Embedding Dimension

Embedding spaces define notions of semantic similarity and distance. We study whether those embeddings reflect physical measurements of mass, distance, time and volume, which admit a unique, objective notion of semantic equivalence and distance. We find that physical measurement is only weakly modeled in the embedding space, and that instead quite peculiar measurement patterns can be observed. Further analysis indicates that embedding representations of physical measurements are strongly influenced by superficial string similarity, and recalibration of similarity does not substantially improve the alignment.

An advanced retrieval-augmented generation pipeline is typically assembled from three or four independently operated systems: an approximate nearest-neighbour index, a full-text search engine, a graph database, and a relational document store. Each contributes its own deployment surface, configuration model, and failure modes, and the integration logic that binds them is written anew in every project. In this work, we present \textsc{Quanta}, an open-source Python library, which unifies dense vector search over 4-bit quantised embeddings, BM25 full-text retrieval, and knowledge-graph traversal behind a single retrieval API. Quanta makes two design commitments, which distinguish it from existing hybrid retrieval stacks. First, signals are combined by \emph{weighted reciprocal rank fusion} rather than by normalising heterogeneous scores onto a shared range, which we argue is ill-posed because such normalisations are query-dependent. Second, the graph is a \emph{candidate expander and not a relevance scorer}: traversal widens the candidate pool, and the newly admitted documents are re-scored by the dense indexes under an identifier allowlist, so structural adjacency determines what is considered while content evidence determines how it ranks.

Cognitive Diagnosis Models (CDMs) play a pivotal role in personalized online learning. Traditional CDMs rely on discrete, ID-based embeddings to represent students, exercises, and concepts. This paradigm diverges from the nature of learner cognition, where knowledge is not stored and retrieved as isolated symbols. As a result, CDMs suffer from semantic limitations when new exercises or concepts appear. In this paper, we propose a Process-aware Language Cognitive Diagnosis (PLCD) framework that uses language-derived structures as cognitive priors and response records to calibrate student posterior states. PLCD leverages large language models (LLMs) to construct concept schemas and cognitive process graphs, and uses target-conditioned semantic memory to retrieve historical responses that are relevant to each target exercise. A process-grounded Language-to-Cognition Mapper with DA-MoE experts and process-level contrastive learning then maps the textual evidence into a unified cognitive space. Experimental results show that PLCD not only outperforms traditional baselines in predicting student performance but also exhibits strong cognitive transfer capabilities. These results connect the computational power of LLMs with the psychometric goal of measuring latent knowledge states, suggesting that structured language priors calibrated by response records can improve cold-start robustness and cognitive grounding.

Graph representation learning has largely focused on designing increasingly sophisticated models to transform graph topology into vector representations, or embeddings. However, the extent to which embedding quality depends on model learning, rather than on the underlying topological transformations, remains unclear. Here, we show that informative embeddings can be derived without complicated model design and gradient-based training. Propagating random features through implicit hierarchical structures induced by random walks and anonymous walks yields embeddings that capture node proximity and structural role, respectively. These two training-free embeddings preserve complementary aspects of graph organization and perform competitively with classic and recent methods across various node-, edge-, and graph-level tasks. They often require substantially less computation, resulting in a favorable quality-efficiency trade-off. Combining the two types of embeddings further improves inference quality of some tasks compared with using either embedding type alone. Our results suggest that informative graph embeddings can arise from carefully chosen topological transformations before any learning operation is applied.

An image may be worth a thousand words, but most captioning models describe it in only a few. Modern vision-language models produce fluent high-level captions, yet routinely miss the attributes, counts, textures, materials, and spatial relations that make an image visually specific. Recent multi-stage systems recover some of these details through generation, decomposition, verification, and rewriting, but they do so at the expense of substantially higher inference latency. We propose SimLoss, a reference-free embedding-space objective for single-pass fine-grained image captioning. SimLoss trains a vision-language model to align its projected hidden-state representation with a frozen image embedding through an InfoNCE contrastive loss, supplying a dense visual supervision signal before any text is decoded, and requiring neither human-written fine-grained captions nor pseudo-captions from a multi-stage pipeline. We instantiate it as SimLoss FFT, which backpropagates through a locally available embedding model, and SimLoss GRPO, which treats that model as a black-box reward. Compared with single-pass, multi-stage verification, reward-optimized, and perception-aware baselines, the fully differentiable fine-tuning variant, SimLoss FFT, achieves the highest precision while nearly matching the F1 score of the multi-stage method, all while retaining single-pass inference and running roughly 20 times faster than the multi-stage pipeline. The reward-based variant SimLoss GRPO attains the strongest recall. Together, these results show that embedding-space supervision can recover the quality of multi-stage verification at the latency of a single-pass captioner.

By introducing RSLM (Rotated Scaled Lloyd-Max), a family of training-free vector quantization codecs compressing embeddings to 1--4 bits per dimension, we reduce memory cost and memory bandwidth of a typical large-scale Approximate Nearest Neighbor (ANN) search system, while reducing its complexity and keeping or improving recall across multiple benchmark datasets. State-of-the-art systems filter candidates using coarse partitions, approximately score them to narrow the set, and then rescore the best with higher precision representations (often >=8 bits per dimension). Our relativized codecs can bring this down to 2--4 bits per dimension. We use the properties of the ANN system to encode residual vectors instead of full vectors, both for the approximate scoring phase and the rescoring phase. Since Maximum Inner Product Search (MIPS) is very sensitive to vector norms, we correct the $L_2$ norms of quantized vectors. Our major innovation is that we correct the $L_2$ norm of the final reconstructed vector rather than just the residual. Our rescaling replaces more complicated schemes, such as Anisotropic loss. The residualization scheme gives us a more favorable quality vs size trade-off than generic quantization methods. Our high-performance implementation leverages a block-wise cascaded Fast Walsh-Hadamard Transform (FWHT) with linear-like complexity, AVX SIMD-optimized codebooks, and a steganographic encoding of scaling factors for perfect cache-line alignment.

Molecular self-supervised learning uses chemical structures to guide which molecular embeddings should be similar. We study whether explicitly encoding a molecule's Bemis-Murcko scaffold and using it to supervise the molecular embedding changes what the model learns. We further test whether this effect depends on the embedding geometry by comparing Euclidean and Lorentz contrastive objectives. Across two augmentation strengths, scaffold-supervised models consistently organize molecules according to both identical and structurally related scaffolds. The resulting embeddings also improve molecular property prediction on several tasks, while the exact gains depend on the predicted property. The effect of scaffold supervision on molecular organization is stronger under Lorentz objectives, but neither geometry provides a consistent overall advantage. These results show that explicitly teaching the relation between a molecule and its structural core can reliably shape the organization of molecular embedding space, while the extent of usefulness of this organization remains task dependent.

Hyperbolic embeddings provide compact geometric representations of complex networks in hyperbolic spaces, but systematic comparisons of methods developed in machine learning, network science, and algorithmics remain rare. We benchmark 13 unsupervised hyperbolic graph embedders under a unified protocol for link prediction and topology reconstruction on synthetic and empirical networks. The protocol captures both missing-link recovery and the preservation of local and global network structure. Maximum-likelihood and representation-learning-based approaches, including hybrid variants, achieve the strongest overall performance, although no method dominates across all tasks and structural regimes. Performance is more strongly associated with embedding paradigm than with disciplinary origin. We identify the network regimes in which different paradigms succeed or fail and provide practical guidance for method selection in downstream applications.

We propose Zero-phase Component Analysis (ZCA) whitening as a geometric pre-processing step for the Word Embedding Association Test (WEAT). WEAT is a bias measurement method widely used in both computational social science and AI fairness research. It relies on cosine similarity as a measure of semantic association, which assumes that the embedding space is approximately isotropic. However, prior work has reported that many widely used language models do not satisfy this assumption, raising concerns about the reliability of bias measurements. ZCA whitening transforms the covariance of the embedding space into the identity matrix while minimizing perturbation to the original vectors. This transformation restores the isotropy condition on which WEAT relies. We evaluate our approach on ten standard WEAT test suites and seven models spanning three architectural families, yielding 70 model-task combinations. The results show that ZCA whitening substantially reduces the anisotropy of the embedding spaces across all models. Particularly for highly anisotropic models, we further observe improvements on standard semantic similarity benchmarks, indicating that the calibrated space better captures semantic associations. After calibration, over 30% of WEAT results change significance status, and effect sizes shift in both directions depending on bias category. These shifts suggest that uncalibrated measurements may both overestimate and underestimate the associations encoded in the embedding space. These findings indicate that previously reported bias measurements in anisotropic embedding spaces should be interpreted with caution and may benefit from re-evaluation with calibrated methods. Our approach contributes to restoring the measurement foundation of WEAT across both computational social science and AI fairness research.

How can an analyst decide whether a nonlinear dimensionality reduction embedding can be trusted? Existing diagnostics provide only partial answers: projection glyphs characterize local sensitivity, map-continuity scores measure local conditioning, and transport-based analyses reveal path-dependent inconsistencies. However, these methods appear unrelated and provide no common framework for understanding when they agree or not. We show that they are all derived from a single geometric object induced by every differentiable embedding, whether defined implicitly through optimization or explicitly by a learned mapping. This framework provides two complementary geometric views of an embedding. The differential view explains local behavior: its first-order term recovers projection glyphs, while its second-order curvature quantifies how far their linear approximation remains reliable. The integral view follows the same geometry along high dimensional paths and determines whether an embedding depends only on the current state or also on the path taken to reach it. We further show that map-continuity is a prerequisite for the other analyses. The framework is theoretically complete for diagnostics derived from the embedding geometry, and we prove the integral view irreducible: no amount of local measurement at any number of points, to any order of derivative, reproduces what it detects. Classical rank-based metrics form a complementary class based on finite-scale neighborhood relationships. Experiments on synthetic and real datasets validate theoretical predictions, demonstrate accurate curvature-based trust estimates on single-cell embeddings, and show that the integral analysis distinguishes single-valued embeddings from path-dependent optimization-based embeddings in ways that existing pointwise diagnostics cannot.

We propose Kohn-Sham Spectral Embedding (KSSE), an energy-based model replacing the top-layer classifier of convolutional networks with a sparse-graph spectral embedding at the Nishimori temperature of an associated Random-Bond Ising Model the spectral detectability threshold where class structure becomes marginally distinguishable from disorder. Mapping pre-trained features onto quasi-cyclic low-density parity-check graphs, we construct a regularized Laplacian (Bethe-Hessian) as an effective Kohn-Sham Hamiltonian, yielding D independent spectral problems-one per feature channel-solvable in $O(N log N + k_{mode}^{2} N)$ time by FFT on circulant blocks (Pontryagin self-duality), with low-mode Rayleigh-Ritz refinement ($k_{mode}=5$). Physically, this is a k.p effective-mass reduction on a one-dimensional ring crystal: the circulant support is the perfect crystal, the data weights a slowly varying impurity potential, and the Nishimori crossing a Fermi level at the band edge. Star-domain surgery optimizes the graph: instead of eliminating all frustrated cycles impossible without destroying the codewords-edge shifts create certified convexity around codewords with bounded residual frustration, with multi-scale fractal certification (basins $D_{2}<1$ vs rough landscapes $D_{2}>3$). The theory includes a generalized Ihara-Bass identity with a sharp spectral threshold, a non-backtracking growth trichotomy with frustration as a gauge-invariant $Z_{2}$ flux, a trapping-set spectral test, exact channel separability with a cup-product obstruction, plus loop-series, convexity, surgery, and quasi-stationarity bounds. On ImageNet-1000 with frozen EfficientNet-B4 features (D=1792) under a transductive protocol, KSSE achieves 88.93% Top-1 accuracy with ~21.24M parameters-beating Swin-L (197M, 86.4-87.3%) and matching the lower end of ViT-H/14 (632M, 88.0-89.5%) with 10x and 30x fewer parameters.

It is common for two-dimensional embeddings of high-dimensional data to be read far beyond what they can support. Distances in and between clusters, the meaning behind empty spaces, and the amount of structure hidden at each point are generally invisible in the output of methods such as t-SNE and UMAP. This is because the information that could support the meaning of these properties is discarded during the optimisation process. Here, we present FloDR, a dimensionality reduction method that embeds data through an invertible normalising flow. While FloDR only uses the first two output coordinates to create a two-dimensional embedding, it retains the remaining coordinates rather than discarding them. In addition to the embedding, an exact inverse and an exact density are properties of a trained mapping, which enable diagnostic visualisations that are computed from the exact inverse of the model that drew the layout rather than from an approximate one. Specifically, we draw two fields, the conditional spread, which measures how much of the original data remains undetermined at each embedding position in input units, and the hidden contrast, which measures how much information about a labelled contrast the two plotted coordinates discard. Both fields are rendered with a prespecified test against a held out portion of the input data and a bootstrap confidence. A field that fails the test is reported as refused.

Protein fold classification can be approached via sequence-based representations or structural descriptors, but direct comparisons between lightweight handcrafted descriptors and pretrained protein language model embeddings remain limited. We investigate discrete Ricci curvature on Calpha contact graphs as a lightweight structural descriptor for fold classification. Each protein domain is represented by a 22-dimensional fixed-length feature derived from summary statistics and quantiles of Ollivier-Ricci and Forman-Ricci edge curvature distributions. We evaluate on CATH top-10 Topology classification and on the ASTRAL 40%-identity SCOPe top-10 Fold benchmark, comparing against geometry, contact-graph statistics, persistent homology, and mean-pooled ESM-2 (150M) baselines. On both datasets, lightweight structural descriptors substantially outperform mean-pooled ESM-2 embeddings, with a larger performance gap on the ASTRAL 40% SCOPe benchmark. Ricci alone uses 22 dimensions, or 3.4% of the ESM-2 baseline dimensionality, and already outperforms mean-pooled ESM-2 on both datasets. Combining Ricci with persistent homology yields the strongest performance, achieving macro-F1 of 0.71 on CATH and 0.68 on SCOPe with a 112-dimensional feature vector. These results identify a regime where lightweight interpretable graph descriptors offer a practical alternative to pretrained protein language model embeddings.

Generating high-quality triangle meshes is essential for film, gaming, and interactive 3D applications. Mainstream methods rely on mesh serialization and autoregressive processes, which stuggles in effective inference and is sensitive to error accumulation. In this paper, we present Nexus, a diffusion method that achieves holistic mesh generation via decoupled vertex and topology generation. First, we view mesh vertices as sparse voxels organized as an octree and adopt a diffusion model to generate the vertices in a coarse-to-fine manner. Second, for topology modeling, we propose Spacetime Interval, as an extension of Spacetime Distance to encode arbitrary edge and face topology into continuous per-vertex embeddings. It allows for a global and efficient recovery of complex topology. We then employ a diffusion model to generate the continuous embeddings on the generated vertices. Extensive experiments on the Objaverse and Toys4K datasets and in-the-wild images demonstrate that our method outperforms state-of-the-art autoregressive and two-stage baselines, effectively circumventing the inherent limitations of sequential mesh modeling. A blind user study from 3D practitioners confirms strong perceptual preference for our results.

3D anomaly detection has recently emerged as an important research topic in computer vision. Although existing methods have achieved high performance, excessive anomaly responses in normal regions and false positives near object boundaries remain unresolved challenges. To address these challenges, we propose a novel 3D anomaly detection model, Memory-to-Prototype Anomaly Detection (M2P-AD), which effectively models the distribution of normal features while suppressing excessive anomaly scores in normal regions and false positives near object boundaries. Specifically, we introduce a Memory-to-Prototype (M2P) module that learns representative prototypes from normal feature embeddings to preserve important structural information of objects. In addition, a Boundary extraction (BE) module is integrated to identify object boundaries, and a Boundary-aware score refinement (BSR) strategy is applied to recalibrate anomaly scores by incorporating boundary characteristics. The proposed method is evaluated on Real3D-AD, Anomaly-ShapeNet, and MulSen-AD, achieving state-of-the-art performance. Qualitative results demonstrate that excessive anomaly scores in normal regions are reduced and false positives near object boundaries are suppressed, resulting in more accurate and stable anomaly localization. The results indicate that the proposed approach enables more reliable 3D anomaly detection and provides a robust solution applicable to real-world industrial environments.

In this work, we introduce CoCo, a loss function aimed at learning normalized and well-structured representations. The proposed loss encourages intra-class collapse and inter-class contrast while preserving sufficient flexibility for neural networks to approximate geometrically optimal embeddings with large angular separation between classes. We provide a theoretical analysis positioning CoCo with respect to related objectives such as dot regression and cross-entropy, showing that the new proposed loss benefits from closer initialization to the optimal configuration, more informative gradients, and stronger incentives for class-wise representation collapse. Extensive experiments on diverse tabular datasets from the OpenML-CC18 benchmark show that CoCo achieves competitive performance with state-of-the-art methods, including kernel SVM, Random Forest, dot regression, and cross-entropy-based neural networks. In addition, both theoretical arguments and empirical analyses demonstrate that the proposal promotes tighter class clustering and faster convergence. These results highlight CoCo loss as an effective objective for learning discriminative representations while maintaining competitive predictive performance.

Accurately representing atmospheric aerosol populations is essential for simulating aerosol-cloud interactions, radiative forcing, and ice nucleation, yet existing reduced schemes impose structural assumptions that limit their ability to capture composition diversity and mixing state. Machine-learning approaches offer more flexible representations, but standard autoencoders do not preserve the mathematical structure of aerosol populations and therefore cannot support physically meaningful process operators. We introduce AeroMELD (Aerosol Measure Embedding for Latent Dynamics), a mathematically grounded framework for constructing low-dimensional latent variables that retain this structure. We show that any permutation-invariant linear encoder must take a scale-shape decomposition, with total number concentration represented explicitly and latent shape given by a barycentric combination of per-particle embeddings. This aggregated latent state retains the diagnostic expressiveness of a Deep Sets model by moving the nonlinear post-aggregation stage into the learned diagnostic map while preserving latent linearity. Using particle-resolved data as ground truth, we encode weighted particle populations directly rather than binned aerosol states; size-resolved mass and number distributions serve only as diagnostic targets and visual summaries. The latent space accurately reconstructs these distributions, CCN spectra, optical coefficients, and immersion-freezing behavior while preserving the linear population structure needed for hybrid ML-physics models. Although the experiments focus on diagnostic reconstruction, the embedding is designed so that emissions and mixing can be represented exactly and nonlinear microphysical processes learned in a controlled latent space. This work establishes a foundation for learning aerosol-process evolution directly in latent space.

Similarity search is a primary application of embedding models trained by contrastive learning. For one of the most popular contrastive learning loss functions, InfoNCE, we show that the population risk with $k$ negative samples is $O(1/k)$ close to an expected cross-entropy which quantifies deviation between i) a softmax similarity search over unseen data using the learned embedding function, and ii) an idealised softmax search over the same data but using similarity implicitly represented in the positive sample generator. This complements existing interpretations of InfoNCE in the $k\to\infty$ limit which are phrased in terms of mutual information, and alignment versus uniformity in embeddings. To quantify generalisation performance, we introduce a new continuity bound for the InfoNCE loss, obtained via Gâteaux differentiation. The bound preserves the structure of averaging over negative samples present in the loss function and features an ``inverse temperature'' parameter which can be tuned to account for the algorithmic temperature. For embedding functions which are Lipschitz in a parameter, this yields a simple demonstration that the averaging effect of $k$ negative samples in the InfoNCE loss carries over to stabilisation of the generalisation error as $k$ grows.

Designing functional and aesthetically coherent floor plans requires exploring a vast space of possible room arrangements, a task that quickly becomes overwhelming for human designers. In this paper, we propose GRE-Diff, a controllable and interactive diffusion-based framework that automates the creation and editing of apartment floor plans under user-specified constraints. By combining AI-generated suggestions with real-time, human-in-the-loop editing, the system enables users to specify room types, room counts, boundary shapes, and editing operations through LLM-parsed instructions or GUI-based interaction. It then generates a diverse set of plausible and well-structured designs for refinement. At the core of our approach is Gaussian Room Embedding (GRE), a continuous latent representation that models each room as a spatial Gaussian distribution capturing its location and extent. Extensive experiments on the RPLAN dataset show that GRE-Diff produces high-quality, constraint-aware, and editable polygonal layouts, offering a practical step toward bridging AI-driven automation and human creativity in spatial design.

This paper concerns the problem of unsupervised temporal action segmentation for long, untrimmed videos. Recent successful approaches follow a joint representation learning and clustering paradigm, where optimal transport (OT) is adopted to produce pseudo labels for learning frame representations. These approaches alternate between estimating pseudo labels using OT and optimizing the parameters with gradient descent during training, where OT is used for obtaining the final temporal action segmentation. A major limitation of these works is that they learn a deterministic embedding for frame representations. The iterative procedure between learning deterministic embeddings based on pseudo labels and estimating pseudo labels from the learned embedding can thus get quickly stuck in a local optimum. As an alternative, we thus propose to learn a probabilistic embedding for frame representations. The embeddings are modeled by Gaussian distributions and we sample from the distributions before estimating the pseudo labels. We evaluate our approach on several challenging temporal action segmentation datasets and achieve results comparable to, and in some cases, better than the state of the art. Compared to baselines with deterministic embeddings, our approach improves MoF up to 20.7% and F1-score up to 19.0%. Our code is available at https://github.com/derkbreeze/PEOT.

We propose MABLE (Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning), a self-supervised framework for learning node and graph embeddings from large, heterogeneous graphs, demonstrated here on geospatial mineral-exploration data. MABLE combines masked reconstruction with fixed cosine-similarity losses that align matched augmented views while keeping unpaired embeddings well spread. A bi-Lipschitz feature decoder ties a low-dimensional reconstruction component of each node embedding to feature similarity, while matched-node consistency shapes the remaining context used by graph pooling. Lipschitz-controlled pooling helps stabilize graph-level representations under perturbations of retained node embeddings, while augmentation alignment trains robustness to masking, node dropping, and sampling variation. Across local copper and regional Arabian Shield studies, MABLE embeddings provide complementary downstream signal and produce coherent embedding-derived layers for hypothesis generation without learned discriminators or hard-negative selection.

Training in artificial neural networks can be viewed as a trajectory evolving through a high-dimensional loss landscape. However, the large number of trainable parameters makes the direct analysis of these dynamics challenging. In this work, we treat such training trajectories as temporal networks and apply recently proposed strategies for the scalar embedding of temporal networks. We investigate whether such a scalar embedding provides a meaningful low-dimensional representation of neural network training dynamics. Using a multilayer perceptron trained on the MNIST classification task, we show that the embedding preserves the main dynamical features observed in the original parameter space, including the emergence of sensitivity to initial conditions for specific learning rate regimes and an accurate reconstruction of the network's maximum Lyapunov exponent. We then use the embedded scalar trajectory to define a characteristic time, analogous to a Lyapunov time, after which the exponential separation between initially close embedded trajectories saturates. This characteristic time captures the typical decorrelation time between initially close network trajectories in the original high-dimensional system. Finally, we investigate the statistical organization of asymptotic training states through a spacing observable defined in the embedded space. We find that the distributions of rescaled asymptotic spacings collapse onto a common form across initial conditions and are compatible with a skew lognormal distribution. Altogether, our results suggest that scalar low-dimensional embeddings provide a useful framework for studying and visualizing the dynamical properties of neural network optimization trajectories.

Pathology foundation models (PFMs) have demonstrated strong potential across clinical and scientific applications, yet their performance is often hindered by batch effects, which are non-biological variations across tissue source institutions (TSIs) that distort learned feature representations and impair generalization. Conventional mitigation strategies, such as stain normalization, offer limited success in addressing these high-dimensional, complex artifacts. We present GLMP (General-purpose LLM-Mediated Pathology model), a novel framework that generates robust numerical embeddings from histology image patches through an intermediate textual representation. By leveraging pretrained general-purpose multimodal large language models (MLLMs) and text encoders, GLMP effectively prioritizes biologically meaningful signals over TSI-specific artifacts, thereby improving cross-institutional generalization. To our knowledge, GLMP is the first pathology model to use text descriptions of histological features as an intermediate representation for generating numerical embeddings from histology images. Our results highlight the untapped potential of broad-domain, non-specialized MLLMs in computational pathology and introduce a new paradigm for building versatile, generalizable, and robust pathology models.

Autoregressive Transformers dominate high-quality mesh generation by producing artist-worthy topologies, yet their inherent sequential decoding induces substantial computational overhead, falling orders of magnitude slower than parallel generative models. On the other hand, while continuous diffusion and flow-matching methods support efficient parallel synthesis across a variety of domains, they cannot be directly applied to meshes: mesh connectivity is inherently discrete and incompatible with standard continuous noise injection and denoising operations. To resolve this fundamental incompatibility, we introduce a compact topology embedder that projects discrete mesh vertex positions and normals into continuous per-vertex embeddings, where the original discrete adjacency information can be faithfully recovered via spacetime distance thresholding. After pretraining and freezing this embedder, any raw mesh can be fully converted into a continuous per-vertex state space unifying position, normal, and implicit topological attributes. Built upon this novel continuous mesh representation, we present PolyFlow, a Transformer-based flow-matching framework that achieves fully parallel vertex state denoising conditioned on extracted point-cloud features. During inference, our model completes generation rapidly via an ODE solver, and supports explicit, precise control over output mesh resolution by directly specifying the target vertex count. Extensive evaluations on the Toys4K benchmark demonstrate that PolyFlow surpasses state-of-the-art autoregressive baselines in both Chamfer Distance and Hausdorff Distance.

Large language models (LLMs) are attractive for context-aware time series forecasting because they can integrate heterogeneous textual signals, yet their discrete, language-oriented tokenization and embedding interfaces are misaligned with continuous numerical values, often harming numerical ordering and forecasting reliability. We propose TempoWave, a plug-and-play temporal wavelet digit interface that maps each scalar observation into digit-wise embeddings constructed from multi-wavelet, multi-scale coefficients. By directly overriding standard token representations, TempoWave seamlessly exposes both fine-grained local fluctuations and macro global structures in a transformer-compatible form, ensuring that precise numerical formatting, distinct digit identity, and robustness to common normalization operations are maintained throughout the LLM pipeline. Experiments across five context-enriched forecasting benchmarks demonstrate that TempoWave consistently improves LLM-based forecasters over standard numeric tokenization and alternative embedding interfaces, achieving a new state-of-the-art. These results highlight the numeric interface as a key bottleneck and suggest that principled multi-resolution embeddings can better couple LLMs' contextual reasoning with precise forecasting. Our code is available at https://github.com/DC-research/TempoWAVE and our model can be accessed at https://huggingface.co/Melady/TempoWAVE.

Chess engines have evolved from search-based systems optimized solely for strength to neural policies capable of modeling human decisions across much of the rating spectrum. Maia-3, the strongest human-like move policy for chess, models the typical moves of a given rating but does not model high Elo strength well (2500+ Lichess Elo) nor has an extensible architecture for modeling individual play style. On the other hand, search-based engines like Stockfish are far stronger than any known human but struggle to model human-like play. To solve these problems, we present Matilda, a permutation-invariant set transformer that re-ranks the full legal-move distribution produced by a frozen Maia-3 and improves it along both dimensions with one 1.7M-parameter model. Matilda uses Maia-3 to provide both global context and search candidates. Context is encoded from Maia-3's hidden representation, time control, and an optional 32-dimensional player-style vector, while the top-16 candidate moves are optionally rescored by Stockfish. A zero-initialized head scatters per-candidate adjustments back into the policy logits, so the untrained model is exactly Maia-3 and every gain is value-added under full-vocabulary NLL. On a 2500+ Elo benchmark from Lichess, Matilda improves on Maia-3 by +0.5-0.6% below 2800 but +4.3%, +11.9%, and +21.9% at 2800-2900, 2900-3000, and 3000+, respectively, and an additional +0.41% overall from player-style embeddings. Ablations show that the improvements are primarily driven by the engine-derived features, the mechanism is not engine-specific, and the gains survive memorization, sibling, and account audits while preserving Maia-3 at 1000-2500 Elo. Because search supervision is modular, Matilda naturally supports interchangeable search engines, demonstrated by replacing Stockfish with an AlphaZero-family engine.

Location encoders transform geographic coordinates into high dimensional embeddings for downstream machine learning, but it is unclear how well these representations capture interpretable spatial effects. We benchmark whether GeoShapley, a game-theoretic explainer that treats all location features as a single joint player, can recover spatially varying coefficients from models built on location-encoder embeddings. Eleven encoders from the TorchSpatial framework are evaluated against a synthetic process with known coefficients, across three scales (grid, county, global), with and without raw coordinates alongside the embedding, and under untrained and contrastively trained conditions. Measuring recovery as the correlation between estimated and true coefficients, we report how it varies with scale and encoder architecture and compare the embeddings against a raw-coordinate baseline. Recovery of the primary coefficient is consistently high across encoders, whereas recovery of a secondary coefficient is more scale-dependent, differing most at the global scale; the raw-coordinate baseline remains competitive throughout.

Numbers have algebraic structure that standard neural embeddings often fail to expose. We introduce Prime Fourier Embeddings (PFE), which encode integers as prime-indexed (cos, sin) pairs derived from the harmonic analysis of Q, providing a pre-structured representation in which modular arithmetic reduces to selecting the relevant prime channel rather than discovering algebraic structure from scratch. We prove that any linear map equivariant with respect to the product group action on PFE must be block-diagonal with one independent block per prime -- a consequence of Schur's lemma applied to the resulting character decomposition. For square-free composite moduli, the Chinese Remainder Theorem predicts which prime channels are task-relevant. Both predictions are confirmed empirically: ablation studies show specialization ratios exceeding 500x between task-relevant and task-irrelevant channels, with perfect in-distribution test accuracy across all square-free composite moduli tested.

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.

We propose a spectral-based, unsupervised representation learning framework to derive low-dimensional embeddings for clinical concepts and patients in rare disease cohorts from electronic health records, where data are high-dimensional but sample sizes are limited. To overcome this challenge, we incorporate a knowledge matrix extracted from a broader population that shares a partially overlapping subspace with the rare-disease cohort. Our method departs from existing approaches by relaxing restrictive one-to-one signal-alignment assumptions between the latent data matrix and knowledge matrix, allowing more flexible and realistic forms of structured sharing. We introduce a novel two-step spectral embedding procedure: first, we identify and remove irrelevant components from the knowledge matrix; then, we apply a projection-based method to separately recover shared and heterogeneous components. Simulations and an analysis of a real-world multiple sclerosis cohort show that the proposed method outperforms competing approaches, particularly in challenging scenarios where shared signals are weak and only partially aligned, as is common in rare-disease data.

We present a quantum--classical hybrid pipeline for polarimetric material classification that casts this as a point-matching problem. Voxel cubes, containing polarized light reflections, are used to train an encoder to produce 32-dimensional embeddings for the voxels of the cubes. At inference, the encoder head is discarded and the embeddings are encoded as probability amplitudes of quantum states. Next, a SWAP-test circuit estimates the fidelity between each of the 32D embeddings from the query cube and a dataset of anchor cubes. The aggregated fidelity serves as materials similarity scores, and the class of the anchor with highest aggregated fidelity is deemed as the class of the queried material. We evaluate our approach on a dataset of 23 materials ($\approx$800 samples each) derived from their Mueller matrices. The point-matching approaches from the proposed quantum SWAP-test and a classical classifier using Optimal Transport are compared. Our results demonstrate the competitive classification accuracy alongside open-set discrimination potential, establishing it as a viable path toward NISQ-based material recognition.

Principal component analysis (PCA) is one of the most widely used unsupervised dimension reduction techniques. We study PCA for data from multiple related domains. Since principal components generally differ across domains, one way to obtain a shared low-rank embedding is to perform PCA on the pooled data. However, this approach can focus on spurious directions that exhibit high variation in only a few domains. To find a robust embedding that still explains most variance in unseen but similar domains, we propose instead to focus on shared directions of variation. To this end, we introduce Anchor PCA which trades off overall explained variance with agreement between the shared and domain-specific low-rank embeddings. Anchor PCA amounts to PCA on a modified target matrix and thus can be solved efficiently. Moreover, we show that Anchor PCA recovers a maximal invariant subspace and admits a minimax reconstruction interpretation under bounded domain-specific covariance inflations. On simulated and real-world gas sensor data with temporal drift, we demonstrate, respectively, that Anchor PCA recovers the maximally invariant subspace and yields embeddings that explain more variance on unseen domains than the pooling baseline and a worst-case alternative. Taken together, these findings establish Anchor PCA as a promising approach to robust unsupervised dimension reduction from multi-domain data.

Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings. Designing descriptors that are both expressive and broadly applicable, however, remains challenging. We study persistent homology (PH) as a general-purpose representation for MD and introduce the masked Flood complex, a protein-tailored modification of a recently introduced simplicial complex construction that emphasizes inter-residue structure at low computational cost. Vectorized persistence diagrams then provide information-rich, geometry-aware summaries of protein conformations, which we evaluate on protein class prediction, frame-level observable regression, and Markov state model (MSM) estimation from learned low-dimensional coordinates in a single shared representation space. Results on the mdCATH dataset show that PH-based descriptors are competitive across tasks, with masked Flood PH yielding the most consistent overall performance. Further, when using topologically-informed MSMs as a drop-in replacement within the recent MarS-FM framework for generative modeling of protein conformations, we obtain consistently better ensemble statistics than MSMs based on physical observables. Finally, we explore the transferability of the generative model to qualitatively different, fast folding, proteins.

Many practically relevant applications of quantum machine learning involve classical data, for which performance depends critically on how inputs are embedded into quantum states. Yet the use of a fixed embedding circuit ansatz remains standard practice. We propose an energy-based generative learning framework that synthesizes gate sequences to optimize embedding structures and refine data-tailored parameters, using a fidelity-based surrogate objective to guide the search toward improved class distinguishability. Empirically, the method improves classification performance across diverse settings, while also revealing datasets where architecture search within the present embedding family yields only limited additional gains. We explain this saturation by deriving bounds on the achievable empirical risk in terms of the Wasserstein distance in the input space, showing that classical data geometry provides an \emph{a priori} diagnostic for regimes in which substantial gains from embedding optimization are unlikely. The results establish a practically useful and theoretically motivated framework for searching effective quantum data embeddings through generative optimization, with the attainable gains diagnosed through the geometry of the underlying classical data.

Traditional multi-modal financial forecasting often relies on scalar sentiment scores, which fail to capture the nuances of financial news. To address this information loss, this paper explores high-dimensional representation learning by replacing discrete polarity ratings with dense FinBERT embeddings within a Transformer-based forecasting architecture. We benchmarked various embedding strategies on the FNSPID dataset, including raw embeddings, attention-weighted aggregation, and a custom Siamese network. While the attention-based mechanism struggled with the low signal-to-noise ratio typical of financial data, the integration of Siamese-optimized embeddings outperformed both the scalar baseline and raw embedding approaches, demonstrating that preserving high-dimensional narrative context yields improved predictive accuracy for short-term stock price movements.

Numeric tabular datasets are the dominant data format in scientific practice, yet large language models lack native mechanisms for representing numeric datasets in a meaningful way across heterogeneous feature spaces. Existing approaches either target predictive modeling over individual datasets, which requires a shared set of variable definitions, or lack mechanisms for interpretable cross-dataset alignment. The proposed methodology characterizes numeric tabular datasets through structured exploratory data analysis descriptors, embeds those descriptors into a shared vector space using a pretrained sentence transformer, and quantifies cross-dataset similarity via Canonical Correlation Analysis (CCA). Furthermore, a penalized formulation of CCA is applied to recover sparse, interpretable variable-level correspondences between datasets, identifying which statistical descriptors or variable-level quantities drive cross-dataset alignment without requiring shared variable names or feature conventions. Differential privacy is optionally applied to the descriptor set prior to embedding, supporting deployment in sensitive data contexts without requiring access to raw observations at time of comparison. The methodology is evaluated across 15 datasets spanning general-purpose benchmarks, materials informatics, and nuclear-grade graphite characterization. Results demonstrate a total P@1 score of 0.9, with known nearest-neighbor retrieval and cluster structure remaining robust across embedding ablations and differential privacy budgets. The proposed framework provides a principled pathway for integrating heterogeneous numeric data into retrieval-augmented generation pipelines while preserving statistical context, with direct applications to data-driven algorithm selection and simulation model initialization for unknown datasets.

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.

A fundamental open question in self-supervised learning (SSL) is the explicit characterization of the optimal geometry of the learned representations. Recently, LeJEPA identified isotropic Gaussian embeddings as optimal for minimizing downstream prediction risk in Euclidean spaces. However, the corresponding problem for distributions supported on lower-dimensional manifolds, such as the hypersphere, remains unexplored. In this work, we demonstrate that extending this minimax analysis to smooth distributions on Riemannian manifolds fundamentally changes the optimal solution. We show that, under a worst-case formulation, both k-nearest neighbors and kernel ridge regression induce hyperspherical uniformity. More precisely, we show that uniform distributions on manifolds are optimal for k-nearest neighbors, and that the uniform distribution on the sphere is optimal for kernel ridge regression with both the exponential dot-product kernel and the linear kernel. This theoretical insight reveals a fundamental limitation of Gaussian embeddings: their non-uniform density induces anisotropic k-NN neighborhoods, severely biasing the estimator. To correct this, we introduce SPHERE-JEPA, a theoretically grounded SSL framework. We adapt LeJEPA's Cram{é}r-Wold projection mechanism to enforce hyperspherical uniformity rather than a Gaussian prior. Empirically, SPHERE-JEPA yields significant improvements, boosting texture retrieval mAP by over 6%, while consistently matching or outperforming LeJEPA on standard benchmarks-including a +1.8% linear probing gain on ImageNet-1K (ViT-B/14).

Hepatocellular carcinoma (HCC) is biologically heterogeneous, shaped by the interplay between hepatic functional reserve and tumor-related oncologic factors; thus, similar survival outcomes may reflect fundamentally different underlying biological processes. Prognostic modeling in HCC is informed by rich multimodal information from multiparametric MRI and radiology reports from routine clinical practice. Existing prognostic vision-language models (VLMs) learn a single entangled latent representation that blends hepatic and tumor-related factors, limiting both accuracy and biological interpretability. We present BioFact-MoE, a biologically factorized Mixture of Experts (MoE) framework that explicitly decomposes liver and tumor factors via biologically supervised experts within a residual MoE survival architecture. On a HCC cohort of N=588 patients (pretrained on 4,582 3D MRI image-report pairs), BioFact-MoE consistently improves survival prediction over all baselines across time horizons, achieving 12-, 18-, and 24-month AUCs of 75.33%, 75.85%, and 73.96%. Beyond scalar risk prediction, gated expert weights enable phenotype-aware risk stratification. Pathway-informed gating uncovers clinically meaningful treatment-associated survival heterogeneity. In held-out validation, hepatic and tumor embeddings show selective associations with liver function and tumor burden markers, respectively (p<0.05), without supervision. The code is available at https://github.com/jy-639/BioFact-MoE.

Museums are important sites for the dissemination of culture and art. They are institutions rooted in history and tradition; their exhibitions are often designed to highlight these aspects. Recently, a new approach is being explored in the field: emotion-based exhibitions. These exhibitions are designed specifically to elicit emotions in the visitors, in order to maximize engagement, and as a way to democratize access to art and attract a wider, more diverse audience. To do so, the emotional content of the artworks must first be extracted, however, manually annotating the artworks by experts is a prohibitively labor-intensive process, and risks introducing the personal bias of curators. To assist the museum curators in their design of these exhibitions, we wish to develop a tool that can predict the emotional response evoked by a work of art. In this article, we leverage a continuous bi-dimensional emotion space to enhance emotion representations and the training process of deep learning models. Drawing inspiration from existing categorical and dimensional emotion representations, we introduce a new representation, Dimensional Distribution Emotion State (DDES), along with a pipeline for multi-dataset training. We show that DDES provides multiple advantages compared to widely used representations while exhibiting similar baseline performance.

Why does the low dimensionality of representations, typically $d\approx 1000$, not prevent modern embedding-based retrieval models from scaling to billions, or even trillions, of data points? To answer this question, we study maximal-margin embeddings in the following retrieval model, classically studied in communication complexity [PS86] and more recently in embedding-based retrieval [WBNL26]. Let $A\in \{0,1\}^{N\times n}$ be a matrix indicating whether each of $N$ queries is relevant to each of $n$ documents. We are interested in the largest margin $m>0,$ denoted by $\mathsf{m}^{\mathsf{rd}}(d, A),$ for which there exist unit norm embeddings of the queries and documents $\{U_j\}_{j = 1}^N, \{V_i\}_{i = 1}^n$ with the following property. $\langle U_j, V_i\rangle \ge m$ whenever $A_{ji} = 1$ and $\langle U_j, V_i\rangle \le -m$ otherwise. A large margin is a key proxy for representation quality: it controls both robustness to perturbations and compositional generalization across queries. Our main theorem establishes that the best possible margin without a restriction on the dimension, $\mathsf{m}^{\mathsf{rd}}(+\infty, A),$ can be nearly achieved in dimension $d = O(\mathsf{m}^{\mathsf{rd}}(+\infty, A)^{-2}\log n)$ which improves a theorem of [BDES02]. Together with a matching lower bound in Theorem 1.5, we conclude that when $A\in \{0,1\}^{\binom{n}{k}\times n}$ is the matrix containing all possible $k$-sparse rows once, dimension $d = O(k\log (n/k))$ is necessary and sufficient for the maximal possible margin $\mathsf{m}^{\mathsf{rd}}(+\infty, A) = Θ(k^{-1/2})$ in this setting. This fully resolves the setup of [WBNL26]. We also give several constructions for large margins when $d = o(k\log (n/k)).$ Finally, we empirically test the InfoNCE and sigmoid losses for producing large margin embeddings and demonstrate a clear advantage of the sigmoid loss.

Recent advancements in instructional fine-tuning have injected noise into embeddings, with NEFTune (Jain et al., 2024) setting benchmarks using uniform noise. Despite NEFTune's empirical findings that uniform noise outperforms Gaussian noise, the reasons for this remain unclear. This paper aims to clarify this by offering a thorough analysis, both theoretical and empirical, indicating comparable performance among these noise types. Additionally, we introduce a new fine-tuning method for language models, utilizing symmetric noise in embeddings. This method aims to enhance the model's function by more stringently regulating its local curvature, demonstrating superior performance over the current method, NEFTune. When fine-tuning the LLaMA-2-7B model using Alpaca, standard techniques yield a 29.79% score on AlpacaEval. However, our approach, SymNoise, increases this score significantly to 69.04%, using symmetric noisy embeddings. This is a 6.7% improvement over the state-of-the-art method, NEFTune (64.69%). Furthermore, when tested on various models and stronger baseline instruction datasets, such as Evol-Instruct, ShareGPT, OpenPlatypus, SymNoise consistently outperforms NEFTune. The current literature, including NEFTune, has underscored the importance of more in-depth research into the application of noise-based strategies in the fine-tuning of language models. Our approach, SymNoise, is another significant step towards this direction, showing notable improvement over the existing state-of-the-art method.

Vector quantization is a fundamental primitive for scalable machine learning systems, enabling memory-efficient storage, fast retrieval, and compressed inference. Recent rotation-based quantizers such as EDEN, RabitQ, and TurboQuant have introduced strong guarantees and empirical performance, but the surrounding comparisons have been difficult to interpret because they rely on different distortion criteria, probability regimes, and implementation assumptions. As our first contribution, we provide a unified theoretical comparison of these methods and show that their relative advantages are criterion-dependent rather than absolute: EDEN and TurboQuant are favorable for MSE distortion, EDEN is also effective for expected inner-product distortion, and RabitQ provides strong high-probability control. This comparison further clarifies that EDEN provides particularly strong guarantees for expected distortion measures. As our second contribution, we introduce Block-Sphere Quantization (BlockQuant), a new rotation-based block quantization algorithm designed around the spherical geometry of randomly rotated vectors. Unlike coordinate-wise quantizers, BlockQuant quantizes blocks on the sphere, preserving the geometry of rotated embeddings more faithfully. We prove that this block-spherical design theoretically improves over the baselines considered in this paper for both reconstruction MSE and expected inner-product distortion. Our experiments on real embedding datasets and long-context LLM inference tasks show practical gains that are consistent with our theoretical improvements.

Binary quantization (BQ) compresses high-dimensional embeddings into one or two bits per coordinate, enabling nearest neighbor search at extreme speed. Yet a striking puzzle persists: BQ achieves competitive recall on contrastive embeddings but fails on others -- and two leading systems adopt diametrically opposite strategies (random rotation vs. preserving coordinate axes) without a common theory explaining when each is appropriate. We address this puzzle by connecting the Gaussian structure recently established for InfoNCE-trained representations to a statistical framework for BQ quality. Our analysis reveals two distinct roles of the covariance matrix. First, the full covariance structure -- not merely its diagonal -- determines the absolute level of ranking fidelity, with off-diagonal correlations contributing 30--50% of the signal. Second, coordinate heterogeneity (the non-uniformity of per-coordinate variances) governs key design choices: how much each additional bit contributes, and whether random rotation helps or hurts. We derive approximate expressions for ranking fidelity under a Gaussian model, show that the magnitude bit carries information proportional to heterogeneity, and show that random rotation destroys precisely the signal that one paradigm exploits while creating the isotropy that the other requires. A phenomenological scaling law predicts fidelity across models and dimensions. Experiments on 18 datasets spanning 9 embedding families support the main predictions and provide, to our knowledge, the first principled design guide for binary quantization systems.

Contrastive learning (CL) aims to preserve relational structure between samples by learning representations that reflect a similarity graph. Yet, the geometry of the resulting embeddings remains poorly understood. Here we show that weighted InfoNCE objectives can be interpreted as Distance Geometry Problems, where the weighting scheme specifies the target geometry to be realized by the representation. This viewpoint yields exact characterizations of the optimal embeddings for several supervised and weakly supervised objectives. In supervised classification, both SupCon and Soft SupCon (a dense relaxation of it where pairs from distinct classes have small non-zero similarity) collapse samples within each class to a single prototype. However, while balanced SupCon recovers the classical regular simplex geometry, class imbalance breaks this symmetry: SupCon induces non-uniform inter-class similarities depending on class sizes, whereas Soft SupCon preserves a regular simplex geometry regardless of class imbalance. In continuous-label settings, our framework reveals a different failure mode: y-Aware CL generally cannot attain its entropic optimum unless the labels lie on a hypersphere, exposing a mismatch between Euclidean label weights and spherical latent similarity. By contrast, geometrically consistent choices such as Euclidean-Euclidean weighting or X-CLR admit unique optimal embeddings. Our results show that the choice of weighting scheme determines whether contrastive learning is geometrically realizable, degenerate, or inconsistent, providing a principled framework for designing contrastive objectives.

Periodic signals are critical for representing physical and perceptual phenomena. Scalar, real angular measures, e.g., radians and degrees, result in difficulty processing and distinguishing nearby angles, especially when their absolute difference exceeds pi. We can avoid this problem by using real-valued, periodic embeddings in high-dimensional space. These representations also allow us to control the nature of their dot product similarities, allowing us to construct a variety of different kernel shapes. In this work, we aim of highlight how these representations can be constructed and focus on the formalization of Dirichlet and periodic Gaussian kernels using the neurally-plausible representation scheme of Spatial Semantic Pointers.

Unobserved confounding prevents standard covariate adjustment from identifying causal response functions in observational studies. Proxy causal learning addresses this problem through bridge equations involving treatment- and outcome-inducing proxies, avoiding direct recovery of the latent confounder. Existing doubly robust proxy estimators combine outcome and treatment bridges, but typically rely on fixed kernels, sieves, or low-dimensional semiparametric models; existing neural proxy methods are more flexible, but are largely single-bridge estimators. We develop a neural doubly robust framework for proxy causal learning with continuous and structured treatments. Our method introduces a neural mean-embedding estimator for the treatment bridge, combines it with a neural outcome bridge, and estimates the doubly robust correction through a final regression stage. The framework covers population, heterogeneous, and conditional dose-response functions, yielding full response-curve estimators rather than binary-treatment effects. The algorithms use two stages for each bridge and history-aware updates of the final linear layers to stabilize stochastic multi-stage training. We prove consistency of the algorithms showing that the doubly robust error is controlled by the final averaging and regression errors together with the smaller of the outcome- and treatment-side weak-norm bridge errors. Across synthetic and image-valued benchmarks, the proposed estimators outperform existing baselines and single-bridge neural estimators, showing the benefit of combining learned outcome and treatment bridges in a doubly robust construction. Our implementation is available at https://github.com/BariscanBozkurt/DRPCL-Neural-Mean-Embedding.

Watermarking for large language models (LLMs) is a promising approach for detecting LLM-generated text and enabling responsible deployment. However, existing watermarking methods are often vulnerable to semantic-invariant attacks, such as paraphrasing. We propose PASA, a principled, robust, and distortion-free watermarking algorithm that embeds and detects a watermark at the semantic level. PASA operates on semantic clusters in a latent embedding space and constructs a distributional dependency between token and auxiliary sequences via shared randomness synchronized by a secret key and semantic history. This design is grounded in our theoretical framework that characterizes a jointly optimal embedding-detection pair, achieving the fundamental trade-offs among detection accuracy, robustness, and distortion. Evaluations across multiple LLMs and semantic-invariant attacks demonstrate that PASA remains robust even under strong paraphrasing attacks while preserving high text quality, outperforming standard vocabulary-space baselines. Ablation studies further validate the effectiveness of our hyperparameter choices. Webpage: https://ai-kunkun.github.io/PASA_page/.

In many practical applications it is important to build symmetries into neural network architectures. Consider the important case of permutation symmetry on point clouds consisting of $n$ points in $d$ dimensions. In this case the network learns a function on a set of $n$ points in $\mathbb{R}^d$, and a natural paradigm for constructing invariant networks is Janossy pooling, which generalizes the popular Deep Sets architecture. We study the universality of this approach, in particular the important question of how large the embedding dimension must be to guarantee universality of this architecture. Specifically, using a novel technique, we prove new lower bounds on the required size of this embedding dimension. For Deep Sets, this gives the correct minimal dimension up to a constant factor for all $d > 1$. For $k$-ary Janossy pooling, we prove the first non-trivial lower bound on the required embedding dimension when $k > 1$.

Embedding-based representations in Euclidean space $\mathbb{R}^d$ are a cornerstone of modern machine learning, where a major goal is to use the \emph{smallest dimension} that faithfully captures data relations. In this work, we prove sharp dimension--accuracy tradeoffs and identify a fundamental information-theoretic limitation: unless the embedding dimension $d$ is chosen close to the ground-truth dimension $D$, accuracy undergoes a sudden collapse. Our main result shows that this phenomenon arises even in standard contrastive learning settings, where supervision is limited to a set of $m$ anchor--positive--negative triplets $(i,j,k)$ encoding distance comparisons $\mathrm{dist}(i,j) < \mathrm{dist}(i,k)$. Specifically, given triplets realizable by an unknown ground-truth embedding in $D$ dimensions, we prove that there exists constant $c < 1$, such that \emph{every embedding of dimension at most $cD$ violates half of the triplets}, yielding accuracy as low as a trivial one-dimensional solution that ignores the input. We complement our information-theoretic bounds with strong computational hardness results: under the Unique Games Conjecture, even if the given triplets are nearly realizable in $D=1$ dimension, no polynomial-time algorithm -- \textit{regardless of its dimension} -- can achieve accuracy above the trivial $50\%$ baseline.

We study query time bounds for the fundamental problem of estimating the kernel mean $\frac1{|X|}\sum_{x\in X}\mathbf{k}(x,y)$ of a query $y$ in a finite dataset $X\subset\mathbb{R}^d$ up to a prescribed additive error $\varepsilon$. The best known bounds for the Gaussian kernel are $O(d/\varepsilon^2)$, $\widetilde O(d+1/\varepsilon^4)$, and $\widetilde O(d+Δ^2/\varepsilon^2)$, where $Δ$ is the diameter of a region containing the points. We prove the new bound $\tilde O(d+\varepsilonΔ^2+1/\varepsilon^3)$, which improves over the previous ones in regimes with small error $\varepsilon$ and intermediate diameter $Δ$. At the center of our proof is a new fast spherical embedding theorem in the sense introduced by Bartal, Recht and Schulman (2011), which limits the embedded data diameter while preserving local Euclidean distances and avoiding ``distance collapse'' at larger scales. This fast embedding theorem may be of independent interest.

Malaria, childhood acute respiratory infection, and child undernutrition together account for over two million deaths annually in children under five, with the burden concentrated in low and middle-income countries where climate variability modulates transmission, exposure, and nutritional outcomes. Routine health surveillance in these settings remains sparse and reactive. Satellite-derived representations of the Earth's surface offer a scalable, low-cost complement to traditional covariates, yet their utility as predictors of population health outcomes is poorly characterised. We summarise findings from three studies evaluating AlphaEarth Foundations 64-dimensional satellite embeddings as predictors of population health outcomes, focusing on vulnerable populations. The studies span infectious disease (malaria, respiratory infection) and stunting. In each study, embeddings provide predictive value at sufficient spatial granularity: (i) malaria prediction across Nigeria shows consistent per-region R^2 gains; (ii) childhood acute respiratory infection prediction across 11 DHS countries increases pooled R^2 from 0.157 to 0.206 across three tree-based estimators; (iii) stunting prediction across 35 countries is neutral at country level due to collinearity with fixed effects. The stunting case is currently limited by lack of DHS cluster-level coordinates, which is the next key experiment.

We propose Noise-Based Spectral Embedding (NBSE), a physics-informed framework for selecting informative features from high-dimensional data without greedy search. NBSE constructs a sparse similarity graph on the samples and identifies the Nishimori temperature $β_N$ the critical inverse temperature at which the Bethe Hessian becomes singular. The corresponding smallest eigenvector captures the dominant mode of an intrinsically degree-corrected diffusion process, naturally reweighting nodes to prevent hub dominance. By transposing the data matrix and applying NBSE in feature space, we obtain a one-dimensional spectral embedding that reveals groups of redundant or semantically related dimensions; balanced binning then selects one representative per group. We prove that coloured Gaussian perturbations shift $β_N$ by at most $O(\barσ^2)$, guaranteeing robustness to measurement noise. Experiments on ImageNet embeddings from MobileNetV2 and EfficientNet-B4 show that NBSE preserves classification accuracy even under aggressive compression: on EfficientNet-B4 the accuracy drop is below $1\%$ when retaining only $30\%$ of features, outperforming ANOVA $F$-test and random selection by up to $6.8\%$.

Statistical modeling of popular music presents a unique challenge due to the complexity of song structures, which cannot be easily analyzed using conventional statistical tools. However, recent advances in data science have shown that converting non-standard data objects into real vector-valued embeddings enables meaningful statistical analysis. In this work, we demonstrate an approach based on logistic principal component analysis to construct embeddings from global song features, allowing for standard multivariate analysis. We apply this method to a corpus of Lennon and McCartney songs from 1962-1966, using embeddings derived from chords, melodic notes, chord and pitch transitions, and melodic contours. Our analysis explores how these song embeddings cluster by Beatles album, how songwriting styles evolved over time, and whether Lennon and McCartney's compositions exhibited convergence or divergence. This embedding-based approach offers a powerful framework for statistically examining musical structure and stylistic development in popular music.

Earth observation foundation models encode land surface information into dense embedding vectors, yet the geometric structure of these representations and its implications for downstream reasoning remain underexplored. We characterize the manifold geometry of Google AlphaEarth's 64-dimensional embeddings across 12.1 million Continental United States samples (2017--2023) and develop an agentic system that leverages this geometric understanding for environmental reasoning. The manifold is non-Euclidean: effective dimensionality is 13.3 (participation ratio) from 64 raw dimensions, with local intrinsic dimensionality of approximately 10. Tangent spaces rotate substantially, with 84% of locations exceeding 60\textdegree{} and local-global alignment (mean$|\cosθ| = 0.17$) approaching the random baseline of 0.125. Supervised linear probes indicate that concept directions rotate across the manifold, and compositional vector arithmetic using both PCA-derived and probe-derived directions yields poor precision. Retrieval instead produces physically coherent results, with local geometry predicting retrieval coherence ($R^2 = 0.32$). Building on this characterization, we introduce an agentic system with nine specialized tools that decomposes environmental queries into reasoning chains over a FAISS-indexed embedding database. A five-condition ablation (120 queries, three complexity tiers) shows that embedding retrieval dominates response quality ($μ= 3.79 \pm 0.90$ vs.\ $3.03 \pm 0.77$ parametric-only; scale 1--5), with peak performance on multi-step comparisons ($μ= 4.28 \pm 0.43$). A cross-model benchmark show that geometric tools reduce Sonnet 4.5's score by 0.12 points but improve Opus 4.6's by 0.07, with Opus achieving higher geometric grounding (3.38 vs.\ 2.64), suggesting that the value of geometric characterization scales with the reasoning capability of the consuming model.

Recommender systems have advanced markedly over the past decade by transforming each user/item into a dense embedding vector with deep learning models. At industrial scale, embedding tables constituted by such vectors of all users/items demand a vast amount of parameters and impose heavy compute and memory overhead during training and inference, hindering model deployment under resource constraints. Existing solutions towards embedding compression either suffer from severely compromised recommendation accuracy or incur considerable computational costs. To mitigate these issues, this paper presents BACO, a fast and effective framework for compressing embedding tables. Unlike traditional ID hashing, BACO is built on the idea of exploiting collaborative signals in user-item interactions for user and item groupings, such that similar users/items share the same embeddings in the codebook. Specifically, we formulate a balanced co-clustering objective that maximizes intra-cluster connectivity while enforcing cluster-volume balance, and unify canonical graph clustering techniques into the framework through rigorous theoretical analyses. To produce effective groupings while averting codebook collapse, BACO instantiates this framework with a principled weighting scheme for users and items, an efficient label propagation solver, as well as secondary user clusters. Our extensive experiments comparing BACO against full models and 18 baselines over benchmark datasets demonstrate that BACO cuts embedding parameters by over 75% with a drop of at most 1.85% in recall, while surpassing the strongest baselines by being up to 346X faster.

When task-specific labels are not available, it becomes difficult to select an embedding model for a specific target corpus. Existing labelless measures based on kernel estimators or Gaussian mixes fail in high-dimensional space, resulting in unstable rankings. We propose a flow-based labelless representation embedding evaluation (FLARE), which utilizes normalized streams to estimate information sufficiency directly from log-likelihood and avoid distance-based density estimation. We give a finite sample boundary, indicating that the estimation error depends on the intrinsic dimension of the data manifold rather than the original embedding dimension. On 11 datasets and 8 embedders, FLARE reached Spearman's $ρ$ of 0.90 under the supervised benchmark and remained stable in high-dimensional embeddings ($d \geq 3{,}584$) as the existing labelless baseline collapsed.

Across many scientific fields, measurements often represent the number of times an event occurs. For example, a document can be represented by word occurrence counts, neural activity by spike counts per time window, or online communication by daily email counts. These measurements yield high-dimensional count data that often approximate a Poisson distribution, frequently with low rates that produce substantial sparsity and complicate downstream analysis. A useful approach is to embed the data into a low-dimensional space that preserves meaningful structure, commonly termed dimensionality reduction. Yet existing dimensionality reduction methods, including both linear (e.g., PCA) and nonlinear approaches (e.g., t-SNE), often assume continuous Euclidean geometry, thereby misaligning with the discrete, sparse nature of low-rate count data. Here, we propose p-SNE (Poisson Stochastic Neighbor Embedding), a nonlinear neighbor embedding method designed around the Poisson structure of count data, using KL divergence between Poisson distributions to measure pairwise dissimilarity and Hellinger distance to optimize the embedding. We test p-SNE on synthetic Poisson data and demonstrate its ability to recover meaningful structure in real-world count datasets, including weekday patterns in email communication, research area clusters in OpenReview papers, and temporal drift and stimulus gradients in neural spike recordings.

Previous work has shown that node embedding methods can produce different representations and downstream predictions across repeated training runs, even when trained on the same data with identical hyperparameters. However, the role of embedding dimensionality in this instability remains poorly understood. In this work, we systematically analyze how embedding dimensionality affects the stability of embeddings from five widely used node embedding methods: ASNE, DGI, GraphSAGE, node2vec, and VERSE. We evaluate stability from both representational and functional perspectives across a broad range of dimensions, datasets, and repeated training runs, and relate the resulting stability patterns to predictive performance. Our results show that dimensionality can substantially affect embedding stability, although the observed effects depend strongly on the embedding method and stability notion considered. While node2vec and ASNE generally became more stable at higher dimensions, GraphSAGE and VERSE often exhibited non-monotonic behavior or decreasing stability. We further find that dimensions associated with high stability do not necessarily coincide with those yielding the strongest downstream performance. Overall, our findings demonstrate that embedding dimensionality can have a substantial impact on the stability of node embeddings and downstream predictions.

Deformable 3D Gaussian Splatting (3DGS) has emerged as a popular method for real-time talking head synthesis, offering high-quality renderings at low latency. Tri-planes are a common choice for encoding Gaussians prior to deformation since they provide a compact and continuous representation. However, tri-plane encodings are limited by grid resolution and approximation errors introduced by projecting 3D volumetric fields onto 2D subspaces. Recent work has demonstrated the effectiveness of per-Gaussian embeddings for driving temporal deformations in 4D scene reconstruction. We introduce EmbedTalk, which leverages these embeddings to model speech-driven facial deformations for talking head synthesis. Comprehensive experiments show that EmbedTalk improves rendering quality, lip synchronisation, and motion consistency over previous 3DGS-based methods, while remaining competitive with state-of-the-art generative models. Replacing tri-plane features with embeddings also yields significantly more compact models that achieve 60+ FPS on a laptop GPU (RTX 2060 6 GB). Our code will be placed in the public domain on acceptance.