Hierarchical Representation Learning

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18 papers in the last four weeks, up 260% on the four weeks before. 0.2% of all new papers.

Jul 13Week of Sep 28

Latest papers 154

Aug 1, 2026cs.AI

Gene Ontology-Guided Hierarchical Spatial Gene Expression Prediction from Histopathology Images

Predicting spatial gene expression from histopathology images enables large-scale transcriptomic profiling without the cost of direct measurement. Existing methods decode the target gene set as a flat, unstructured vector, ignoring the inter-gene dependencies arising from shared biological pathways and regulatory programs. Without explicit structural guidance, models must infer these dependencies entirely from limited paired data, constraining prediction quality. We propose MSGR (Multi-Scale Gene Refiner), which bridges this gap by incorporating the Gene Ontology (GO), a curated functional hierarchy of genes, as an explicit structural prior. MSGR organizes target genes into a four-level GO tree. Its GO-guided decoder then progressively refines predictions from coarse functional domains to fine individual genes via residual corrections under scale-weighted supervision. Operating solely on the gene side, the GO-guided decoder serves as a seamless plug-in replacement that consistently improves existing architectures without requiring any image-side modifications. Extensive experiments on nine datasets from the HEST-1k benchmark provide empirical evidence for two central claims: GO-structured decoding consistently outperforms flat decoding, even against a state-of-the-art generative baseline, and the gain is attributable to biological ontology structure rather than hierarchical decomposition per se, as confirmed by a +0.027 margin over a structurally equivalent random hierarchy.

Zhiwen Xu, Xiaoming Yan, Chengkun Wu +3

National University of Defense Technology Changsha, China

Computational Pathology Spatial Transcriptomics Hierarchical Representation Learning Spatial Gene Expression Prediction Genomics Gene Expression Prediction from Histopathology Images

Jul 31, 2026cs.SI

Multi-Granularity Position Embedding of Graphs via Granular-Ball for Link Prediction

Link prediction aims to identify potential or future connections within a given graph structure. Position information is essential for link prediction, as it distinguishes homogeneous nodes through their relative relationships, facilitating the accurate capture of structural patterns and implicit connections. Previous studies derive node positional information as distances to single-granularity landmarks, defined as the centers of homophilic regions, while neglecting the multi-granularity nature of homophilic structures and their hierarchical interrelations. We propose the Multi-Granularity Position Embedding of Graphs via Granular-Ball for Link Prediction (MGLP) method to obtain multi-granularity position embedding of graphs. Specifically, MGLP introduces an Adaptive Granular-Ball Graph Refinement mechanism to adaptively refine the graph into homophilic subdomains with optimal levels of granularity. The central nodes within subdomains are treated as landmarks, which form a Hierarchical Central Graph. Moreover, a novel Multi-granularity Hierarchical Distance encoding mechanism is proposed to capture both the homophilic structures within a graph and their hierarchical correlations, improving the discriminative power of nodes. Experimental results demonstrate that the multi-granularity position embedding generated by our method exhibits excellent performance and strong competitiveness compared to baseline algorithms for link prediction. Our codes are available in https://anonymous.4open.science/r/MGLP-D3C5/.

Sen Zhao, Cheng Liu, Shuyin Xia +4

Chongqing Key Laboratory of Computational Intelligence, Key Laboratory of Big Data Intelligent Computing, Key Laboratory of Cyberspace Big Data Intelligent Security, Ministry of Education, School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China · Chongqing Key Laboratory of Computational Intelligence, Key Laboratory of Big Data Intelligent Computing, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China · Chongqing Ant ConsumerFinance Co,. Ltd, Ant Group, Chongqing, 400065, China

Graph Representation Learning Link Prediction Hierarchical Representation Learning Graph Embedding

Jul 27, 2026cs.CV

TreeAdapter: Hierarchical Taxonomy-Guided Adapter Composition for Fine-Grained Species Image Generation

Although general text-to-image models excel in open-domain generation, their performance degrades significantly in specialized downstream domains, particularly when generating images of rare biological species. Hindered by long-tailed distributions, general models struggle to capture subtle fine-grained details, while per-species fine-tuning methods over-isolate individual species and consequently ignore the shared visual features among closely related taxa. To address this, we propose TreeAdapter, a novel framework that explicitly leverages hierarchical taxonomic data. Rather than using a monolithic model or independent per-species modules, TreeAdapter attaches lightweight adapters to every node of the taxonomic tree. Specifically, leaf-node adapters capture species-specific visual traits, while internal-node adapters encapsulate shared semantics among descendant taxa. We introduce a two-stage training paradigm where ancestor adapters are optimized to model only the residual visual features unexplained by their descendants. This model architecture and training paradigm enable the model to fully leverage hierarchical information, ensuring the accurate generation of visual features for each species. Extensive experiments across three large-scale biodiversity benchmarks demonstrate that TreeAdapter achieves state-of-the-art fine-grained generation quality, outperforming both general-purpose and domain-specific baselines.

Yuze Sun, Zhongjie Duan, Yingda Chen

ModelScope Team, Alibaba Group

Hierarchical Representation Learning Image Generation

Jul 26, 2026cs.LG

A Statistical Difference between Single-Layer Learning and Hierarchical Learning in Wide Neural Networks

Hierarchical neural networks are widely used in artificial intelligence, yet their mathematical properties remain incompletely understood. In the infinite-width limit, two different theoretical frameworks have been proposed. One reduces deep learning to kernel regression with a fixed kernel by assuming that the parameters remain close to their initialization, whereas the other allows the parameters to move away from their initialization, requiring the kernel itself to be optimized. In this paper, we study a three-layer neural network with a finite but large number of hidden units. We show that training the input-to-hidden weights yields a smaller generalization error than keeping them fixed. Furthermore, the latter setting exhibits singularities in the parameter space, whereas the former does not. These findings indicate that singularities play an essential role even in wide neural networks.

Sumio Watanabe

RIKEN Center for Advanced Intelligence Project 1-4-1 Nihonbashi, Chuo-ku, 103-0027, Tokyo, Japan

Neural Network Generalization Hierarchical Representation Learning Neural Network Training Dynamics

Jul 24, 2026cs.CV

Gradient-Based Latent Decomposition Reveals Mechanisms of Feature Degradation in Weakly Supervised Mammography

Weakly supervised hierarchical models exhibit a persistent asymmetry: coarse lesion-type features are preserved under reconstruction while fine-grained malignancy cues degrade---a pattern with direct consequences for the clinical reliability of breast cancer screening pipelines. We introduce gradient-based orthogonal latent decomposition for hierarchical Variational Autoencoders~(H-VAEs) to mechanistically explain this asymmetry. The latent space is partitioned into a task-aligned component~(

z_1

), shaped by coarse supervisory gradients, and an orthogonal residual~(

z_{\text{res}}

) capturing remaining representational capacity. On~~3,550 mammographic Regions of Interest~~(ROIs) from CBIS-DDSM, only~

\sim

4.4% of latent magnitude aligns with supervisory gradients, leaving~

\sim

95.6% in the orthogonal residual upon which fine-grained pathology prediction primarily depends. The model achieves Stage-1~~AUC~~0.866 and Stage 2~~AUC~~0.552, with a reconstruction stability gap of

Δ_{\text{diag}}=5\%

(

p=0.005

) and a classification gap of

Δ_{\text{AUC}}=0.314

(

p{<}0.001

). Latent ablation confirms that features for both tasks reside heavily in~

z_{\text{res}}

, structurally explaining why reconstruction degrades pathology stability disproportionately. Comparisons with Multi-Instance Learning~(MIL) and Multi-Task Learning~(MTL) confirm generalization across architectures and modalities. These findings reveal that in high-dimensional spaces, a single coarse supervisory signal isolates only a sparse 1D latent direction, forcing critical fine-grained features into the vulnerable residual subspace.

Vinceline Bertrand, Ionut Cardei

Florida Atlantic University, Boca Raton, FL, USA

Variational Autoencoders Hierarchical Representation Learning Orthogonal Representation Learning Medical Image Classification Weakly Supervised Learning Mammography

Jul 23, 2026cs.AI

MSBraM: A Multi-scale Self-supervised Brain Foundation Model for Hierarchical EEG Dynamics Learning

Self-supervised foundation models have recently shown strong potential for electroencephalogram (EEG)-based analysis. However, existing approaches struggle to capture the inherently multi-scale temporal structure of EEG signals, where local neural patterns and long-range dependencies jointly encode task-relevant information. This limitation hampers cross-scale representation learning and generalization across diverse downstream tasks. To address this challenge, we propose MSBraM, a Multi-Scale self-supervised Brain foundation Model designed to learn hierarchical EEG representations. MSBraM follows a two-stage pretraining framework. First, a multi-scale neural tokenizer discretizes raw EEG signals into semantic codes at different temporal resolutions via vector-quantized reconstruction. Second, the model is pretrained to predict masked codes using a curriculum multi-scale masking strategy, progressively integrating fine-grained local patterns with global temporal context. We pretrain MSBraM on over 2,400 hours of EEG data and evaluate it across 10 downstream tasks on 12 public datasets. Extensive experiments show that MSBraM achieves superior performance on other state-of-the-art pretrained models, demonstrating strong generalization and transferability. These results indicate that explicitly modeling multi-scale temporal dynamics is critical for effective EEG foundation models.

Tao Zhou, Jing Han, Lingyu Shu +1

Hunan University Changsha, China

Electroencephalography Self-Supervised Pre-Training Hierarchical Representation Learning Multiscale Time-Series Modeling EEG Foundation Models

Jul 18, 2026eess.SP

Hierarchical Wireless Foundation Model for Multi-Task Optimization

The increasing complexity of next-generation wireless networks has driven the integration of artificial intelligence (AI) into wireless communications. However, most existing studies focus on developing task-specific deep learning techniques for single scenarios, which limits their ability to generalize across diverse tasks, channel conditions, and system configurations. To address this generalization bottleneck, we propose a hierarchical wireless foundation model (WFM) for multi-task optimization. The proposed WFM couples an upstream foundation channel encoder (FCE) with a downstream foundation optimization decoder (FOD) via geometry-aware cross-attention. Specifically, the FCE extracts task-agnostic channel representations via self-supervised masked reconstruction while the FOD generates multi-task optimization decisions through differentiable output heads. Moreover, a hybrid supervised-to-unsupervised training strategy is employed to overcome the performance ceiling of purely supervised learning, and the modular architecture of the WFM enables efficient adaptation to unseen communication tasks with minimal parameter overhead. Simulation results show that the proposed WFM learns high-fidelity channel representations and achieves competitive multi-task optimization performance while substantially reducing optimization inference latency relative to numerical baselines. Furthermore, it exhibits robust generalization to unseen propagation environments, varying constraint parameters, and heterogeneous system configurations.

Yangjing Wang, Ouya Wang, Shenglong Zhou +1

Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2BX London, U.K. · School of Mathematics and Statistics, Beijing Jiaotong University, China

Wireless Foundation Models Hierarchical Representation Learning Multi-Task Optimization

Jul 16, 2026cs.SD

MIDI-RAE-JEPA: Hierarchical Representation Learning and Generation for Symbolic Music

Rich internal representations of musical structure are essential for music understanding tasks such as machine-assisted music co-writing, yet self-supervised approaches for symbolic music representation remain underexplored, particularly those that encode the hierarchical multiscale nature of musical structures. We present MIDI-RAE-JEPA, combining a pitch- and time-shift equivariance objective with LeJEPA and a Swin Transformer V2 encoder to learn such hierarchical representations of symbolic music encoded as piano roll images. The time-shift equivariance objective encourages the model to internalize temporal musical relationships. The encoder is trained purely on self-supervised objectives -- including a masked embedding predictor (MEP) -- with collapse prevented via SIGReg. A separate decoder trained on the frozen encoder embeddings achieves reconstruction F1 of 0.995, and a flow matching generative model conditioned on those embeddings produces generations that closely match the pitch register and rhythmic density of the conditioning excerpt, while mismatched conditioning yields unrelated but musically plausible output. Learned representations outperform a Haar scattering transform baseline on a downstream emotion classification task, and embedding distances increase monotonically with pitch and time shift magnitude, confirming measurable equivariance. These results suggest that equivariance-based SSL objectives, combined with sufficient fine-level encoder capacity, provide a viable path toward semantically rich, generatively useful representations of symbolic music.

Scott H. Hawley

Department of Chemistry & Physics, Belmont University, Nashville, TN, USA

Representation Learning Self-Supervised Pre-Training Symbolic Music Generation Hierarchical Representation Learning Equivariant Representation Learning

Jul 13, 2026cs.LG

Mitigating The Effect of Class Imbalance in Data with Hierarchical and Dependable Structure

Classifying cybersecurity vulnerabilities using the Common Weakness Enumeration (CWE) taxonomy is challenging due to extreme class imbalance and strong hierarchical dependencies among weakness categories. Although oversampling techniques such as Synthetic Minority Oversampling Technique (SMOTE) and Adaptive Synthetic Sampling (ADASYN) are widely adopted to mitigate class imbalance, their effectiveness for hierarchical CWE text classification remains largely unexplored. This paper proposes a Hierarchy-Aware RoBERTa framework that explicitly incorporates CWE structural information through learnable parent-class embeddings, preserving taxonomic consistency. Our experiments demonstrate that synthetic interpolation in high-dimensional embedding spaces violates the inherent parent-child constraints of the CWE hierarchy, offering only marginal benefits for classical ML models while consistently degrading deep learning architectures. Evaluated on a CWE Research Concept dataset, the proposed model achieves a weighted F1-score of 0.76 without data augmentation, outperforming all baselines with notable gains on minority classes, including the Class category whose F1-score improved from 0.40 to 0.60 over the BERT baseline. Our results suggest that hierarchy-aware representation learning is a more principled alternative to oversampling for structured vulnerability classification.

Bipin Chhetri, Deepika Giri, Avishek Kadel +2

Department of Computer Science1, Texas Tech University1 · Cumberland University2 · Yeshiva University3 +1

Class-Imbalanced Learning Hierarchical Classification Software Vulnerability Detection Hierarchical Representation Learning

Jul 10, 2026cs.CV

HiHR: Hierarchical Hyperbolic Representation for Aerial-Ground Person Re-Identification

Aerial-Ground Person Re-IDentification (AG-ReID) aims to retrieve the same person across heterogeneous aerial and ground camera platforms. Although great progress has been made, existing methods remain suboptimal due to the direct feature alignment across views, overlooking view-specific cues. To address this issue, we propose a novel Hierarchical Hyperbolic Representation (HiHR) framework for AG-ReID. More specifically, we first extract multi-granularity features based on pre-trained visual-text encoders. Then, we propose a Text-guided Multi-granularity Fusion (TMF) to fuse multi-granularity features and enhance the representation ability of identity features. Furthermore, we introduce the Hierarchical Hyperbolic Learning (HHL) to construct a hierarchical feature structure in a hyperbolic space. This hierarchy includes a coarse level that ensures identity separability and cross-view consistency, and a fine level that preserves view-specific discriminative cues. As a result, our proposed framework can effectively aggregate view-invariant and view-specific discriminative features for AG-ReID. Extensive experiments on four AG-ReID benchmarks demonstrate the effectiveness of our framework. The source code is available at https://github.com/YangQiWei3/HiHR.

Qiwei Yang, Pingping Zhang

Dalian University of Technology, Dalian, China

Hierarchical Representation Learning Hyperbolic Representation Learning Person Re-Identification

Jul 9, 2026cs.CV

HSA: Hierarchical Slot Attention for Multi-granularity Scene-Decomposition

Slot attention is a powerful framework for object-centric learning, decomposing visual scenes into latent slots through iterative competitive attention. However, existing methods share two critical limitations: they decompose scenes into a flat set of slots at a single granularity, and this decomposition is based on appearance rather than semantics. Yet humans understand scenes through semantic hierarchies: separating foreground from background, recognizing object categories, and identifying individual instances. Crucially, such semantic hierarchies cannot emerge without supervision, because category names are human constructs, not visual patterns. We propose Hierarchical Slot Attention (HSA), which learns multi-granularity semantic scene decomposition from a single model. HSA decomposes scenes at three levels: holistic (foreground/background), semantic (object categories), and panoptic (individual instances). Using only 10% labeled data, combined with hierarchical alignment loss, HSA learns all three levels jointly. We further introduce grouping purity and containment to measure whether the hierarchy is encoded in representation space, not just output masks. Experiments on COCO and PASCAL VOC demonstrate that HSA outperforms the strongest flat baseline by up to \textbf{

+

41.5} ARI at holistic, \textbf{

+

14.6} at semantic, and \textbf{

+

10.4} at panoptic level on COCO, with even larger gains on Pascal VOC, while requiring a single model instead of three. Code will be made available upon acceptance.

Neelu Madan, Rongzhen Zhao, Andreas Mogelmose +4

1Aalborg University, Denmark · 2Pioneer Centre for AI, Denmark · 3Aalto University, Finland +2

Panoptic Segmentation Hierarchical Representation Learning Object-Centric Representation Learning Slot Attention

Jul 8, 2026cs.CV

Navigating Hierarchy: Hyperbolic Learning on Brain Graphs for Disorder Diagnosis

Functional brain networks exhibit a hierarchical organization across ROI, community, and whole-brain levels, supporting local processing, inter-community coordination, and global integration. Recent studies have demonstrated that brain community-aware modeling is beneficial for both diagnosis and biomarker identification of brain networks. However, existing brain graph modeling methods often struggle to model ROI-community interactions, thereby failing to fully exploit the hierarchy across ROI, community, and whole-brain network levels. To address this issue, inspired by deep hyperbolic learning in modeling hierarchical structures, we propose a novel framework, termed Hyperbolic Learning on Brain Graphs (HLBG), for brain network analysis. The core idea of HLBG is to exploit the inherent hierarchical geometry of hyperbolic space to model the hierarchical relationships among ROIs, functional communities, and the whole-brain network, thereby learning hierarchy-aware and highly discriminative representations for brain network data. Specifically, HLBG first projects representations from ROIs, communities, and the whole-brain network into Lorentzian hyperbolic space. Then, the multi-level hierarchy is imposed via two geometric entailment constraints. In addition, we introduce a new Graph-aware Mamba (GaMamba) model, which incorporates topology-derived structural prompts into Mamba to capture long-range dependencies while preserving graph topological information. Experiments on ABIDE-I and REST-MDD demonstrate that HLBG outperforms state-of-the-art methods and identifies disorder-relevant functional biomarkers.

Yapeng Li, Bo Jiang, Ziyan Zhang +2

School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, China

Medical Diagnosis Hierarchical Representation Learning Neuroimaging Hyperbolic Representation Learning Brain Network Analysis

Jul 8, 2026cs.CV

HPR-SAM: Hierarchical Probabilistic Representation Learning for Prompt-free SAM-based Medical Image Segmentation

Prompt-free adaptation of the Segment Anything Model (SAM) has emerged as a promising paradigm for automatic medical image segmentation. Existing methods mainly focus on prompt generation, while overlooking that prompt quality is fundamentally constrained by the expressiveness of anatomical representations. However, deterministic prototypes or semantic tokens are insufficient to jointly capture global anatomical priors, intra-structure diversity, and local structural reliability. To address this limitation, we propose the Hierarchical Probabilistic Representation (HPR) framework, which learns complementary anatomical representations through Distributional Anatomical Representation (DAR), Multi-component Anatomical Representation (MAR), and Local Reliability Representation (LRR), and integrates their predictions via Hierarchical Prediction Fusion (HPF) while remaining compatible with the original SAM decoder. Experiments on the Synapse, LA, and PROMISE12 datasets demonstrate that HPR-SAM achieves state-of-the-art performance on Synapse and the best performance under few-shot settings on LA and PROMISE12, validating the effectiveness of the proposed hierarchical probabilistic representation learning framework for prompt-free medical image segmentation. Code is available at https://anonymous.4open.science/r/HPR-SAM-E4AF.

Yingzhen Hu, Yiheng Zhong, Keying Zhu +5

Yale University, United States

Medical Imaging Foundation Models Representation Learning Hierarchical Representation Learning Medical Image Segmentation

Jul 7, 2026cs.CV

RFHNet: Relational and Frequency-Aware Hashing Network for Large-Scale Fine-Grained Food Image Retrieval

Fine-grained food image retrieval is a key task in computational gastronomy, with applications in food traceability, dietary monitoring, and smart catering systems. Although hashing-based retrieval is attractive for large-scale search due to its storage efficiency and fast Hamming-distance computation, existing methods often perform poorly in fine-grained food scenarios, where subtle local semantics and frequency-sensitive visual cues are essential. To address this challenge, we propose RFHNet, a cascaded hierarchical hashing network that captures both global structure and fine-grained local details through multi-level representations. RFHNet includes three components: (1) Fine-grained Relation Modeling (FRM) to capture subtle visual differences among similar food components; (2) Multi-Frequency Modulated Fusion (MFMF) to extract informative multi-frequency features; and (3) Hierarchical Semantic Synergy (HSS) to adaptively integrate multi-level representations and generate discriminative hash codes. Experiments on six food-specific benchmarks show that RFHNet consistently outperforms state-of-the-art hashing methods, with mAP gains of 4.44% to 17.20% at 12 bits. These results validate the effectiveness of RFHNet for large-scale visual food retrieval and smart catering applications. The source code will be released upon publication.

Junsong Wang, Weiqing Min, Guorui Sheng +3

College of Computer Science and Artificial Intelligence, Ludong University Yantai, China · Institute of Computing Technology, Chinese Academy of Sciences Beijing, China · University of Chinese Academy of Sciences Beijing, China

Image Matching Fine-Grained Image Retrieval Hierarchical Representation Learning Fine-Grained Visual Perception

Jul 6, 2026cs.CV

Is the Geometry Doing the Work? An Operating-Point Audit of Hierarchy in Hyperbolic Vision-Language Models

Whether a hyperbolic representation model uses its geometry cannot be inferred from curvature alone: what matters is the dimensionless operating point

\sqrt{c}ρ

and whether the radial and cone mechanisms are operational there. We develop necessary-condition diagnostics and audit three published hyperbolic vision-language families -- MERU, HyCoCLIP, and PHyCLIP -- across released checkpoints and matched interventions. All converged checkpoints remain near-Euclidean (

H(u)\approx1

; none reaches

\sqrt{c}ρ>1

), and releasing the curvature floor changes

c

and norms without leaving this regime or substantially degrading downstream performance. Entailment cones are inactive or saturated, and graded traversal fails under controlled readouts, including the models' native distance metrics. External parent-child ordering shows no shuffle-controlled pair-specific radial signal at quantified sensitivity; the only surviving pair-specific signal, a statistically detectable but small residual on the GRIT box-to-full-caption relation, remains non-operative under the evaluated readouts. Taxonomy correlations show no detectable norm contribution beyond cosine, and coarse-retrieval gains co-vary with box/compositional supervision without establishing an active radial mechanism. Gradient diagnostics expose a low-curvature, wide-cone shortcut in the entailment objective. A closed-form aperture identity places the saturation edge at

\sqrt{c}ρ\le2K

: with the floor released, all trained relation-level parent means lie at or below this edge, leaving the parent cones fully or nearly saturated. Entailment-off runs pass the edge and continue contracting. The shortcut is the dominant accelerator of collapse, not its sole cause. These audited formulations do not show an operative radial/cone mechanism under our diagnostics. We distill the audit into a five-number geometry report for hierarchy claims.

Jaeyoung Kim, Eunseok Kim, Dongsuk Jang

MADI

VLM Evaluation Vision-Language Models Hierarchical Representation Learning Hyperbolic Representation Learning

Jul 6, 2026cs.LG

Hierarchical Scaffolding Enables Human-Like Cognitive Selectivity under Data Scarcity

Modern machine learning systems demand extensive datasets for visual recognition. Conversely, humans learn with high efficiency despite severe data limitations, often by acquiring broad categorical structures before refining finer distinctions. Inspired by this contrast, we introduce SCALA (Scaffolded Cognitive Architecture for Learning under limited dAta), a hierarchical learning framework grounded in cognitive psychology that guides models from coarse conceptual structures to fine-grained recognition. Our model exhibits human-like cognitive selectivity by effectively prioritizing task-relevant features while suppressing background distractors, a mechanism that induces a fundamental shift in representation learning. This shift is characterized by accelerated cluster formation, reduced intra-class dispersion, and enhanced semantic separability. Empirically, SCALA achieves significant accuracy improvements under severe data scarcity. Furthermore, this hierarchical scaffolding promotes robust generalization to unseen classes and accelerates the acquisition of novel categories. Collectively, our results establish SCALA as a powerful framework for achieving human-level sample efficiency and resilient category generalization in data-constrained environments.

Juhyoung Park, Jaehyuk Bae, Hyeonbo Yang +1

School of Computing 2Department of Brain and Cognitive Sciences Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea · Department of Brain and Cognitive Sciences Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea

Hierarchical Representation Learning Data-Efficient Learning

Jul 5, 2026cs.CV

HASSL: Hierarchy-Aware Self-Supervised Learning Framework for Single Cell Microscopy

Hierarchical structure is common in image data, where fine-grained clusters often merge into larger, coarser semantic groups. In biological cell images, current self-supervised learning models often suppress this hierarchy, as coarse factors such as imaging modality can obscure finer morphological attributes in the latent space. We propose a hierarchy-aware self-supervised training framework to address this problem. Our method combines two components: a distillation framework with a segmentation teacher to improve morphological awareness in the latent space, and a hierarchy-aware contrastive loss based on HDBSCAN to improve decision boundaries between closely related subtypes at different hierarchical levels. Together, these components reduce the tendency of self-supervised learning to overemphasize coarse factors and instead align embeddings with semantic and morphological cues. This yields biologically meaningful sub-clusters driven by fine morphological detail. We train and evaluate our method on a curated corpus of 2.3 million single cells aggregated from 20 microscopy datasets, both labeled and unlabeled, covering 208 cell classes. Our method improves over baseline and counterpart methods, increasing average top-K accuracy by 2.8%, top-9 retrieval on the dataset with the deepest hierarchy by 6.3%, and downstream F1-score for biologically relevant drug classification from perturbed cell morphology by 7.8%.

Julius Riel, Vishwa Mohan Singh, Sai Anirudh Aryasomayajula +10

TUM.ai, Munich, Germany · Ludwig-Maximilian-University, Munich, Germany · Technical University of Munich, Munich, Germany +6

Contrastive Learning Hierarchical Representation Learning Medical Image Representation Learning Self-Supervised Visual Representation Learning Microscopy Image Analysis

Jul 4, 2026cs.LG

Omni-Sleep: A Sleep Foundation Model via Hierarchical Contrastive Learning of CNS-ANS Dynamics

Sleep physiology arises from the coordinated dynamics of the central nervous system (CNS) and autonomic nervous system (ANS), as reflected by multimodal polysomnography signals including EEG, EOG, EMG, ECG, and respiration. However, existing sleep foundation models often fuse heterogeneous biosignals in a topology-agnostic manner, overlooking their physiological organization. We introduce Omni-Sleep, a sleep foundation model that uses the CNS/ANS partition as a physiological prior for topology-constrained representation learning. Omni-Sleep learns structured representations through three objectives: intra-system consistency, which captures shared subsystem-level factors within neural and cardio-respiratory signals; inter-system synchronization, which aligns subsystem trajectories to model brain--body dynamics; and latent-space masked temporal modeling, which captures long-horizon sleep dynamics. Pre-trained on over 100,000 hours of multi-center multimodal PSG data, Omni-Sleep is evaluated on sleep staging and multi-disease classification. Across datasets and modality-ablation settings, Omni-Sleep outperforms strong foundation-model baselines, showing improved label efficiency, cross-dataset generalization, and robustness to missing modalities. These results highlight the value of physiological hierarchy for generalizable sleep representation learning. Code is available at https://github.com/AutoBrain-sleep/OmniSleep.

Zhoujie Hou, Song Wang, Kexin Lou +3

Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China · Omni-Intelligence, Shenzhen, China · Shenzhen Loop Area Institute, Shenzhen, China

Sleep Stage Classification Latent Dynamics Modeling Hierarchical Representation Learning Multimodal Contrastive Learning Time Series Representation Learning

Jul 3, 2026cs.CR

LLM-Enhanced Hierarchical Heterogeneous Graph Representation Learning for Malicious Python Package Detection

Malicious Python packages have become a major threat to software supply chain ecosystems due to the widespread adoption of open-source repositories such as PyPI. Existing learning-based detection methods struggle to capture the hierarchical organization and heterogeneous interactions among different program entities. Although Large Language Models (LLMs) have demonstrated strong capabilities in code understanding and semantic reasoning, they are rarely integrated with structural program representations for fine-grained malicious behavior analysis. In this paper, we propose an LLM-enhanced hierarchical heterogeneous graph representation learning framework for malicious Python package detection. The framework constructs a hierarchical heterogeneous code graph that explicitly models heterogeneous code entities and different types of structural dependencies. LLMs are further leveraged to infer function-level semantic roles, introducing an additional layer of semantic heterogeneity. Based on this graph, we develop a hierarchical heterogeneous graph neural network that performs type-aware message passing over different node and edge categories, effectively modeling malicious behavior propagation for accurate package-level classification. The framework also incorporates a function-level attribution mechanism which, combined with LLM reasoning, automatically identifies suspicious functions and localizes fine-grained malicious behaviors without human expert intervention. Extensive experiments on real-world datasets show that our framework consistently outperforms traditional machine learning methods, graph-based detectors, and state-of-the-art LLMs across packages with varying sizes and dependency complexities, while providing accurate, robust, and interpretable malicious behavior localization.

Hang Gao, Xiaoyu Chen, Baoquan Cui +4

Institute of Software, Chinese Academy of Sciences · University of Chinese Academy of Sciences

Heterogeneous GNNs Hierarchical Representation Learning Software Supply Chain Security Malware Analysis Malware Detection

Jul 3, 2026cs.LG

The Multiscale Single-Index Model: A Stylized Model for Hierarchical Feature Learning

We consider the Multiscale Single-Index Model (MSIM), first introduced in \cite{oymak2021learning}, as a stylized model for hierarchical learning with \emph{scale separation}. Each layer extracts a shared single-index feature at one physical scale and passes it to the next, thus defining a tractable setting in which to study how deep architectures learn multiscale representations. Under non-degeneracy and delocalization assumptions on the link function and planted features respectively, for fixed depth

K

and local scale

d

, the first Wiener chaos of the target behaves as a perturbed spiked tensor, where the perturbation of order

d^{-1/2}

comes from the non-linearity -- revealing the MSIM as a natural non-linear analogue of the Tensor PCA model \cite{montanari2014statistical}. While this perturbative picture is sufficient to enable efficient spectral recovery based on Tensor unfolding (as already observed in \cite{oymak2021learning}), it is not precise enough for the analysis of backpropagation gradient-based methods. In this work, we address this limitation by performing a fine-grained analysis of the Wiener chaos using Edgeworth expansions. In the first chaos, this gives a finite-rank hierarchy at scales

d^{-q/2}

. In higher chaoses, balanced flattenings exhibit staircase singular-value plateaus of size

d^{-ρ/2}

and multiplicity

d^ρ

under a natural higher-chaos non-cancellation condition. Using this higher-chaos structure, and under an additional slow Hermite-energy tail condition, we first establish shallow-network approximation lower bounds, quantifying the benefit of depth in this model. Next, and most importantly, we prove that online SGD on the correlation objective, where all layers evolve in the same timescale, achieves

1 - o_d(1)

recovery with

n = \widetilde{O}( d^{K-1})

samples, recovering the same sample complexity as in the linear counterpart.

Joan Bruna

Courant Institute School of Mathematics, Computing and Data Science, New York University

Single-Index Models Hierarchical Representation Learning Stochastic Gradient Descent

Jul 3, 2026cs.CV

Learning Taxonomic Trees with Hierarchical Representation Regularization for Large Multimodal Models

Taxonomies provide key information about the semantic relationships between concepts and the inherent organization of vision and language. Despite their impressive capabilities, large multimodal models (LMMs) often lack taxonomic knowledge, leading to low hierarchical visual recognition (HVR) consistency. These models typically only rely on language modeling objectives during fine-tuning and lack explicit taxonomy-aware regularization. To address this, we propose Hierarchical Representation Regularization (

HiR^2

), a simple plug-and-play regularizer that improves hierarchical consistency in LMMs. Specifically, we introduce a semantic-aware visual tree construction framework that extracts coarse-to-fine visual features from intermediate LLM layers guided by textual cues. The regularizer combines two complementary objectives: a taxonomic entailment loss that enforces hierarchy via hyperbolic entailment cones in the Lorentz model, and a discriminative dispersive loss that promotes angular separation of semantically similar embeddings on the unit sphere without disturbing the radial hierarchical structure. Extensive experiments demonstrate that

HiR^2

effectively captures taxonomic structures across diverse LMMs and fine-tuning methods. Code is available at https://github.com/PKU-ICST-MIPL/HiR2_ICML2026.

Hulingxiao He, Zhi Tan, Yuxin Peng

Wangxuan Institute of Computer Technology, Peking University

Hierarchical Representation Learning Multimodal Large Language Models

Jul 2, 2026cs.LG

HERMES: A Multi-Granularity Labeling Substrate for Pre-training Data Mixtures

Most data-mixing methods assume the corpus has already been partitioned into groups, and the choice of those groups determines what a mixer can express. Existing labels, including provenance, topic or format taxonomies, and flat embedding clusters, commit to one semantic axis at one granularity; changing the resolution rebuilds the labels. We argue the bottleneck is the label system, not the mixer, and provide a hierarchical one. HERMES is a data-derived labeling substrate: a Learned Semantic Transform followed by 3-stage residual vector quantization annotates each document once into a coarse-to-fine code whose prefix length controls granularity up to approximately 130k cells. At coarse granularity HERMES sits at a plateau with KMeans-family methods on standard clustering metrics, so the contribution is the substrate, not the clusterer. On 1B-parameter, 25B-token pre-training, the hierarchy exposes an interaction fixed-granularity pipelines cannot test: at one prefix length, a combined Stage-2 rule contrast, equal-subbucket coverage versus size-proportional within-bucket quality top-30%, lifts a 16-task capability macro-average by +0.0253; at the next finer level, the same rule loses its measurable edge as candidate pools contract approximately 5x. HERMES reframes data mixture design from choosing among fixed label sets to navigating a reusable, data-derived granularity hierarchy.

Ziyun Qiao, Yue Min, Ruining Chen +1

Wizard Quant, Beijing, China · University of Science and Technology of China, Hefei, China

Language Model Pretraining Training Data Curation Hierarchical Representation Learning Data Mixture Optimization

Jul 2, 2026cs.LG

SA-HGNN: Sample-Adaptive Hyperbolic Graph Neural Network for EEG-Based Depression Recognition

Graph Neural Networks (GNNs) have been widely used to capture spatial functional connectivity patterns to improve electroencephalography (EEG)-based depression recognition performance. However, the functional connectivity of brain networks in patients with depression exhibits an inherent hierarchical structure, making it difficult to capture accurate connection patterns. To address these issues, this paper proposes a novel model named Sample-Adaptive Hyperbolic Graph Neural Network (SA-HGNN), which aims to accurately extract the authentic hierarchical structure of depression-affected brain networks. Specifically, the proposed model comprises three core modules. First, a Sample-Adaptive Graph Construction module dynamically constructs personalized brain network topologies to capture more complex spatial relationships within the brain network. Second, hyperbolic graph convolution is employed to overcome the representation bottlenecks of Euclidean space, leveraging hyperbolic geometry to precisely capture latent hierarchical relationships within the brain network. Finally, an Attention Pooling module adaptively filters out highly redundant noise channels in EEG signals, effectively mitigating the interference of inherent noise on the authentic hierarchical topology. Extensive experiments on public EEG datasets demonstrate the superior performance of our method across resting-state and task-related paradigms, validating its robustness to noise and efficacy in capturing abnormal functional connectivity patterns in brain networks of patients with depression.

Yang Li, Pan Hu, Yan Zhang +3

School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China

Graph Structure Learning Electroencephalography Graph Neural Networks Depression Detection Hierarchical Representation Learning

Jul 1, 2026cs.LG

Hierarchical Self-Supervised Representation Learning Framework for Multivariate Time Series Grounded in ECG Analysis

Data analysis in the medical domain often encounters scenarios involving a limited target dataset and a large, unannotated dataset with a general distribution. Under such circumstances, self-supervised learning (SSL) methods are highly effective for utilizing large datasets, making them a popular choice for electrocardiogram (ECG) analysis. This work presents the Event Reconstruction Joint-Embedding Predictive Architecture (ER-JEPA), a lightweight SSL framework for multivariate time series, whose name and two-fold hierarchical structure are inspired by the diagnostic approach of cardiologists. At its core, ER-JEPA features: (1) a two-stage structure that constructs representations for each time interval and subsequently processes these representations as a univariate time series, (2) the hierarchical integration of two Joint-Embedding Predictive Architectures (JEPAs), and (3) a Vision Transformer (ViT) backbone. The structural concatenation of two JEPAs categorizes the model as a Hierarchical JEPA (H-JEPA), designed to encode multiple levels of abstract representations for enhanced prediction on complex tasks. This study reports a successful application of H-JEPA to 12-lead ECG data as a multivariate time series, alongside an analysis of the sensitivity of hierarchical representation during the pretraining stage. Pretrained on approximately 180,000 10-second recordings, the model achieves state-of-the-art downstream performance on the ST-MEM benchmark, with rapid computation and minimal resource usage.

Siwon Kim

Research Institute of Basic Sciences, Seoul National University, Seoul, Korea

Electrocardiography Self-Supervised Time Series Representation Learning Joint-Embedding Predictive Architecture Hierarchical Representation Learning

Jun 30, 2026cs.CV

HyperVLP: Enhancing Hierarchical Surgical Video-Language Pre-training in Hyperbolic Space

Surgical vision-language foundation models typically adopt educational materials, such as surgical lecture videos, to transfer surgical knowledge encoded in language into visual representations. These knowledge are multi-dimensional and hierarchical: fine-grained action cues appear in narration, mid-level key steps are summarized in subsection headings, and global procedural context, such as patient history and surgical strategy, is described in abstract texts. Prior work largely collapses these heterogeneous signals into a single flat embedding space, implicitly assuming independence across hierarchy levels. However, this is suboptimal because it ignores cross-level semantic containment, e.g., actions belong to steps, steps compose phases, weakens long-range dependency modeling. To this end, we propose a hyperbolic surgical video-language pre-training framework that explicitly preserves the hierarchical structure by mitigating structural false negatives induced by procedural context and enforcing semantic consistency between parent phases and their constituent child steps. Extensive experiments on multiple surgical benchmarks show consistent gains in zero- and few-shot phase recognition across procedures and institutions.

Yaojun Hu, Kun Yuan, Nassir Navab +3

Zhejiang University, Hangzhou, China · University of Strasbourg, CNRS, INSERM, ICube, UMR7357, Strasbourg, France · IHU Strasbourg, Strasbourg, France +1

Hierarchical Representation Learning Surgical Video Understanding Medical VLMs Vision-Language Alignment Hyperbolic Representation Learning

Jun 29, 2026cs.LG

ScaleAware-JEPA: Latent Representation for Discovery in Multiscale Physical Fields

Continuous physical fields represent a large fraction of data under scientific investigation. Their multiscale structures are central to discovery, yet useful coordinates are not known in advance. Standard self-supervised methods define context and targets in fixed image coordinates, posing a predictive task misaligned with fields organized across a continuous scale hierarchy. We introduce ScaleAware-JEPA, a framework that constructs dense, label-free latent coordinates for continuous scalar fields. Constrained Diffusion Decomposition (CDD) separates each field into pixel-registered scale components and provides the scale coordinates that define the masking geometry. The resulting JEPA objective predicts hidden structure with a context footprint tied to the diffusion scale of each component rather than to an arbitrary patch size. Across MHD turbulence, interstellar molecular gas and urban nighttime-light structure, the learned geometry maps back to coherent morphology, forming dense structural atlases without labels or predefined segmentation rules. By tying latent prediction to the scale hierarchy of a field, ScaleAware-JEPA constructs latent coordinates through which complex physical patterns can be inspected before their relevant structures have been prescribed. Code is available at https://github.com/gxli/SA-JEPA.

Guang-Xing Li

Representation Learning Joint-Embedding Predictive Architecture Hierarchical Representation Learning Predictive Representation Learning

Jun 27, 2026cs.LG

MOSAIC: Orchestrating Collaborative Knowledge Tracing with Hierarchical Semantic Alignment

Knowledge Tracing (KT) is important for personalized education but traditionally suffers from two key limitations: a reliance on shallow ID-based representations that neglect semantic depth and a restriction to single-granularity mastery estimation that overlooks hierarchical knowledge dependencies. To address these challenges, we propose MOSAIC (Multi-granularity Online Semantic AI for Collaborative Knowledge), a novel framework that orchestrates LLM-driven semantic alignment with sequential modeling. Unlike methods that use LLMs solely as predictors, MOSAIC leverages a frozen LLM to generate dynamic, context-aware embeddings and hierarchical prediction prompts, explicitly capturing collaborative signals and peer interactions. Furthermore, we introduce a cross-granularity consistency objective that jointly regularizes mastery estimation across concept, topic-cluster, and global proficiency levels. Extensive experiments on ASSISTments, EdNet, and a newly collected large-scale MOOC dataset demonstrate that MOSAIC establishes new state-of-the-art results. Specifically, our method achieves AUC improvements of up to 3.4% and Accuracy gains of up to 2.5 % across all benchmarks. Notably, MOSAIC exhibits superior robustness in collaboration-rich environments and long-sequence scenarios (AUC 0.862 on MOOC), offering both high predictive precision and semantically grounded interpretability.

Xinjin Li, Mengyue Wang, Yuzhen Lin +4

Columbia University, New York, USA · University of California, Berkeley, Berkeley, USA · School of Information Systems and Management, Carnegie Mellon University, Pittsburgh, PA, USA +4

Intelligent Tutoring Systems Hierarchical Representation Learning Knowledge Tracing

Jun 25, 2026cs.LG

Prism Transformer: Progressive Head Schedules for Hierarchical Attention Processing

Multi-head attention conventionally partitions the hidden dimension equally across all heads at every layer, enforcing an identical representational subspace dimension (dh = dmodel/h) throughout the models depth. In this work, we identify this uniform allocation as a fundamental structural bottleneck: due to their restricted dimensional space, early-layer heads are unable to faithfully capture complex, high-dimensional contextual patterns. To resolve this, we introduce the Prism Transformer, a novel architectural paradigm that replaces the static, uniform head configuration with a progressive head schedule. By monotonically increasing the head count across layers, the Prism Transformer naturally establishes a local-to-global representational hierarchy: early layers leverage fewer, exceptionally wide heads to capture complex, local compositional patterns, while deep layers deploy many, narrow heads to decompose these patterns into specialized linguistic features. Crucially, this structural shift is parameter-neutral, compute-neutral, and introduces zero training or inference overhead, preserving identical weight matrices and FLOP budgets as the standard Transformer. Across three model scales (124M, 354M, and 757M), the Prism Transformer consistently outperforms uniform baselines, achieving consistent reductions in validation loss alongside consistent gains on downstream zero-shot benchmarks (including PIQA, HellaSwag, ARC-Easy, and WinoGrande). Our findings demonstrate that non-uniform subspace allocation unlocks latent capacity within the standard Transformer budget, enabling more effective use of model capacity.

Shubham Aggarwal

Hierarchical Representation Learning Transformer Attention Multi-Head Attention

Jun 22, 2026stat.ML

Sublinearly Structured Deep Neural Networks Achieve Feature Learning Consistency for Compositional Functions

Over the past decade, deep neural networks (DNNs) have achieved remarkable success on complex machine-learning tasks, yet the theoretical foundations of their performance remain incomplete. From a statistical viewpoint, a natural question is: can DNNs attain feature-learning and prediction consistency comparable to that of classical models? While a full characterization is open, we provide positive results for a broad subclass. We establish feature-learning consistency guarantees for sublinearly structured DNNs-architectures whose input/output dimensions and number of hidden neurons grow sublinearly with the sample size-when learning hierarchically compositional target functions. Importantly, this consistency still holds even in the conventional "over-parameterized" regime where the total number of parameters exceeds the number of training samples. Empirically, sublinearly structured DNNs match or surpass wide DNNs in prediction. A structural audit further indicates that widely used convolutional neural networks (CNNs), including AlexNet, VGGNet, ResNet, GoogLeNet, are sublinearly structured on their image classification benchmarks. We further prove that the sublinearly structured DNNs achieve universal approximation for hierarchically compositional functions in the large-sample limit. Moreover, images exhibit an inherent hierarchical, compositional structure. Taken together, these results explain, through a statistical lens, why many large-scale deep learning models succeed after adequate training on massive image datasets.

Sehwan Kim, Yan Sun, Faming Liang

Ewha Womans University, Seoul 03760, Republic of Korea · New Jersey Institute of Technology, Newark, NJ 07102, USA · Purdue University, West Lafayette, IN 47907, USA

Neural Network Generalization Hierarchical Representation Learning Statistical Learning Theory Compositional Representation Learning

Jun 22, 2026cs.LG

Do Sparse Autoencoders Learn Meaningful Concept Hierarchies?

Sparse autoencoders (SAEs) have become an important tool for unsupervised concept discovery in large models. To make the resulting feature spaces more interpretable and manageable, recent approaches have begun imposing hierarchical structure, either explicitly or as an implicit effect of training constraints, yet rigorous comparison remains difficult. There are no agreed-upon requirements for what a meaningful feature hierarchy should satisfy, and evaluation has largely relied on qualitative illustrations with fragmented quantitative protocols. To address this, we derive a set of key requirements for generalization/specialization hierarchies in unsupervised concept discovery, drawing on semantic net and taxonomy research alongside recent SAE work, and use them to derive a concrete evaluation protocol. Applying this protocol to current SAE approaches trained on visual data, we find that while feature spaces generally provide a basis for sensible hierarchies, establishing good hierarchical structure remains challenging. In particular, feature absorption, both in its well-known hard form and in a continuous, soft form, systematically compromises hierarchy quality, pointing to a fundamental tension that future approaches will need to navigate.

Nils Grandien, David Steinmann, Felix Friedrich +1

Computer Science Department, TU Darmstadt · Hessian Center for AI (hessian.AI) · Black Forest Labs +1

Hierarchical Representation Learning Sparse Autoencoders