Spatial transcriptomics enables spatially resolved gene expression analysis from slide-level images while preserving morphological features, providing valuable information for studying disease mechanisms and developing treatments. However, spatial gene expression profiling typically requires expensive and time-consuming tests. While existing image-based prediction optimizations mostly revolve around including positional embeddings and further image-based changes, text-based optimizations remain relatively unexplored. We present GATE-ST, which incorporates text-based inputs into image-based spatial gene expression predictions. With this approach, generated text descriptions of genes are utilized to better spatial transcriptomics prediction results. Gene summaries are put through a text encoder, generating embeddings that integrate with image embeddings through cross-attention layers to align with morphological features. We demonstrate the effectiveness of such text inputs by benchmarking performance against random gene embeddings and multiple other image-text fusion architectures, and show that GATE-ST outperforms these alternatives. Our results demonstrate the effectiveness of GATE-ST in pathology imaging, which may greatly reduce the time and cost of accurate spatial transcriptomic predictions, proving the potential of text-guided spatial gene expression prediction.
https://arxiv.org/abs/2609.38690
Effective AI adoption in cyber-physical systems (CPS) depends on embedding design knowledge into engineering practice. Yet as AI-enabled components increasingly replace analytically derived control laws, this occurs without a systematic understanding of how controller architectures differ or remain similar across paradigms. We address this gap with an empirical study of traditional and AI-enabled Simulink controllers, guided by a literature-derived taxonomy of ten structural categories and nine functional roles. The study analyzes 62 real-world models spanning 8 controller types and 10 application domains, and surveys 13 practitioners, identifying three architectural tensions. First, subsystem organization dominates all controller structures regardless of paradigm, occupying 68-72% of controller footprint, while core control logic occupies minimal space. Second, AI-enabled controllers rely heavily on discrete dynamics and user-defined abstraction, categories largely absent from AI literature, exposing a gap between described and implemented architectures. Third, constraint enforcement blocks largely disappear from AI-enabled models despite practitioner expectations. This reveals a misalignment where safety mechanisms shift from explicit structure to implicit training-time artifacts, breaking traceability.
https://arxiv.org/abs/2609.38504
Multi-user voice agents must track who said what across dialogue sessions. Text LLMs are attractive backbones for such agents, but transcripts alone do not expose acoustic speaker identity, leaving the model without a persistent reference for linking information to speakers across sessions. We address this gap by introducing Speaker Handles, soft-token representations that expose acoustic speaker identity to a frozen text LLM for cross-session speaker-dependent reasoning. A three-stage curriculum trains a lightweight projector, with fewer than 0.1% of the backbone's parameters, to map speaker embeddings into these handles. Establishing whether the resulting handles truly support cross-session speaker-dependent reasoning is challenging with existing benchmarks because textual cues can partially reveal fact ownership. We therefore present SpeakerBind, a controlled shared-agent benchmark in which overlapping facts across users require correct cross-session speaker attribution. Speaker Handles achieve 97.40-98.36% accuracy on VoxCeleb1 and 70.40% on SpeakerBind, close to the 71.88% topline. These results show that the proposed Speaker Handles provide an efficient way to integrate acoustic speaker identity into frozen text LLMs for speaker-content reasoning.
https://arxiv.org/abs/2609.38501
This paper presents an explainable approach to pedestrian routing, in which perceived safety is estimated from street-level imagery through an explicit natural-language intermediate representation. A vision--language model caption is generated and stored before any scoring is undertaken, and the perceived-risk class is derived entirely from structured features of that stored text, so that every segment score remains inspectable by the user. Nine captioning conditions across five model families are benchmarked against a direct Contrastive Language--Image Pre-training (CLIP) image-embedding baseline under an identical downstream pipeline, and the caption-mediated representation is found to reach parity with the image embedding rather than to trail it. The approach was deployed over 654,115 images covering 36 electoral wards in two locations in Northern England (Manchester and Huddersfield). Independent field validation against 3,669 locally collected ratings of 494 images across 70 participant sessions established agreement that is statistically significant but modest, at $r=0.262$, against a measured noise ceiling of 0.737 imposed by disagreement between raters. A single-use confirmatory test then found that a pipeline 44\% stronger on the supervised benchmark did not produce measurable improvement in the field ($r=0.250$, $p=0.84$), so the benchmark gains did not predict the deployment gains in this case. Routing behaviour varies systematically with journey length. There is negligible change below 1\,km, reaching a median increase of 12.78\% in low-risk route length for a median detour of 2.73\% on journeys of 3 to 6 km.
https://arxiv.org/abs/2609.38479
Retrieval-Augmented Generation (RAG) is now the standard way to ground Large Language Models (LLMs) in external knowledge, yet the design space of retrieval pipelines is large and the trade-offs between variants are not well understood, especially on domain-specific corpora at realistic scale. In this work, we present a controlled comparison of six retrieval strategies for scientific question answering: (i) classic top-k dense retrieval, (ii) LLM-based query rephrasing, (iii) query rephrasing followed by LLM-based reranking, (iv) multi-query fusion via Reciprocal Rank Fusion (RRF), (v) an agentic tool-call pipeline in which the generator decides for itself whether to retrieve, and (vi) late-interaction retrieval with ColBERTv2. All six pipelines share the same generator (Meta-Llama/Llama-3.1-8B-Instruct), prompt, and evaluation protocol; the five single-vector pipelines additionally share SPECTER2 embeddings and a Chroma vector store; and all six retrieve from the full corpus of 463,971 arXiv papers dated 2024-2025. To support reproducible, large-scale evaluation, we also release a synthetic question dataset of 19,484 problem-statement and methodology questions generated by Llama-3.1-8B-Instruct from a random sample of 10,000 papers across academic domains (query generation succeeded for 9,742 of them), and every strategy is evaluated on this same query set. We describe the architecture and implementation of each pipeline, release the code and the synthetic question dataset, and evaluate each strategy with an LLM-as-a-judge protocol along multiple quality dimensions, together with direct gold-paper retrieval metrics. The result is an open testbed for studying the cost and quality trade-offs of RAG design choices on a research-literature corpus, and a basis for future work on faithfulness, retrieval robustness, and agentic retrieval.
https://arxiv.org/abs/2609.38473
The development of Financial Natural Language Processing (NLP) systems for Brazilian Portuguese is hindered by the scarcity of domain-specific datasets. To address this, we present a large-scale corpus of approximately 160,000 Brazilian Portuguese financial news articles collected from web sources. To establish initial benchmarks for a weakly supervised multi-class classification approach based on semantic similarity, we annotated subsets of this corpus both manually and using a Large Language Model (LLM). We evaluated three similarity-based methods -- cosine similarity, K-Nearest Neighbors (KNN), and FAISS-based nearest-neighbor search -- using multilingual semantic embeddings. Our experiments reveal that the task is highly sensitive to label quality and class distribution. On the manually labeled subset, KNN achieved the best performance (47.3% accuracy, 31.9% F1-score), closely followed by FAISS. Conversely, on the LLM-annotated subset, while accuracy reached approximately 50%, F1-scores dropped to near 20%, highlighting the negative impact of label imbalance and noisy weak annotations. These findings establish foundational baselines for a challenging task, underscoring the critical need for high-quality manual annotations. Ultimately, this dataset and our preliminary results provide a reference point for future research in Brazilian Portuguese Financial NLP.
https://arxiv.org/abs/2610.20630
Random exploration reveals how an environment can be traversed before a goal is specified. Can this experience support long-range planning without policy-improvement training? Our random-walk analysis explains what temporal relations contain: short horizons reveal geodesic geometry in the diffusion limit, while longer horizons reveal connectivity between regions before mixing removes these distinctions. We learn these relations with a conditional energy-based model that estimates temporal log-density ratios through horizon-conditioned embeddings. The model is trained on observation pairs by noise-contrastive estimation, without action or reward labels. The planner queries these learned relations at different horizons as it moves toward the goal. At test time, a separate local dynamics model predicts candidate action outcomes, and the temporal model evaluates their progress toward the goal by selecting or aggregating estimated improvements across horizons. The agent executes one action and replans with both models fixed. Experiments demonstrate long-range maze planning from random exploration using states and images. Learned score fields, embedding probes, and planned routes exhibit properties of a multiscale cognitive map. We further demonstrate egocentric navigation from random exploration and manipulation planning from suboptimal data.
https://arxiv.org/abs/2609.38383
AI-enabled Cyber-Physical Systems (CPS) are highly vulnerable to adversarial and anomalous inputs, where small perturbations can induce cascading errors and unsafe control actions. Existing approaches, such as rule-based filtering, training-time regularization, or diffusion-based reconstruction, either operate outside the model or lack mechanisms to incorporate formal security specifications into the prediction process. In this paper, we take the first step toward embedding security properties directly into AI-enabled CPS, enabling predictive models to enforce system-level constraints during inference rather than relying on external defenses. We introduce a logic-conditioned bi-stage diffusion framework that integrates Signal Temporal Logic (STL) specifications into forecasting. STL serves as a first-class conditioning signal that guides both an input repair stage and an output refinement stage, allowing the model to jointly mitigate adversarial perturbations and enforce desired temporal behaviors to satisfy security-critical properties. We evaluate our approach on two real-world multivariate CPS forecasting datasets under a diverse set of physical sensor and cyber attacks. Across sensor faults, gradient-based attacks, adaptive attacks, and varying attack strengths, our method consistently improves robustness and specification compliance, degrades more gracefully as attack strength increases, and generalizes better to unseen attacks. Ablation studies on specification coverage and quality further show that embedding logical security properties yields gains unattainable by reconstruction-based methods alone, highlighting a new direction for integrating formal methods with generative models in secure CPS.
https://arxiv.org/abs/2609.38381
Representing scientific papers as points in a space lets us search for similar papers and inquire about how fields relate to one another and drive innovation. Beyond search, the vector space of papers invites generation: mixing papers through simple vector operations creates new points, mirroring combinatorial novelty, the recombination of existing ideas into new ones. However, a mixed point often represents an idea no paper has yet realized, with no papers nearby to identify the idea. We propose representing each paper by a LoRA adapter generated by the Doc-to-LoRA hypernetwork. Every point in the space, including mixtures, thus represents a large language model (LLM) open to questions and instructions in natural language. On papers from the American Physical Society (APS), we instruct the LLM at the average of each subfield to name the field in a few words and obtain labels closer to the official names than the labels of five baselines, as judged by word overlap and a panel of five LLM judges. We also ask the LLMs at points between two APS papers to write an abstract and obtain descriptions shifting from one paper to the other in step with the mixing weight. While Doc-to-LoRA is trained for generation, a small invertible transform makes the embeddings competitive for search, on par with SPECTER2 and EmbeddingGemma and close to SBERT. Because the transform is invertible, every point in the transformed space still maps back to an LLM. The embeddings thus serve both search and generation, enabling researchers to question the idea at any point in the space as a starting point for generating new ideas.
https://arxiv.org/abs/2609.38374
Quantifying collective fish behavior requires accurate trajectories, yet multi-view 3D tracking remains challenging due to frequent occlusions, visually similar individuals, and the long-standing scarcity of identity annotations. We present TrackFish3D, a geometry-driven self-supervised framework for dense multi-camera 3D tracking of schooling fish. Instead of relying on appearance-based re-identification or manually annotated identities, TrackFish3D turns calibrated multi-view geometry into supervision: triangulation and reprojection consistency provide pseudo-associations, while a geometric encoder and global association transformer learn all-to-all cross-view correspondence within each frame. To make these associations identity-aware, TrackFish3D introduces a self-supervised contrastive objective that separates co-visible individuals in the embedding space, together with a temporal predictor that preserves identities and bridges short occlusions across frames. The resulting model is trained once on unlabeled footage and applied directly to unseen test videos, requiring no cross-view identity labels, temporal annotations, 3D ground truth, appearance features, or test-time optimization. On our benchmark, TrackFish3D improves 3D Multi-Object Tracking Accuracy from 87.7% for the strongest baseline to 95.8%. On the 3D-ZeF zebrafish benchmark, it achieves 81.1% MOTA, compared with 77.4% for the best geometric baseline. TrackFish3D also generalizes beyond fish, achieving strong results on real-world bird tracking.
https://arxiv.org/abs/2609.38347
Continuous diffusion generates complete reasoning solutions through iterative refinement in latent space. We introduce the Continuous Embedding Diffusion Reasoner (CEDR), an ELF-based training and inference recipe. Our experiments show that accurate decoding alone does not ensure strong reasoning performance. We therefore learn compact representations from multiple layers of a strong autoregressive teacher. Their decomposition also enables asynchronous denoising at different rates. We show that prompt encodings need only preserve the information required for the correct text-conditional score, rather than exactly match teacher features, and use a staged curriculum to learn a compact prompt encoder that replaces the teacher Transformer at inference. We adapt DiffusionNFT to learned self-conditioning guidance and incorporate gold-solution endpoints to supplement sparse rewards. Our supervised models outperform reported results from recent continuous-diffusion baselines at comparable backbone scales on mathematical reasoning and HumanEval code generation. With a 638M-parameter denoising backbone and learned prompt conditioning, post-NFT CEDR-L achieves 63.74% pass@1 on GSM8K and 24.6% on MATH500 at 64 denoising steps, and 32.85% on HumanEval and 30.18% on HumanEval+ at 128 denoising steps. Code will be available at: this https URL.
https://arxiv.org/abs/2609.35694
Turning decoder-only large language models (LLMs) into strong dense retrievers typically requires some form of retriever training. In this paper, we ask whether LLMs can instead be prompted to produce effective representations for dense retrieval given only a few in-context examples. To answer this, we introduce RICE (Representations from In-Context Examples), a simple "training-free" approach that extracts high-quality dense representations from LLMs. To do so, RICE conditions the LLM on examples that provide a shared context for query and document encoding. Our results demonstrate that RICE embeddings can substantially improve the accuracy of prompt-based LLM embeddings, establishing it as a simple method to build LLM-based dense retrievers that do not require training. We release our code at this https URL.
https://arxiv.org/abs/2609.38099
Interactive panoramic video generation aims to synthesize immersive 360\textdegree{} videos that remain visually coherent while following user-specified camera trajectories during exploration. However, progress is limited by a coupled data-and-model gap: existing panoramic video datasets are often short, weakly annotated, or lack camera trajectories, while existing camera-controlled video generation models are designed for perspective videos and do not directly support panoramic geometry. In this paper, we introduce MUGEN and Wan360 to address these limitations. MUGEN is a large-scale real-world panoramic video dataset tailored to interactive 360-degree world exploration, comprising over 1,300 hours of at least 4K panoramic videos with rich semantic and geometric annotations. Built on MUGEN, we further present Wan360, a camera-controllable interactive panoramic video generation model. Panoramic videos are commonly represented by EquiRectangular Projection (ERP), which unfolds a spherical 360-degree view into a rectangular frame with cyclic longitude seams and pole distortions. To this end, Wan360 introduces three parameter-free ERP-aware components: periodic longitude RoPE for seam-consistent positional encoding, ERP-aware padding for reducing boundary artifacts, and random roll yaw for consistent learning. For camera control, Wan360 uses a panoramic Plücker embedding that represents camera motion with ERP rays rather than perspective pinhole rays. Experiments show that MUGEN serves as a data foundation for panoramic world exploration, and that Wan360 enables high-quality, temporally coherent, camera-controllable 360-degree video generation.
https://arxiv.org/abs/2609.38077
Physics-Informed Neural Networks (PINNs) embed governing equations into deep learning, but enforce them only through loss residuals, leaving highly oscillatory wave behavior to be discovered by optimization. As a result, methods that achieve relative $L_2$ errors below $10^{-3}$ on standard manufactured Helmholtz benchmarks can fail on practical radiation problems involving singular excitations, absorbing boundaries, and wave fields spanning tens of wavelengths. Architectural physics embedding addresses this limitation by factorizing the field into analytically derived oscillatory kernels and learnable envelopes. However, the kernel dictionary must be manually constructed and scales with the number of elementary units, growing exponentially with the depth of hierarchically structured systems such as antenna arrays and metasurfaces. We propose PE-EK-PINN (Physics Embedded with Evolving Kernels), which treats physics kernels as reusable learned representations rather than fixed analytical inputs. A converged subsystem field is frozen and promoted to an evolved kernel, whose transformed copies are reused to represent higher-level configurations without deriving new governing equations. The resulting hierarchy makes the peak number of active kernels independent of system size and reduces cumulative training cost from $O(N)$ to $O(\log N)$. Experiments on dipole arrays, composite line-source geometries, and cross arrays demonstrate the dramatic training cost reduction, while achieving a reduced or comparable relative $L_2$ error. One notable example is PE-EK-PINN solves a $256$-dipole array more than 30 times faster than direct PE-PINN.
https://arxiv.org/abs/2609.38023
Class-Incremental Learning (CIL) requires models to recognize new classes over time without forgetting previously learned ones. With the rise of vision-language pre-training, CLIP has become a strong foundation for CIL. A common design in CLIP-based CIL is to construct textual classifier weights by encoding class-name templates with the CLIP text encoder, and then classify visual features by image-text cosine similarity. This design is appealing: since CLIP aligns images and text in a shared embedding space, textual weights appear to provide an off-the-shelf classifier for incremental classes. However, we show that this seemingly natural design is not always beneficial, as a modality gap can still separate the two modalities and make textual classifier weights deviate from visual class distributions. Empirically, under identical task-wise CIL training, initializing the cosine classifier with visual class centers yields lower loss and better incremental accuracy than using CLIP textual this http URL by these observations, we propose VIS, a visual-only method for CLIP-based CIL that removes the deployed textual branch and constructs the incremental classifier entirely in the visual space. To obtain stronger task-adaptive visual representations, VISuses only base-session data to enhance CLIP's final visual representation with informative visual-layer features. Built on the enhanced visual representation, VISemploys a simple kernelized incremental least-squares SVM, whose classifier weights are solved in closed form from additive sufficient statistics. When new classes arrive, VISaccumulates their sufficient statistics and recomputes the classifier weights for all seen classes, enabling efficient incremental updates while preserving historical class knowledge. Extensive experiments show that VISachieves state-of-the-art performance without a textual branch.
https://arxiv.org/abs/2609.37888
Geometric representation learning predominantly scaffolds representations onto flat Euclidean subspaces or compact product tori ($\mathbb{T}^K$). However, flat manifolds possess vanishing curvature and polynomial volume growth, inherently suffering from metric distortion when embedding multi-scale, tree-like visual hierarchies. While hyperbolic spaces ($\mathbb{H}^m$) circumvent this via constant negative curvature ($K<0$) and exponential volume expansion, prior hyperbolic deep architectures are hindered by computationally cumbersome Riemannian optimization, non-linear gyrovector calculus, and floating-point instabilities. In this work, we introduce \textbf{Minkowski Attractor Networks (MAN)}, an operator-splitting-inspired framework that embeds representations within pseudo-Riemannian Minkowski spacetime ($\mathbb{R}^{1,m}$). By framing hyperbolic manifolds as quadric level sets, MAN resolves hyperbolic geometry by combining linear Lorentz group transport with non-linear cone lifting and closed-form radial rescaling, evaluating in a single forward pass without numerical ODE solvers or iterative retractions. We establish \textbf{MAN-2D} ($\mathbb{R}^{1,1} \to \mathbb{H}^1$) as our primary, high-throughput visual backbone, which maximizes channel factorization granularity into $D/2$ independent two-dimensional Minkowski blocks. We further formulate \textbf{MAN-4D} ($\mathbb{R}^{1,3} \to \mathbb{H}^3$) as a spacetime extension, leveraging a commuting Cartan-subalgebra parameterization of $\mathrm{SO}^+(1,3)$ to evaluate 4D Lorentz isometries via two commuting 2D planar maps without matrix-exponential overhead.
https://arxiv.org/abs/2609.37817
Inpainting 3D Gaussian Splatting scenes, a key challenge in 3D editing, requires generating plausible content within a masked region of 3D space. Prior approaches rely on 2D diffusion models to produce one or several inpainted reference views, making them susceptible to challenges associated with multi-view inconsistency and lengthy optimization times. Departing from these approaches, we introduce a reference-free Gaussian splatting inpainting method operating natively in 3D. Our method leverages the embedding space of a large, pre-trained 3D prior, combined with a structure completion network to feed a generative prior which reconstructs the missing region's geometry and appearance. Performing content generation entirely in 3D, it avoids the need to reconcile inconsistencies of multiple inpainted reference images, and is faster than related 2D-based methods. We demonstrate the effectiveness of our method qualitatively and quantitatively, through extensive experiments and a user study. To the best of our knowledge, this work is the first Gaussian splatting inpainting method to operate in the learned representation space of a 3D-native generative prior without relying on inpainted reference views.
https://arxiv.org/abs/2609.37816
Satellite observations, precomputed embeddings, and map products describe the same evolving Earth, yet are stored as independent, petabyte-scale data products. Their continued growth calls for compact representations of multiple products while preserving spatial and temporal detail. We introduce Planetary Feature Fields (PFFs), which exploit redundancy across data products by modeling them jointly as continuous functions of space and time at planetary scale. PFFs are spatially local explicit-implicit (hybrid) neural fields. Each field shares a factored feature volume---a decomposition of an explicit 3D grid with smaller factors---across products, while lightweight implicit decoders reconstruct individual products across multiple timesteps. PFFs reconstruct EO products over space and time more accurately than single-product fields at matched compression rates. At $1800\times$ compression relative to the uncompressed source data, reconstructed features retain approximately $90\%$ or more of the performance achieved with the original features on pixel-level segmentation, change detection, and patch-level classification tasks. PFFs can add new timesteps by extending their factored feature volumes and add new products by attaching new decoders, while leaving existing outputs unchanged. PFFs reduce end-to-end feature access latency by an order of magnitude relative to evaluated API and cloud-storage pipelines.
https://arxiv.org/abs/2609.37784
Large language models (LLMs) have shown strong potential as training-free text encoders for long-context embeddings. Existing approaches primarily improve information flow under causal attention and typically construct embeddings by uniformly averaging all token representations. However, for long documents, such mean pooling can dilute salient semantic information with abundant redundant or weakly informative content. To this end, we propose SCSP, a training-free framework that leverages semantic compression for informative token selection in long-context embedding. Specifically, SCSP first partitions a document into sentence-aware chunks and appends a semantic compression prompt to each chunk. A prompt-isolated attention mask preserves information flow among document tokens while restricting each prompt to its corresponding local context. We then use the attention patterns elicited by these prompts to estimate token importance, select informative tokens, and aggregate their intermediate-layer representations into the final embedding. Extensive experiments on long-context embedding benchmarks demonstrate that SCSP can be integrated into both zero-shot and fine-tuned models in a plug-and-play manner, consistently improving their performance.
https://arxiv.org/abs/2609.37782
Seizure detection and prediction from EEG are clinically important but challenging because seizures are rare, temporally localized, and propagate as coordinated events across multiple channels. Recent dynamic graph neural networks model this by running a temporal model over a sequence of per-time-step pairwise channel edges. However, this pairwise construction misses the spatiotemporal coupling that constitutes a seizure, at substantial training cost. We propose HyBrain, which summarizes spatiotemporal EEG evidence through a small set of soft hyperedges rather than pairwise edges. A per-channel Mamba backbone produces one token per (channel, second), and a spatiotemporal hyperedge block pools these tokens into E_h shared group embeddings through soft memberships and broadcasts them back. The same encoder serves three downstream tasks: window-based detection, one-second point-wise detection, and preictal seizure prediction. On TUSZ and CHB-MIT, HyBrain achieves the best AUROC on every reported setting against ten baselines, with the largest gap on long-clip preictal prediction. It also matches the most efficient baselines in training time and peak GPU memory. A qualitative analysis shows that even a single learned hyperedge cleanly captures the preictal -> ictal -> postictal trajectory on a real seizure clip.
https://arxiv.org/abs/2609.37730