Hierarchical Representation Learning

Sheaf Neural Networks (SNNs) generalize Graph Neural Networks (GNNs) by replacing scalar node signals with stalk-valued signals and by using restriction maps to measure compatibility across edges. Unlike standard graph diffusion, which encourages neighboring node features to become similar, sheaf diffusion promotes consistency through the restriction maps and can therefore model more general relationships between neighboring nodes. However, existing sheaf neural architectures mainly operate at a fixed graph resolution and do not provide a principled pooling mechanism for building hierarchical representations. In this paper, we introduce Hierarchical Sheaf Pool (HiSP), a sheaf-aware pooling framework based on local spectral coarsening. Given a partition of the graph, HiSP constructs each coarse stalk by projecting fine stalk-valued features onto the low-frequency eigenmodes of the cluster-internal sheaf Laplacian. These local modes define a cochain-level prolongation map, which allows the fine sheaf energy to be represented on the coarse space through a Galerkin operator. We further analyze the approximation induced by coarsening by separating truncation loss, due to discarded local modes, from realization loss, due to representing the projected operator as a coarse sheaf. Finally, we implement HiSP as a GNN pooling layer compatible with SNNs and provide a PyG implementation supporting batching, lifted sheaf Laplacians, and hierarchical architectures.

Long-form narratives are challenging for long-context models because their structure is implicit: events, characters, and plotlines interact across hundreds of pages without the explicit cues that guide navigation in structured documents. We address this by constructing storyline trees, hierarchical representations that organize narratives from global themes and major plotlines to fine-grained events. We first segment chapters into contiguous narrative segments, or scenes, and use them as the basic units for tree construction. We then infer storyline trees through complementary top-down and bottom-up procedures that derive, refine, cluster, and summarize storylines at multiple levels of abstraction. We showcase the utility of this representation for question answering: storyline trees enable adaptive retrieval, allowing models to iteratively inspect high-level narrative structure and retrieve scene-level evidence on demand. Experiments on three long-context narrative QA benchmarks show that adaptive retrieval outperforms strong baselines, including post-trained long-context models and agentic chunk-based methods. Ablations confirm that scenes are more effective basic units than chapters or generic segmentation, and that gains persist under matched retrieval budgets

Computing geometric representations of data is a cornerstone of modern machine learning, typically achieved by training dual encoders which map queries and documents into a shared embedding space. Recent work of You et al. [NeurIPS '25] has extended this approach to hierarchical retrieval, where relevance is determined by the ancestor-descendant relationships in a Directed Acyclic Graph (DAG). While previous work has shown that valid embeddings exist when the number of descendants is small, these bounds degrade significantly for deep hierarchies, requiring dimensions as large as the total number of nodes. In this paper, we investigate compact reachability embeddings for more general graph classes and provide theoretical guarantees for representing hierarchies using embeddings whose dimension depends on structural graph parameters. We prove that for any directed tree, there exists a reachability embedding in constant dimension 3, independent of the tree's size or depth. We generalize this result to graphs characterized by treewidth $t$, constructing embeddings of dimension $O(t \log n)$, where $n$ is the number of nodes. Complementing these upper bounds, we provide matching or near-matching lower bounds, showing that dimension $Ω(n)$ is necessary for general DAGs and $Ω(t/\log(n/t))$ is required for graphs of treewidth $t$. We also obtain upper and lower bounds parameterized by the number of cross-edges in the DAG. We additionally show that our embeddings can be constructed on real world datasets, and that they give much smaller dimensions in high recall regimes compared to prior embeddings with theoretical guarantees.

The application of machine learning models in practical tasks faces challenges such as class imbalance and multidimensional noise. This paper proposes RGNet, a neural network architecture based on the concept of the renormalization group (RG), for hierarchical coarse-graining of the feature space. The model sequentially compresses the input dimensionality and concatenates all scales before classification, allowing it to capture both local details and global patterns. The notion of RG-flows is introduced - interpretable low-dimensional representations whose visualization via t-SNE reveals a discrete curvilinear structure confirming the effectiveness of coarse-graining. Experimental results are presented on the imbalanced AI4I dataset. The obtained results demonstrate that RGNet is a universal, interpretable, and competitive solution for fault prediction in applications with imbalanced classes.

Deep neural networks are widely believed to derive their expressive power from their ability to form \textbf{hierarchical representations}, capturing progressively more abstract and compositional features across layers. In language modeling, \textbf{transformers} have emerged as the dominant architecture, with early layers capturing local syntactic patterns and later layers encoding more complex clause-level dependencies. While this intuition has shaped model design, there remains a lack of rigorous theoretical work demonstrating \textbf{how} deep transformers represent such hierarchical structures. In this work, we analyze the expressiveness of deep transformer models through the formal lens of bounded-depth, non-recursive context-free grammars. For this class of grammars, we explicitly construct transformers with positional attention whose depth grows linearly with grammar depth, while the neuron count scales with the number of derivation-tree shapes and quadratically with the number of production rules. Our theoretical results support the linear representation hypothesis by demonstrating that these architectures possess the structural capacity to encode abstract grammatical states into low-dimensional, linearly separable subspaces within the residual stream.

We ask whether the representational hierarchy seen in perception, from local primitives such as edges to higher level structures such as parts and objects, can be established for motion. In humanoid control, low level actions specify immediate motor commands, while meaningful behavior is organized over longer temporal scales, including contacts, gait fragments, balance recovery, reaching, and whole body skills. We introduce MotionPyramid, a hierarchical action representation that learns such structure from motion data. Starting from a motion tracking teacher, it trains a recursive stack of latent decoders: low level latents decode to immediate full body motor commands, while higher level latents unfold through lower levels into temporally extended motion programs. After pretraining, the hierarchy is frozen and reused by downstream reinforcement learning policies as a family of action interfaces at different control resolutions. Experiments show the learned levels form a motion hierarchy: coarser interfaces improve early learning and motion regularity by constraining exploration to structured segments, while finer interfaces preserve feedback control and final task precision. Representation probes show the hierarchy supports traversal, interpolation, transition, and qualitative composition, exposing editable control handles across temporal scales. Finally, we introduce Residual Interfaces, letting a downstream policy maintain coarse, segment level, and frame level residual commands through the frozen hierarchy. Analogous to residual or skip connections in deep networks, this allows coarse motion programs and fine residual corrections to coexist within one controller. MotionPyramid shows that motion, like perception, can be organized into a reusable multi level representation, providing structured abstraction without sacrificing controllability.

Fine-grained aerial object detection, driven by the intrinsic granularity of real-world object categories, is crucial for advanced scene understanding in remote sensing. Existing methods largely inherit the paradigm of coarse-grained object detection, relying solely on single-label supervision and thus struggling to distinguish model-level categories with subtle structural differences. However, for each specific model (e.g., Boeing 787), structured prior knowledge such as attributes and hierarchies offers discriminative semantics across multiple granularities. Motivated by this, we present ExpertDet, a scheme that incorporates expert-informed cues to enhance fine-grained aerial object detection. Specifically, we design Vision-aware Masked Attribute Modeling (VMAM), which aligns attribute semantics with visual structures by reconstructing randomly masked attributes from visual cues, enabling the detector to capture subtle structural distinctions. We further propose Hierarchical Visual Instance Promotion (HierVIP), which builds a visual prototype tree based on hierarchical relations and imposes taxonomy-aware constraints to preserve cross-level semantic continuity while enhancing category discrimination. Moreover, we curate a new fine-grained object detection benchmark for Precise recognition of model-specific Ships and Planes from aerial imagery, PSP, covering 106 ship classes and 30 airplane models, respectively, featuring the most extensive collection of model-specific categories among existing aerial object detection datasets to date. We benchmark state-of-the-art object detection algorithms on the PSP benchmark. Extensive evaluation demonstrates that ExpertDet consistently outperforms other fine-grained competitors across hierarchy levels. The dataset, benchmark, and code are available at https://nnnnerd.github.io/PSP-Benchmark/.

Multimodal Large Language Models (MLLMs) have demonstrated strong performance on vision-language tasks, yet their internal visual representations remain difficult to interpret. Sparse Autoencoders (SAEs) provide a scalable way to decompose dense model activations into sparse, interpretable features. However, existing SAE architectures primarily recover flat feature dictionaries and are less suited for explicit multi-level concept organization. In this paper, we introduce a cascaded sparse autoencoder architecture, dubbed SAE++, for learning hierarchical visual concepts in MLLMs. Rather than nesting or stacking SAE sparse activation codes, SAE++ trains a second-level SAE directly on the decoder weights of the first-level SAE, treating learned low-level feature directions as inputs for higher-level abstraction. This design enables SAE++ to learn "concepts of concepts" while avoiding drawbacks from the shared-prefix coupling of nesting, Matryoshka-style hierarchies and the bottlenecks of naively stacked SAEs. Experiments across Qwen3-VL, Gemma-3, and LLaVA on multiple visual datasets show that SAE++ improves interpretability in terms of hierarchical concept coherence over state-of-the-art SAE baselines. Results on concept steering further demonstrate that the learned concept groups support effective group-level interventions in MLLM outputs. Code is available at https://github.com/Wang-ML-Lab/sae-plus-plus.

Constructing mathematically tractable function spaces that capture hierarchical compositional representations remains a central challenge in statistical learning theory. We introduce Brownian kernel ladders (BKLs), a recursively defined hierarchy of integral reproducing kernel Hilbert spaces generated through Brownian-kernel integral constructions. Starting from linear functionals, each layer is obtained by integrating Brownian kernels over probability measures supported on subsets of the previous layer, yielding a recursive function-space model in which depth is encoded directly through the hierarchy. Based on this framework, we define canonical BKL spaces together with an associated complexity functional. We establish several analytical and statistical properties of these spaces. In particular, we show that BKL spaces form quasi-Banach spaces, satisfy depth-dependent Hölder regularity estimates, and exhibit strict monotonicity with respect to depth. We further prove existence results for regularized empirical risk minimization and derive Gaussian complexity bounds that remain uniformly controlled with respect to both the ambient dimension and the hierarchy depth. A key ingredient of the analysis is a combinatorial proof technique based on recursive subset decompositions and Brownian-kernel threshold representations. These estimates yield excess-risk guarantees of near-parametric order for regularized empirical risk minimization over BKL spaces. Our results provide a mathematically tractable hierarchical function-space framework for studying compositional representations in deep learning.

Electronic health record foundation models typically treat ICD diagnosis codes as flat tokens, overlooking the clinically meaningful hierarchical structure that captures disease families, subcategories, and fine-grained diagnostic detail. As a result, existing EHR representation learning methods do not explicitly exploit the hierarchical structure already present in the coding system. In this work, we study ICD-10-CM hierarchy as a general inductive bias for clinical representation learning. We investigate two complementary mechanisms for incorporating hierarchy: first, by augmenting diagnosis sequences in a BERT-style transformer with tokens corresponding to different levels of the ICD hierarchy, and second, by injecting hierarchy into graph-based code representations through hierarchy-aware edges combined with diagnosis co-occurrence structure. Across these settings, we evaluate whether explicit hierarchy improves downstream prediction, which levels of the hierarchy are most useful, whether hierarchy encoding improves transfer across datasets, and how hierarchy reshapes embedding similarity structure. We conduct experiments on two large-scale real-world clinical datasets: MIMIC-IV, used for pretraining and in-domain evaluation, and eICU, used to assess cross-dataset transfer via frozen encoder probing. Our findings show that explicitly encoding ICD hierarchy improves over flat code representations in both in-domain and cross-dataset settings, while revealing that the most useful level of hierarchy depends on both the task and the modeling approach. More broadly, we focus on hierarchy-aware EHR representation learning and show that the benefits of encoding hierarchy are generalizable across modeling settings and hierarchy levels.

Generative recommendation models that formulate the task as sequence generation overcome the objective fragmentation problem of traditional cascade architectures, yet existing approaches still suffer from flat semantic representations lacking hierarchical structure for multi-step reasoning and an externally constructed chain-of-thought (CoT) that requires expensive annotations and remains disconnected from the generation objective. We propose HoloRec, an endogenous chain-of-thought recommendation mechanism that unifies representation, reasoning, and generation by constructing a hierarchical semantic encoding matrix via multi-granularity nested residual quantization optimized by a holistic reconstruction loss. HoloRec supports two inference modes: a non-thinking mode that uses lightweight multi-granularity supervised alignment for fast prediction, and a thinking mode that employs an interleaved reasoning scheme to generate CoT steps on the fly, directly embedding reasoning into the generation process without external data. Experiments on multiple public recommendation datasets demonstrate that HoloRec consistently outperforms baselines, with especially significant gains in sparse scenarios, and the thinking mode achieves better accuracy than the non-thinking mode with only modest inference overhead.

Visual perception of urban streetscapes underpins evidence-based decisions in landscape planning, public health, and place-making. Yet models trained on a few well-photographed metropolises systematically misjudge underrepresented districts, propagating geographic bias into downstream policy. We address this gap with HVSP-LL, a lifelong learning framework that couples a stratified visual-semantic pivoting module with an equity-aware rehearsal mechanism. The pivoting module organises landscape concepts along a three-tier ontology (macro structure, meso composition, micro element) and aligns image features to learnable semantic anchors at each tier, providing transferable representations that resist distributional drift. The lifelong adaptation component sequentially absorbs new urban regions while constraining inter-region perception gaps through a worst-region sample-reweighting objective and a structurally-aware exemplar buffer. We evaluate HVSP-LL on a panoramic streetscape benchmark assembled from twelve cities across four continents and seven perceptual dimensions. The framework attains 0.834 Spearman correlation on the held-out city sequence, an absolute 6.1 point improvement over the strongest continual baseline, and shrinks the inter-city perception gap to 0.094 -- a 38% reduction relative to the strongest continual baseline (0.151) and a 57% reduction relative to a representative regularisation baseline (0.218). Ablations confirm that each tier of the pivoting hierarchy contributes monotonically, and the equity-aware rehearsal converts mean backward transfer from -0.038 (without retention) to +0.013, eliminating catastrophic forgetting on the held-out sequence. Our results indicate that hierarchical anchoring is a practical pathway toward geographically equitable streetscape inference at city scale.

Spatial transcriptomics (ST) links gene expression with tissue morphology but remains expensive and low-throughput, motivating surrogates that infer expression from routine histology. Whole-slide H&E-to-ST inference pairs a gigapixel image with gene measurements at a sparse, irregular set of locations, making multiscale modeling challenging without incurring dense-grid overhead or quadratic token mixing. We propose HiST, a hierarchical sparse transformer that treats measured locations as a lattice-indexed sparse field and builds a dyadic encoder--decoder directly on the active tissue footprint. HiST combines sparse window attention for local geometric correspondence with resolution-changing operators for rapid multiscale context integration. For a fixed window size, the dominant runtime and memory scale with the number of observed locations rather than the dense slide area. To mitigate slide-specific acquisition variation, HiST adds a bottlenecked global conditioning pathway via a \emph{slide calibration token} that summarizes slide-level context and conditions local representations. On a multi-organ benchmark spanning diverse tissues and acquisition sources, HiST improves predictive performance over recent baselines while reducing runtime and peak memory.

Protein-ligand binding affinity (PLA) prediction is critical in drug discovery. Despite the notable advancements in machine learning-based approaches, existing methods struggle to jointly characterize local geometric organization and globally coordinated cross-molecular interactions, limiting their ability to model complex binding mechanisms. Here, we propose RicciBind, a geometric representation framework that integrates curvature-guided hierarchical structure learning with optimal transport (OT)-based cross-domain alignment to model molecular interactions. Specifically, RicciBind leverages Ricci curvature to capture local interaction tightness within molecular structures, enhancing structural awareness and organizing atomic interactions into curvature-aware hierarchical representations. An OT-based cluster matching mechanism then aligns protein and ligand clusters across heterogeneous domains under geometric constraints, enabling globally consistent correspondences and revealing higher-order interaction patterns beyond local neighborhoods. By coupling curvature-guided structure encoding with OT-driven cross-domain alignment, RicciBind effectively models complex interaction semantics and substantially improves both the accuracy and interpretability of binding affinity prediction. Extensive experiments demonstrate that RicciBind achieved superior predictive performance and generalization across PLA benchmarks and virtual screening tasks. Ablation studies further confirmed the essential role of Ricci curvature in enhancing molecular interaction representations.

Compositional data -- vectors encoding relative proportions -- arise across scientific domains, including ecology, geochemistry, and genomics. The features in these data often come with known hierarchical structure (e.g., taxonomies, phylogenies, ontologies), yet existing methods either ignore this structure, discard the intrinsic Aitchison geometry, are designed for binary trees, or yield incomplete coordinate systems. We describe PolyILR, a canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology. Our construction defines a weighted local geometry at each internal node capturing full branching structure, then lifts these to a global orthonormal basis where every coordinate corresponds to a specific tree location. On microbiome and single-cell benchmarks, PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution. We also establish a novel theoretical connection to softmax classifiers, suggesting possible applications to probabilistic modeling.

Neural fields parameterize data as functions from coordinates to values, providing a unified framework for representation learning across modalities. Existing approaches are dominated by per-sample meta-learning, which scales poorly due to memory-intensive inner-loop optimization. The natural alternative -- feed-forward encoding -- typically introduces modality-specific assumptions, sacrificing the generality that makes learning with neural fields attractive. We argue that locality and hierarchy are useful priors for learning field representations that can be injected without compromising modality-agnosticism. We propose LH-NeF, a framework to learn general-purpose tokenized representations of continuous signals. A locality-preserving hierarchical encoder maps raw coordinate-value field observations to structured tokens, from which the field is reconstructed during training. By replacing meta-learning's inner loop with a single forward pass, LH-NeF uses 42$\times$ less memory and supports 133$\times$ larger batches than the strongest modality-agnostic baseline. Across images, 3D shapes, and climate fields, our learned representations match or exceed performance of modality-agnostic, modality-specific, and specialized generative neural field baselines on both reconstruction and downstream tasks.

Open-vocabulary audio-visual event localization (OV-AVEL) jointly models audio-visual cues to recognize and temporally localize events, including categories unseen during training. Existing methods primarily learn joint audio-visual representations in Euclidean space, but still face two significant challenges. First, the lack of supervision signals for unseen categories makes it difficult to maintain audio-visual consistency across multiple temporal scales. Second, the lack of hierarchical constraints between segment- and video-level semantics prevents the model from establishing semantic consistency across different levels. To address these challenges, we propose a hierarchical semantic constrained heterogeneous graph (HSCHG) for audio-visual event localization framework. We first construct a heterogeneous hierarchical graph in Euclidean space, which includes audio and visual segment nodes and their corresponding video-level nodes. We use multi-directional temporal edges to capture complete temporal information within each modality. Simultaneously, we employ a dual-threshold filtering gated fusion strategy, introducing cross-modal information only when the alignment confidence is high. Furthermore, we introduce bidirectional semantic constraints between segment- and video-level representations to achieve semantic consistency across different levels. Based on this, we map the multi-level audio-visual representations and text prototypes uniformly into hyperbolic space. We use a hierarchical entailment regularization loss to characterize the hierarchical relationships between videos and segments. Extensive experimental results show that our method outperforms existing methods on the OV-AVEL benchmark. Ablation studies further validate the effectiveness of our method.

Learning semantics is essential for deep learning models to be interpretable and better aligned with human reasoning. Concept-based models approach this by representing classes through meaningful semantic abstractions, but typically treat all concepts as a flat, unstructured set learned at a single neural network layer. This overlooks a fundamental property of human semantic understanding: concepts being organized hierarchically, from general to specific. While deep networks do learn a hierarchy of visual features, this structure is rarely aligned with explicit semantic hierarchies. Drawing on Formal Concept Analysis, we demonstrate that formal concept lattices provide principled semantic scaffolds to guide neural network learning. These lattices naturally identify where in the network concepts should be learned based on their level of generality. This allows the model to develop staged, semantically grounded representations throughout its depth. Empirical results on real-world datasets show that our models produce more interpretable embeddings, support more effective interventions, and learn concept representations that are both meaningful and hierarchically structured.

Understanding the relationship between deep visual representations and the human visual system is a fundamental challenge in computational neuroscience. While modern vision models achieve strong performance in image recognition, their correspondence with the hierarchical organization of the human visual cortex remains an open question. In this study, we propose CHASMBrain, a novel hierarchical two-stage framework for image-to-fMRI encoding. Our architecture leverages a dual-stream Mamba design to explicitly separate and process global semantic tokens and local spatial patches, motivated by the functional organization of the visual cortex. A coarse-to-fine strategy is employed: Stage 1 predicts denoised ROI-level activations, while Stage 2 refines these coarse responses into full voxel-level predictions using a Mamba-VAE. Experiments on the Natural Scenes Dataset (NSD) demonstrate that our method achieves a Pearson correlation of 0.429 and an MSE of 0.261, outperforming all evaluated baselines including ridge regression and DINOv2 linear probes. Beyond predictive performance, causal branch-ablation experiments reveal an asymmetric specialization: the patch stream is specifically locked to early visual cortex (retinotopic regions), while the CLS stream contributes broader semantic context to higher-order areas -- a correspondence that holds causally, not merely correlationally. Cross-subject transfer experiments further show that the learned backbone generalizes across individuals with minimal per-subject adaptation, suggesting the model captures a shared, subject-agnostic visual representation.

Genomic foundation models increasingly adopt large language model architectures, yet almost universally rely on fixed tokenization schemes such as $k$-mers, BPE, or single nucleotides, which impose arbitrary sequence boundaries that may obscure biologically relevant structure. We present LDARNet, a 120M-parameter hierarchical genomic foundation model that adapts H-Net-style dynamic chunking from autoregressive generation to masked language modeling, combining BiMamba-2 state-space layers with local attention, bidirectional routing, and a ratio-based regularizer to induce adaptive token boundaries without supervision. Fine-tuned on 27 tasks from the Nucleotide Transformer and Genomic Benchmarks suites, LDARNet achieves 11/18 wins among compact models ($<$300M parameters) and state-of-the-art results on 5 histone modification tasks, outperforming models up to 20$\times$ larger. A FLOPs-matched controlled experiment isolates learned routing as the source of these gains: learned boundaries beat fixed-grid boundaries by up to 14 percentage points on histone tasks at identical compute. Nucleotide-resolution analysis further shows that the learned boundaries align with canonical promoter motifs and splice junctions without supervision, providing a biological interpretation for adaptive tokenization in genomic foundation models.

Skeleton-based action recognition aims to understand human behaviors from body joint sequences and is especially challenging in the one-shot setting, where only a single labeled exemplar is available for each novel action. A key challenge is learning representations that capture the hierarchical and compositional structure of human motion while aligning effectively with high-level action semantics under extreme data scarcity. Existing approaches, largely based on Euclidean embeddings and low-level motion cues, struggle to model the tree-like organization of skeleton data, limiting cross-modal alignment and generalization to unseen action categories. We propose SkelHCC, a unified skeleton hyperbolic CLIP-driven cache adaptation framework for one-shot skeleton-based action recognition. SkelHCC introduces an Explicitly Hierarchical Hyperbolic CLIP (EH-HCLIP) module that embeds skeleton sequences and action language into a shared hyperbolic space. By leveraging the negative curvature and exponential volume growth of hyperbolic geometry, EH-HCLIP naturally encodes the joint-part-body hierarchy of human anatomy and yields structurally consistent cross-modal representations. To support efficient one-shot adaptation, SkelHCC further integrates a training-free LLM-guided Multi-granularity Voting Cache (LMV-Cache) for context-aware inference. Experiments on NTU RGB+D 60, NTU RGB+D 120, and PKU-MMD demonstrate that SkelHCC consistently outperforms state-of-the-art methods.

Protein-protein interactions (PPIs) are essential for many biological processes. However, existing PPI prediction approaches suffer from two major limitations: they overlook the hierarchical organization of proteins, particularly meso-scale motifs that critically regulate PPIs, and fail to effectively integrate sequence, structure, and function modalities. To address these limitations, we propose MMM-PPI, a Hierarchical Motif-based Multi-Modal protein Encoder for PPI Prediction that constructs PPI embeddings in a bottom-up multi-modal manner across three scales. At the micro-scale, we encode three modal residue features; at the meso-scale, a novel multimodal motif encoder aggregates residues into spatially-informed motif embeddings; at the macro-scale, a multimodal protein encoder integrates motifs into protein embeddings by jointly modeling motif importance and inter-modal correlations. The pre-trained encoder can be used off-the-shelf for large-scale PPI prediction. Extensive experiments on multiple PPI datasets show that MMM-PPI outperforms state-of-the-art multi-label PPI prediction models, particularly under challenging data partitions and limited data scenarios. Codes are in https://github.com/yzf-code/MMM-PPI.

Although multi-scales representation learning enables elastic-dimension embeddings, nested subspaces often suffer from dimensional redundancy and spectral collapse. To address this, we introduce MIC, a framework that optimizes the geometric landscape of multi-granular embeddings through isotropic subspace alignment. MIC employs Soft Collapse Regularization (SCR) to mitigate redundancy between prefix and residual subspaces via cross-correlation penalties, alongside Spectral Isotropy Regularization (SIR) to ensure hyper-spherical uniformity in low-dimensional prefixes. By unifying these strategies through a self-distillation objective, MIC generates semantically dense representations that maintain high discriminative power. Our experiments demonstrate that MIC significantly outperforms standard baselines, particularly in high-compression scenarios where maintaining informational capacity is most critical.

Generative models, from diffusion models to large language models, achieve remarkable performance but at a cost in training data orders of magnitude larger than what biological learners require. An alternative paradigm has emerged in which networks are trained to predict their \emph{own} latent representations of related views or masked regions, as in data2vec and JEPA -- an idea related to predictive-coding accounts of the cortex. Despite strong empirical results, the theoretical understanding of these methods remains limited. Central questions include: by how much does latent prediction actually improve data efficiency? Is there a benefit to stacking such methods into multi-scale hierarchies? We answer both using as data a tractable probabilistic context-free grammar that captures the compositional structure of natural language and images. Such a grammar generates strings of visible tokens by recursively applying production rules along a tree of hidden symbols of depth $L$. For such data, supervised or token-level SSL require a number of samples \emph{exponential} in $L$ to recover the latent tree; we prove that latent prediction achieves this with a number of samples \emph{constant} in $L$, up to logarithmic factors. We confirm this bound with (i) a hierarchical clustering algorithm, (ii) an end-to-end neural network whose predictor-clusterer modules predict their own latents at each level via gradient descent, and (iii) the first sample-complexity analysis of data2vec, which we show implicitly performs hierarchical latent prediction. This suggests that explicit stacking such as H-JEPA is largely redundant.

High-fidelity computational fluid dynamics is essential for aerospace design, but engineering-scale simulations of practical three-dimensional aircraft remain computationally expensive. Learning-based flow-field initialization can improve efficiency by reducing the numerical distance between the initial and converged solutions, yet existing deep learning approaches remain difficult to scale to large three-dimensional aircraft flows with multiscale regional heterogeneity. Most prior studies therefore focus on two-dimensional problems, surface quantities, integral aerodynamic coefficients, or simplified three-dimensional cases with limited grid resolution.Here we propose MHLF, a multigrid-hierarchical learning framework for accelerating engineering-scale aircraft flow simulations while preserving high-fidelity numerical accuracy. MHLF combines a topologically consistent geometric multigrid representation with a hierarchical strategy that captures regional flow heterogeneity during both prediction and subsequent CFD correction. Across three engineering-scale aircraft cases spanning Mach 0.15 to 6.0 and covering subsonic, transonic and supersonic regimes, MHLF accelerates convergence without sacrificing flow-field accuracy, achieving a 3 to 8 times efficiency improvement over conventional initialization. These results demonstrate practical full-flow-field prediction for large three-dimensional aircraft within the CFD domain and provide a foundation for data-driven acceleration of high-fidelity aircraft flow simulation.

Realistic physical systems are characterised by emergent interactions across multiple length and time scales, posing a significant challenge for predictive machine learning (ML) models. Most scientific ML models focus on a narrow range of interactions. While machine learning force fields (MLFFs) offer near-quantum accuracy, the ubiquitous message-passing layers miss long-range many-body effects. Here we introduce the Multiscale Structural Ensemble (MuSE), a hierarchical model that uses Soft Coarse-Graining Pooling to construct coarse representations from smooth fractional assignments of atoms to coarse nodes, enabling MLFF modules to operate across multiple scales. MuSE is architecture-agnostic and coupled with SO3krates, MACE, and PaiNN MLFFs for both molecules and materials. We demonstrate the power of MuSE through Hessian-based benchmarks, folding trajectories for biomolecules, and energy profiles in molecule-graphene nanostructures, where MuSE accurately captures quantum-mechanical interactions at relevant scales -- unlike other recent long-range ML models.

The ability of deep neural networks to learn hierarchical features is widely regarded as a key mechanism underlying their success in high-dimensional learning. Existing theory partially supports this view by establishing approximation rates based on parameter counts and sample complexity guarantees for compositional models without incurring the curse of dimensionality (CoD). To study overparameterized regimes, where the number of parameters exceeds the sample size, we develop a framework that measures complexity via the parameter norm. Within this approach, we establish approximation rates and excess risk bounds for learning sparse compositional functions whose compositional structure is represented by directed acyclic graphs (DAGs), using Frobenius norm-constrained deep neural networks. Our results have broad applicability since every function that is efficiently Turing computable admits sparse compositional representations. In particular, we cover a range of representative models, including multi-index models, binary tree structures, and general compositional architectures. The rates we derive show that deep networks can exploit the compositional structure of the target functions, effectively avoiding the CoD through hierarchical representations.

Deep neural networks trained with backpropagation have achieved outstanding performance in vision tasks but remain biologically implausible, computationally demanding, and difficult to interpret. The Forward-Forward (FF) algorithm offers a promising alternative by training each layer independently through local goodness objectives. However, its purely local optimization lacks hierarchical coordination across layers, and the decoupling of goodness from features leaves the representations unconstrained and semantically ambiguous. We propose a Hierarchical and Contrastive Learning FF framework (HCL-FF) to address these limitations. HCL-FF introduces (1) a coarse-to-fine hierarchical learning strategy that guides representations from low-level cues to high-level semantics, and (2) a supervised contrastive objective that enforces class-discriminative alignment after goodness decoupling. Experiments on CIFAR-10, CIFAR-100, and Tiny-ImageNet demonstrate that HCL-FF achieves new state-of-the-art performance among FF-based methods, with notable accuracy gains of +5.46%, +17.00%, and +12.51%, respectively.

We propose a distributional theory of how hypernymy -- the ``is-a'' relation between general and specific concepts -- is encoded geometrically in language representations. Starting from the empirically verified assumption that words closer on the WordNet hypernym graph co-occur more often, we characterize theoretically the spectrum of the resulting embedding Gram matrix of word2vec embeddings. Under mild positivity and decay conditions on the co-occurrence kernel, we prove that the leading eigenvectors first separate broad taxonomic branches and then progressively finer sub-branches, producing a \emph{hierarchical splitting geometry} with a coarse-to-fine spectral organization that mirrors the tree. We confirm these predictions in word2vec embeddings across many sampled WordNet subtrees, and show that the same signature extends strikingly well to Gemma 2B unembeddings. Our results indicate that hierarchical concept geometry in LLMs need not reflect a hierarchy-specific functional mechanism, but emerges from the spectral structure of pairwise word statistics.

Foundational Models pretrained on huge amount of data learn representations that evolve across depth, forming a hierarchy of embeddings with distinct semantic content and geometric structure. Contrary to the widespread practice of using only the final layer or shallow mixtures, we show that task-relevant information is distributed non-monotonically across layers and cannot be recovered by naïve aggregation. Through a geometric and empirical study across multiple modalities, we show that effective transfer depends on identifying which layers encode task-discriminative structure and how their embeddings are geometrically organized. We introduce Layer-wise Optimal Embedding Selection (LOES), a constructive spectral method that identifies task-discriminative subspaces by minimizing residual error under orthogonality and isotropy constraints. To align fine-tuning with this selection principle, we further propose Geometric Regularization Loss (GeoReg), which enforces a simplicial structure on class manifolds and stabilizes representation geometry during fine-tuning. Across a wide range of architectures, depths, modalities, and data regimes, LOES consistently outperforms standard baselines, with gains that grow as model depth increases. Beyond accuracy, our method reveals how semantic factors are distributed across layers, thereby enabling cross-lingual and cross-modal interpretability analyses. Together, our results provide strong evidence that layerwise embedding geometry is not incidental but central to how deep models represent and transfer knowledge.