribution (OOD) settings for transformers. By systematic experiments, we present a mechanistic framework for delineating the precise contours of transformer model robustness. We find that OOD inputs, including subtle typos and jailbreak prompts, drive language models to operate on an increased number of fallacious concepts in their internals. We leverage this device to quantify and understand the degree of distributional shift in prompts, enabling a mechanistically grounded fine-tuning strategy to robustify LLMs. Expanding the very notion of OOD from input data to a model’s private computational processes—a new transformer diagnostic at inference time—is a critical step toward making AI systems safe for deployment across science, business, and government.
A long-standing question in physical reasoning is whether video-based models need to rely on factorized representations of physical variables in order to make physically accurate predictions, or whether they can implicitly represent such variables in a distributed manner. While modern video world models achieve strong performance on intuitive physics benchmarks, it remains unclear which of these representational regimes they implement internally. Here, we present the first interpretability study to directly examine physical representations inside large-scale video encoders. Using layerwise probing, subspace geometry, patch-level decoding, and targeted attention ablations, we characterize where physical information becomes accessible and how it is organized within encoder-based video transformers. Across architectures, we identify a sharp intermediate-depth transition— which we call the \emph{Physics Emergence Zone}—at which physical variables become accessible. Physics-related representations peak shortly after this transition and degrade toward the output layers. Decomposing motion into explicit variables, we find that scalar quantities such as speed and acceleration are available from early layers onwards, whereas motion direction becomes accessible only at the Physics Emergence Zone. Notably, we find that direction is encoded through a high-dimensional population structure with circular geometry, requiring coordinated multi-feature intervention to control. These findings suggest that modern video models do not use factorized representations of physical variables like a classical physics engine. Instead, they use a distributed representation that is nonetheless sufficient for making physical predictions.
Social Aspects · Accountability, Transparency, and Interpretability
Large language models can represent a variety of personas but typically default to a helpful Assistant identity cultivated during post-training. Across several different models, we find an “Assistant Axis" in their activation space, which captures the extent to which a model is operating in its default Assistant mode. Steering towards the Assistant direction reinforces helpful and harmless behavior; steering away increases the model’s tendency to identify as other entities. Measuring deviations along the Assistant Axis predicts “persona drift,” a phenomenon where models slip into exhibiting harmful or bizarre behaviors that are uncharacteristic of their typical persona. We find that persona drift is often driven by conversations demanding meta-reflection on the model’s processes or featuring emotionally vulnerable users. We show that restricting activations to a fixed region along the Assistant Axis can stabilize model behavior in these scenarios—and also in the face of adversarial persona-based jailbreaks. Our results suggest that post-training steers models toward a particular region of persona space but only loosely tethers them to it, motivating work on training and steering strategies that more deeply anchor models to a coherent persona.
Applications · Time Series
Contrastive learning has advanced the representation learning across domains, yet its success relies on data augmentations that preserve semantic contents while providing the view diversities. Multivariate time series, however, are inherently noisy, non-stationary, and lack such intuitive semantic cues. Consequently, standard heuristic augmentations that ignore semantic parts may risk destroying critical temporal dependencies. Though some recent approaches attempt to isolate informative components, they typically rely on an implicit neural mechanism to infer semantics, thus limiting the interpretability and controllability. To address this, we propose ProSAR, an information-theoretic framework that leverages the explicit prototype alignment to guide semantic augmentations, and establish a feedback loop between the augmentation, contrastive learning, and prototype updates. Specifically, grounded in our proposed Prototype-Conditioned Information Bottleneck principle, we leverage the time-domain prototypes as explicit anchors to localize semantic segments, and develop a time–frequency augmentation strategy that retains prototype-consistent information while discarding noise. To promote semantically consistent prototypes for a reliable view generation, we design a dual-prototype loop where the augmented views are encoded into representations and then the learned representations are clustered to update latent prototypes, whose decoded feedback refines the time-domain prototypes for the next round of augmentation. Experiments on diverse time-series benchmarks demonstrate that ProSAR outperforms the other contrastive learning methods on downstream forecasting and classification tasks.
Applications · Health / Medicine
Effective DNA modeling demands the integration of complex patterns such as local motifs, long-range dependencies, and periodic signals. Yet, architectures like CNNs, Transformers, and SSMs are hindered by static or time-domain-exclusive designs, which limit their representational flexibility. To address this, we introduce the **Synergistic Plasticity Unit (SPU)**, a scalable architecture that achieves multi-level plasticity through three synergistic layers. Specifically, SPU integrates a *Locus Plasticity Layer* (LPL) to capture fine-grained local motifs via token-specific convolution operations, while utilizing a *Domain Plasticity Layer* (DPL) to form multi-domain global features by concurrently modeling sequential (time) and spectral (frequency) patterns. Furthermore, it incorporates a *Saliency Plasticity Layer* (SPL) to optimize information flow through dual-axis saliency scoring. Supported by theoretical analysis, extensive empirical validation, and in-depth biological interpretation, this unified design enables SPU to achieve state-of-the-art performance with quasi-linear complexity, establishing a robust and principled paradigm for DNA modeling. Code will be available upon acceptance.
Deep Learning · Large Language Models
The transition from single-turn models to Multi-Agent Systems (MAS) promises enhanced problem-solving capabilities, yet the centralized orchestration topology remains a critical point of fragility. To analyze this, we propose a Mean-Field Entropy Dynamics framework, modeling the orchestration process as a system governed by the competing forces of task resolution and cumulative context loading. To facilitate high-resolution validation, we introduce Inverse Workflow Generation (IWG), a multi-agent pipeline that synthesizes process-verifiable, high-complexity benchmarks with dense intermediate checkpoints. We demonstrate that our entropy dynamics model fits empirical trajectories, providing physically interpretable parameters that quantify system stability and performance collapse. Crucially, our analysis uncovers a ``Reasoning Trap": while reasoning-heavy models excel in isolated tasks, they frequently fail as orchestrators due to context squeezing. By elucidating the physical mechanisms underlying the Orchestrator and quantifying systemic uncertainty, our findings offer insights for the architectural design development of Multi-Agent Systems in prospective research.
Designing biological sequences such as proteins and DNA for desired properties is challenging due to vast search spaces and limited wet lab evaluation budgets. Current evolutionary approaches ignore sequential dependencies and rely on random mutations, which scale poorly for long sequences. In contrast, reinforcement learning (RL) and generative models explicitly model sequence structure but require large datasets to guide generation toward the target properties. These limitations suggest the need for a method that combines the sample efficiency of evolutionary approaches with the ability to exploit sequential structure. In this work, we propose a novel evolutionary approach, $\texttt{IDEAS}$, in which mutations are guided by an explainable model. The model identifies critical motifs in high-fitness sequences and uses them to mutate non-critical positions. Across six continuous-property datasets, seven baselines, and three evaluation budgets, $\texttt{IDEAS}$ achieves a 19% acceleration in design while maintaining a favorable position on the Pareto curve balancing acceleration, diversity, and novelty.
Social Aspects · Accountability, Transparency, and Interpretability
Activation steering offers a computationally efficient mechanism for controlling Large Language Models (LLMs) without fine-tuning. While effectively controlling target traits (e.g., persona), coherency degradation remains a major obstacle to safety and practical deployment. We hypothesize that this degradation stems from intervening on the residual stream, which indiscriminately affects aggregated features and inadvertently amplifies off-target noise. In this work, we identify a sparse subset of attention heads (only three heads) that independently govern persona and style formation, which we term *Style Modulation Heads*. Specifically, these heads can be localized via geometric analysis of internal representations, combining layer-wise cosine similarity and head-wise contribution scores. We demonstrate that intervention targeting only these specific heads achieves robust behavioral control while significantly mitigating the coherency degradation observed in residual stream steering. More broadly, our findings show that precise, component-level localization enables safer and more precise model control.
Applications · Language, Speech and Dialog
Masked diffusion models (MDMs) are a potential alternative to autoregressive models (ARMs) for language generation, but generation quality depends critically on the generation order. Prior work either hard-codes an ordering (e.g., blockwise left-to-right) or learns an ordering policy for a pretrained MDM, which incurs extra cost and can yield suboptimal solutions due to the two-stage optimization. Motivated by this, we propose order-expressive masked diffusion model (OeMDM) for a broad class of diffusion generative processes with various generation orders, enabling the interpretation of MDM, ARM, and block diffusion in a single framework. Furthermore, building on OeMDM, we introduce learnable-order masked diffusion model (LoMDM), which jointly learns the generation ordering and diffusion backbone through a single objective from scratch, enabling the diffusion model to generate text in context-dependent ordering. Empirically, we confirm that LoMDM outperforms various discrete diffusion models across multiple language modeling benchmarks.
Deep Learning · Sequential Models, Time series
Interpretable time series deep learning systems are often assessed by checking temporal consistency on explanations, implicitly treating this as evidence of robustness. We show that this assumption can fail: Predictions and explanations can be adversarially decoupled, enabling targeted misclassification while the explanation remains plausible and consistent with a chosen reference rationale. We propose TSEF (Time Series Explanation Fooler), a dual-target attack that jointly manipulates the classifier and explainer outputs. In contrast to single-objective misclassification attacks that disrupt explanation structure and spread attribution mass broadly, TSEF achieves targeted prediction changes while keeping explanations consistent with the reference. Across multiple datasets and explainer backbones, our results consistently reveal that explanation stability is a misleading proxy for decision robustness and motivate coupling-aware robustness evaluations for trustworthy time series deployments.
Applications · Computer Vision
Despite significant progress in multi-modal Re-Identification (ReID), existing methods tend to emphasize low-frequency cues. Consequently, they focus on attributes such as color, illumination, and coarse appearance, while overlooking mid- and high-frequency structures that encode geometric, textural, and identity-discriminative details. This imbalance leads to incomplete spectral representations and unstable cross-modal alignment. To overcome these limitations, we introduce FUSE, a frequency-domain framework that reformulates multi-modal ReID as a two-stage process of spectral disentanglement and energy alignment. The proposed Spectral Decomposition Module (SDM) adaptively partitions features into low, mid, and high-frequency subspaces, enabling hierarchical spectral modeling. The Cross-Modal Alignment Module (CAM) further enforces energy alignment and subspace complementarity across modalities via frequency-consistency regularization. In addition, FUSE incorporates learnable frequency modulation to enhance robustness under varying illumination and heterogeneous sensor conditions. Extensive experiments on RGBNT201, RGBNT100, and MSVR310 show that FUSE achieves 9.1% mAP and 9.5% Rank-1 improvements, establishing an interpretable frequency-domain paradigm for multi-modal representation learning.
Applications · Computer Vision
High-quality geometric diagram generation presents both a challenge and an opportunity: it demands strict spatial accuracy while offering well-defined constraints to guide generation. Inspired by recent advances in geometry problem solving that employ formal languages and symbolic solvers for enhanced correctness and interpretability, we propose GeoLoom, a novel framework for text-to-diagram generation in geometric domains. GeoLoom comprises two core components: an autoformalization module that translates natural language into a specifically designed generation-oriented formal language GeoLingua, and a coordinate solver that maps formal constraints to precise coordinates using the efficient Monte Carlo optimization. To support this framework, we introduce GeoNF, a dataset aligning natural language geometric descriptions with formal GeoLingua descriptions. We further propose a constraint-based evaluation metric that quantifies structural deviation, offering mathematically grounded supervision for iterative refinement. Empirical results demonstrate that GeoLoom significantly outperforms state-of-the-art baselines in structural fidelity, providing a principled foundation for interpretable and scalable diagram generation.
Deep Learning · Graph Neural Networks
Hypergraph contrastive learning is an effective paradigm for representation learning on higher-order relational data, yet existing methods largely ignore that hyperedges link nodes with multi-level semantics. Standard contrastive objectives emphasize instance discrimination via hyperspherical uniformity and tend to push embeddings apart in an indiscriminate manner. We show that this leads to a *Hierarchy–Uniformity Conflict*, whose geometric manifestation is *Semantic Flattening*, where the semantic depth of hyperedges collapses into a nearly flat cloud of instances. To address this issue, we introduce **HyperDepth**, a hypergraph contrastive learning framework that moves representations towards a hierarchy–uniformity equilibrium by jointly coordinating spectral and geometric signals. HyperDepth employs a decoupled spectral encoding scheme with adaptive gating so that high-frequency components focus on local instance discrimination while low-frequency components capture global hierarchical structure. On top of this, an energy-based hierarchical Alignment module attaches a learnable prototype tree to the representation space and minimizes an interpretable energy functional to recover the semantic depth of hyperedges. Theoretically, under a mild frequency-separation assumption, we show that the local contrastive and global hierarchical objectives operate on orthogonal spectral components and admit equilibrium embeddings that preserve semantic depth while still retaining instance-level discrimination. Experiments on 15 hypergraph datasets and 17 supervised and self-supervised baselines, spanning homophilic and heterophilic regimes, show that HyperDepth attains strong performance with the best average rank.
Hypergraph contrastive learning is an effective paradigm for representation learning on higher-order relational data, yet existing methods largely ignore that hyperedges link nodes with multi-level semantics. Standard contrastive objectives emphasize instance discrimination via hyperspherical uniformity and tend to push embeddings apart in an indiscriminate manner. We show that this leads to a *Hierarchy–Uniformity Conflict*, whose geometric manifestation is *Semantic Flattening*, where the semantic depth of hyperedges collapses into a nearly flat cloud of instances. To address this issue, we introduce **HyperDepth**, a hypergraph contrastive learning framework that moves representations towards a hierarchy–uniformity equilibrium by jointly coordinating spectral and geometric signals. HyperDepth employs a decoupled spectral encoding scheme with adaptive gating so that high-frequency components focus on local instance discrimination while low-frequency components capture global hierarchical structure. On top of this, an energy-based hierarchical Alignment module attaches a learnable prototype tree to the representation space and minimizes an interpretable energy functional to recover the semantic depth of hyperedges. Theoretically, under a mild frequency-separation assumption, we show that the local contrastive and global hierarchical objectives operate on orthogonal spectral components and admit equilibrium embeddings that preserve semantic depth while still retaining instance-level discrimination. Experiments on 15 hypergraph datasets and 17 supervised and self-supervised baselines, spanning homophilic and heterophilic regimes, show that HyperDepth attains strong performance with the best average rank.