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01.
arXiv (CS.AI) 2026-06-16

SciText2Eq: Assessing LLMs for Explainable Equation Generation for Scientific Creativity

arXiv:2606.16003v1 Announce Type: new Abstract: This work investigates the ability of large language models (LLMs) to generate mathematical equations from scientific texts. Prior work faces challenges in unstructured grounding, multi-equation dependency, and humanaligned evaluation. To this end, we construct a dataset of AI research papers, pairing contextual passages with ground-truth equations and variable descriptions. We develop an explainable equation generation workflow and evaluate it across diverse open- and closed-source LLM backbones. We introduce an evaluation protocol combining automatic metrics, LLM-based rubrics, and human judgments to assess accuracy, explainability, and human-LLM alignment. Results indicate that LLMs perform moderately on lexical- and syntactic-based similarity, while struggling with semantic accuracy. Comparisons between LLM-based evaluations and human judgments reveal limited alignment, highlighting challenges in using LLMs to assess equation quality. These findings offer insights for improving equation generation models and developing more reliable evaluation methods for scientific text. We provide code and data for reproducibility.

02.
arXiv (CS.CV) 2026-06-11

Learning Instance-Adaptive Low-Rank Orthogonal Subspaces for Clothes-Changing Person Re-Identification

Clothes-changing person re-identification (CC-ReID) aims to recognize individuals despite drastic appearance changes caused by clothing variation. While existing methods rely on adversarial learning to disentangle clothing features, we propose Ortho-ReID, which explicitly models a low-rank clothing subspace from VLM text descriptions and extracts clothing-invariant representations via direct geometric constraints. A critical component is our transformer-based Basis Maker, which refines a shared, low-dimensional clothing prior into an instance-adaptive low-rank subspace through cross-attention with image patches, enabling robust clothing feature extraction even under varying visibility conditions. This instance-adaptive subspace is supervised via alignment with clothing text embeddings, while identity features are extracted via a learnable projection head and geometrically constrained to be strictly orthogonal to it. Extensive experiments demonstrate state-of-the-art performance on PRCC (+5.9% top-1), Celeb-reID-light (+3.5%), and LaST (+5.3%), with competitive results on LTCC.

03.
arXiv (CS.CV) 2026-06-12

BSViT: A Burst Spiking Vision Transformer for Expressive and Efficient Visual Representation Learning

Spiking Vision Transformers (S-ViTs) offer a promising framework for energy-efficient visual learning. However, existing designs remain limited by two fundamental issues: the restricted information capacity of binary spike coding and the dense token interactions introduced by global self-attention. To address these challenges, this work proposes BSViT, a burst spiking-driven Vision Transformer featuring a Dual-Channel Burst Spiking Self-Attention (DBSSA) mechanism. DBSSA encodes queries with binary spikes and keys with burst spikes to enhance representational capacity. The value pathway adopts dual excitatory and inhibitory binary channels, enabling signed modulation and richer spike interactions. Importantly, the entire attention operation preserves addition-only computation, ensuring compatibility with energy-efficient neuromorphic hardware. To further reduce spike activity and incorporate spatial priors, a patch adjacency masking strategy is introduced to restrict attention to local neighborhoods, resulting in structure-aware sparsity and reduced computational overhead. In addition, burst spike coding is systematically integrated across the network to increase spike-level representational capacity beyond conventional binary spiking. Extensive experiments on both static and event-based vision benchmarks demonstrate that BSViT consistently outperforms existing spiking Transformers in accuracy while maintaining competitive energy efficiency.

04.
arXiv (CS.CL) 2026-06-16

Your "Pro" LLM Subscription May Actually Be "Free": Exposing Fingerprint Spoofing Risks in LLM Inference Services

As Large Language Model (LLM) APIs become ubiquitous, users increasingly rely on black-box fingerprinting to verify that providers are serving the advertised premium models. However, these methods may overlook adversarial providers who manipulate model weights to cheat the fingerprint process. We introduce a novel threat termed fingerprint spoofing, where a malicious provider stealthily serves a weaker model that has been parameter-efficiently fine-tuned to mimic a stronger model, thereby evading user-side fingerprinting. We first formally prove that user-side resource constraints (i.e., finite query budgets and weak fingerprinting classifiers) make current fingerprinting vulnerable to fingerprint spoofing. Guided by this theoretical analysis, we propose GhostPrint, a cost-effective attack framework leveraging surrogate modeling, reward-ranked fine-tuning, and knowledge distillation. Extensive evaluations in both static and continual fingerprinting settings demonstrate that GhostPrint allows weak models to consistently bypass representative fingerprint methods while maintaining utility at a low fine-tuning cost, exposing a critical vulnerability in current LLM fingerprinting pipelines.

05.
arXiv (CS.LG) 2026-06-16

Efficient Reinforcement Learning by Guiding World Models with Non-Curated Data

arXiv:2502.19544v3 Announce Type: replace Abstract: Leveraging offline data is a promising way to improve the sample efficiency of online reinforcement learning (RL). This paper expands the pool of usable data for offline-to-online RL by leveraging abundant non-curated data that is reward-free, of mixed quality, and collected across multiple embodiments. Although learning a world model appears promising for utilizing such data, we find that naive fine-tuning fails to accelerate RL training on many tasks. Through careful investigation, we attribute this failure to the distributional shift between offline and online data during fine-tuning. To address this issue and effectively use the offline data, we propose two techniques: i) experience rehearsal and ii) execution guidance. With these modifications, the non-curated offline data substantially improves RL's sample efficiency. Under limited sample budgets, our method achieves nearly twice the aggregate score of learning-from-scratch baselines across 72 visuomotor tasks spanning 6 embodiments. On challenging tasks such as locomotion and robotic manipulation, it outperforms prior methods that utilize offline data by a decent margin.

06.
arXiv (CS.CL) 2026-06-18

Notation Matters: A Benchmark Study of Token-Optimized Formats in Agentic AI Systems

Large language models in Agentic AI systems consume tool schemas and execution results and emit tool invocations as structured data. The default language for that exchange, JSON, was designed for application-to-application interchange rather than token efficiency, so its structural elements impose substantial token overhead. Recent work proposes token-optimized alternatives such as TOON (Token-Oriented Object Notation) and TRON (Token Reduced Object Notation) as more compact replacements, but these formats have been evaluated only on isolated comprehension or generation tasks. Whether their token reductions hold inside end-to-end agentic loops therefore remains an open question. We evaluate TOON and TRON on four agentic benchmarks (BFCL, MCPToolBenchPP, MCP-Universe, StableToolBench) and five open-weight LLMs, decoupling input compression from output compression to measure comprehension and generation independently. TRON reduces tokens by up to 27% with accuracy within 14pp of the JSON baseline. TOON achieves up to 18% reduction at a similar 9pp accuracy cost, but additionally cascades on multi-turn parsing failures and collapses parallel tool-call output for most models. The code is available at: https://github.com/lkutschka/notation-matters

07.
arXiv (CS.CV) 2026-06-19

Abstraction in Style: Beyond Texture and Color

Artistic styles often embed abstraction beyond surface appearance, involving deliberate reinterpretation of structure rather than mere changes in texture or color. Conventional style transfer methods typically preserve the input geometry and therefore struggle to capture this deeper abstraction behavior, especially for illustrative and nonphotorealistic styles. In this work, we introduce Abstraction in Style (AiS), a generative framework that separates structural abstraction from visual stylization. Given a target image and a small set of style exemplars, AiS first derives an intermediate abstraction proxy that reinterprets the target's structure in accordance with the abstraction logic exhibited by the style. The proxy captures semantic structure while relaxing geometric fidelity, enabling subsequent stylization to operate on an abstracted representation rather than the original image. In a second stage, the abstraction proxy is rendered to produce the final stylized output, preserving visual coherence with the reference style. Both stages are implemented using a shared image space analogy, enabling transformations to be learned from visual exemplars without explicit geometric supervision. By decoupling abstraction from appearance and treating abstraction as an explicit, transferable process, AiS supports a wider range of stylistic transformations, improves controllability, and enables more expressive stylization.

08.
arXiv (CS.CL) 2026-06-19

LaViSA: A Language and Vision Structural Ambiguity Benchmark

Structural ambiguity arises when a single sentence admits multiple valid interpretations due to its syntactic structure, posing a fundamental challenge for language understanding. Visual scenes serve as useful cues for resolving such ambiguity, and Vision and Language Models (VLMs) need to be capable of deriving possible semantic interpretations from visual scenes. We introduce Language and Vision Structural Ambiguity (LaViSA), a benchmark designed to evaluate the ability of VLMs to resolve structural ambiguity leveraging visual scenes. LaViSA consists of ambiguous sentences, their disambiguated sentences, and corresponding images of these disambiguated sentences across seven ambiguity categories. Using LaViSA, we conduct a comprehensive evaluation of diverse VLMs, including both proprietary and open-source models with varying parameter scales and reasoning capabilities. Experimental results show that although recent VLMs can leverage visual scenes to resolve structural ambiguity to a some extent, they still struggle with certain ambiguity types and visually subtle semantic distinctions, indicating remaining limitations in resolving structural ambiguity using visual scenes.

09.
arXiv (CS.AI) 2026-06-12

PI-Hunter: Automated Red-Teaming for Exposing and Localizing Prompt Injections

arXiv:2606.12737v1 Announce Type: cross Abstract: Large Language Models (LLMs) are rapidly evolving into agentic systems that interact with external tools and environments, introducing new security risks such as indirect prompt injection attacks through untrusted external sources. Existing defenses mainly focus on blocking malicious content at inference time, and current red-teaming methods primarily optimize attack success. As a result, developers have limited visibility into how latent prompt injections emerge and propagate through agents. We propose PI-Hunter, an automated agentic auditing framework for proactive vulnerability exposure in LLM agents. PI-Hunter constructs realistic source-aware test cases and iteratively evolves them through feedback-driven exploration to induce agents to retrieve and reveal latent malicious instructions embedded within external environments. Extensive experiments across multiple benchmarks, agent architectures, attacks, and defenses demonstrate that PI-Hunter substantially improves vulnerability exposure and attack-surface coverage over strong automated red-teaming baselines, while remaining effective under existing prompt injection defenses.

10.
arXiv (math.PR) 2026-06-11

The Statistical Compass

arXiv:2606.11282v1 Announce Type: cross Abstract: This monograph develops probability and stochastic-process ideas as a translation language for statistics: from designed observations and data objects to targets, stability statements, inference, and use. The chapters move from motivating examples and randomization through probability measures, kernels, likelihoods, data objects, weak convergence, empirical fields, functional data, M- and Z-estimation, testing, local approximations, event-time processes, and prediction. Historical and biomedical examples are used to keep abstract objects tied to records, mechanisms, and decisions. The aim is to give readers a common grammar for classical probability, modern data structures, and statistical practice.

11.
arXiv (CS.CL) 2026-06-16

Can LLM Coding Agents Reason About Time Series?

Large language models (LLMs) are increasingly being used for automated decision-making systems in finance, healthcare, or environmental monitoring. Time series data are ubiquitous in these fields, yet hard to process automatically. Can time series be analyzed by LLM agents? We examine three approaches: providing the agent with raw numerical data, using the LLM as a coding agent, or a combination of both. In the coding agent setup, the model iteratively queries the data using Python code. Using two time series understanding benchmarks, we show that agents with code access can outperform models processing raw data by up to 10%. However, even the best performing agent still answers about 22-34% of the questions incorrectly. To get insights into models' strategies and reasoning gaps, we analyze the model outputs with a strong LLM judge. Our analysis reveals that coding agents can select appropriate statistical tests, but often miss important nuances. Meanwhile, models with access to raw data can reach the right conclusions using back-of-the-envelope calculations.

12.
arXiv (CS.AI) 2026-06-11

Automating Geometry-Intensive Compliance Checking in BIM: Graph-Based Semantic Reasoning Framework

arXiv:2606.12065v1 Announce Type: new Abstract: Automating compliance check for geometry-intensive regulations remains a significant technical bottleneck in Building Information Modeling (BIM), primarily due to the semantic disparity between high-level regulatory logic and structured IFC data. Existing methods, often reliant on static rule templates, struggle to traverse multi-hop reasoning chains or resolve latent spatial dependencies across multiple building entities. To address these challenges, a Spatial-Geometric Reasoning System for Building Information Modeling (SGR-BIM) is proposed as an integrative graph-driven reasoning framework. SGR-BIM dynamically constructs a cross-modal knowledge graph that aligns user intent, regulatory semantics, and BIM geometry, enabling interpretable reasoning without rigid hard-coding. Validated on 679 expert-verified queries from fire safety codes, the framework achieves 84.3% accuracy, representing an 8.6% improvement over enhanced-tool single-agent baselines. This research provides a graph-based semantic reasoning paradigm, enhancing the transparency and flexibility of automated geometric compliance check workflows in the Architecture, Engineering, and Construction (AEC) industry.

13.
arXiv (CS.CV) 2026-06-19

Gaussian Process Prior Variational Autoencoder for Endoscopic Videos

Endoscopic video analysis is essential for gastrointestinal diagnosis and computer-assisted interventions, but video sequences are routinely degraded by specular reflections, motion artifacts, and missing frames. These transient corruptions can distract clinicians, reduce image interpretability, and disrupt downstream tasks such as 3D reconstruction and navigation. Effective restoration therefore requires methods that exploit temporal continuity rather than treating frames in isolation. We introduce a Gaussian Process Prior Variational Autoencoder (GPVAE) framework for endoscopic video restoration that replaces the standard factorized latent prior with a temporal Gaussian process prior, enabling interpolation of missing frames with uncertainty-aware reconstruction. The framework combines endoscopy-specific encoders, including a convolutional EndoVAE backbone and pretrained Vision Transformer encoders from GastroNet-5M, with two scalable GP approximations: Hierarchical Prior Approximation (HPA) and Sparse Precision Approximation (SPA). Specular reflections are handled using a DUCKNet-based masking pipeline that excludes corrupted pixels from the reconstruction objective. On the C3VDv2 colonoscopy dataset, the best GPVAE variants reduced image reconstruction RMSE by 21.9\% on average, and by up to 26.1\%, relative to matched VAE baselines. Downstream trajectory RMSE was reduced by 12.7\% on average across classical visual odometry and a pretrained PoseNet, at an average increase of 27.3\% in training time per epoch. Finally, the GP posterior provides per-frame uncertainty estimates that reflect temporal support and offer a confidence signal for restored frames.

14.
arXiv (CS.CV) 2026-06-16

Region-Adaptive Sampling for Diffusion Transformers

Diffusion models (DMs) have become the leading choice for generative tasks across diverse domains. However, their reliance on multiple sequential forward passes significantly limits real-time performance. Previous acceleration methods have primarily focused on reducing the number of sampling steps or reusing intermediate results, failing to leverage variations across spatial regions within the image due to the constraints of convolutional U-Net structures. By harnessing the flexibility of Diffusion Transformers (DiTs) in handling variable number of tokens, we introduce RAS, a novel, training-free sampling strategy that dynamically assigns different sampling ratios to regions within an image based on the focus of the DiT model. Our key observation is that during each sampling step, the model concentrates on semantically meaningful regions, and these areas of focus exhibit strong continuity across consecutive steps. Leveraging this insight, RAS updates only the regions currently in focus, while other regions are updated using cached noise from the previous step. The model's focus is determined based on the output from the preceding step, capitalizing on the temporal consistency we observed. We evaluate RAS on Stable Diffusion 3 and Lumina-Next-T2I, achieving speedups up to 2.36x and 2.51x, respectively, with minimal degradation in generation quality. Additionally, a user study reveals that RAS delivers comparable qualities under human evaluation while achieving a 1.6x speedup. Our approach makes a significant step towards more efficient diffusion transformers, enhancing their potential for real-time applications.

15.
bioRxiv (Bioinfo) 2026-06-22

Few-Shot Classification of C. elegans Developmental Stages via Explainable Hierarchical Hyperbolic Graph Embeddings

Automated, accurate, and fast developmental-stage classification of C. elegans from microscopy-based morphological images is essential for aging research, drug screening, and disease modeling. However, it remains challenging due to morphological similarities between stages and the limited annotated data. In this work, we propose HyperDev, a hyperbolic few-shot learning framework that addresses these limitations by directly encoding developmental hierarchies in the embedding space, unlike conventional Euclidean approaches that treat stages as independent classes. HyperDev uses Poincare ball geometry, combined with a biologically informed developmental prior, to naturally represent stage relationships. We introduce our selfcurated C. elegans dataset spanning seven developmental stages (Egg, L1-L4, Adult, Dauer) with extreme class imbalance (6-8 samples per minority class). HyperDev achieves competitive classification accuracy (76.9-88.3%) while providing intrinsic explainability across nine 7-way few-shot evaluation settings. The learned embeddings exhibited strong biological alignment (Pearson r = 0.669, p < 0.001), while significantly outperforming ProtoNet (r = 0.187), MatchingNet (r = 0.235), and RelationNet (r = 0.464). These results establish hyperbolic geometry as a principled approach to explainable few-shot learning in biological imaging, where understanding learned representations is as critical as predictive performance. Clinical Relevance–By enabling explainable, data-efficient developmental staging from scarce samples, HyperDev supports improved phenotype quantification for aging research, disease modeling, and drug screening. Index Terms–Hyperbolic learning, few-shot classification, developmental staging, Caenorhabditis elegans, interpretability, explainability.

16.
arXiv (CS.LG) 2026-06-19

Low-Energy Reduced RISC-V Instruction Subset Processor for Tsetlin Machine Inference at the Edge

arXiv:2606.19964v1 Announce Type: new Abstract: Tsetlin Machine (TM) is a logic-based machine learning approach that relies on simple bitwise operations and finite-state automata, which makes it attractive for edge AI deployments. Recent work has focused on co-processor and accelerator designs based on Tsetlin Machines (TMs). Although these designs achieve high performance, they typically depend on tightly coupled interfaces, microcode-style programming, and external host processors, limiting flexibility and ease of programming. In this work, we present a domain-specific RISC-V microprocessor architecture and design flow tailored for TM inference. Leveraging the modular structure of RISC-V, we design a reduced instruction subset processor that retains programmability while targeting improved performance and lower energy consumption for TM workloads. Instruction profiling is employed to guide instruction reduction, followed by datapath and control path simplifications tailored to TM inference. Both the baseline RV32IM core and the proposed reduced core are evaluated across multiple datasets and compared with Binarized Neural Networks (BNNs), which serve as a hardware-efficient baseline due to their reliance on bitwise operations during inference. Results show that TM achieves comparable or higher accuracy (e.g., up to 88.18% on CIFAR-2 compared to 60.0% for BNN) while reducing execution time by up to 98% across multiple datasets. Furthermore, the proposed design achieves an average $29.7\times$ reduction in energy consumption, demonstrating its effectiveness for programmable and efficient edge AI systems.

17.
arXiv (CS.AI) 2026-06-12

Decoding the Multimodal Maze: A Systematic Review on the Adoption of Explainability in Multimodal Attention-based Models

arXiv:2508.04427v2 Announce Type: replace-cross Abstract: Multimodal learning has witnessed remarkable advancements in recent years, particularly with the integration of attention-based models, leading to significant performance gains across a variety of tasks. Parallel to this progress, the demand for explainable artificial intelligence (XAI) has spurred a growing body of research aimed at interpreting the complex decision-making processes of these models. This systematic literature review analyzes research published between January 2020 and early 2024 that focuses on the explainability of multimodal models. Framed within the broader goals of XAI, we examine the literature across multiple dimensions, including model architecture, modalities involved, explanation algorithms and evaluation methodologies. Our analysis reveals that most studies are concentrated on vision-language and language-only models, with attention-based techniques being the most commonly employed for explanation. However, these methods often fall short in capturing the full spectrum of interactions between modalities, a challenge further compounded by the architectural heterogeneity across domains. Importantly, we find that evaluation methods for XAI in multimodal settings are largely non-systematic, lacking consistency, robustness, and consideration for modality-specific cognitive and contextual factors. To address these gaps, we not only synthesize findings from the surveyed works but also incorporate a complementary analysis that integrates recent and emerging advances driving multimodal explainability. Based on these insights, we provide a comprehensive set of recommendations aimed at promoting rigorous, transparent, and standardized evaluation and reporting practices in multimodal XAI research. Our goal is to support future research in more interpretable, accountable, and responsible multimodal AI systems, with explainability at their core.

18.
arXiv (CS.AI) 2026-06-12

Pythagoras-Prover: Advancing Efficient Formal Proving via Augmented Lean Formalisation

arXiv:2606.12594v1 Announce Type: new Abstract: Modern Lean theorem provers achieve strong performance only with substantial training and inference compute, driven in part by scarce verified proof data and the long reasoning traces of formal proof search, making both supervised fine-tuning (SFT) and sampling expensive. We introduce Pythagoras-Prover, a compute-efficient open-source family of Lean theorem provers built for practical compute budgets. The family spans two generation paradigms: autoregressive models at 4B and 32B parameters, and a first proof-of-concept diffusion-based prover (4B) that iteratively refines Lean proofs at inference time. For training efficiency, we build a Lean-verified corpus stratified into easy, medium, and hard problems for curriculum SFT, so models acquire proof skills progressively from shorter, simpler proofs to longer, harder ones. During SFT, a dynamic proof-reasoning filtering scheme preserves informative proof traces while keeping each instance within an 8k-token context budget. We also introduce Augmented Lean Formalisation (ALF), which expands scarce verified corpora into variants of formal statements, populated via self-distillation for extra training signal without formally verifying every mutated instance. By perturbing known problems while preserving their formal character, ALF reduces reliance on any statement's surface form. Empirically, Pythagoras-Prover-4B surpasses DeepSeek-Prover-V2-671B at pass@32 on MiniF2F-Test (86.1% vs 82.4%) with ~167x fewer parameters, while Pythagoras-Prover-32B sets the open-source state of the art at 93.0% on MiniF2F-Test and solves 93 of 672 PutnamBench problems. We release MiniF2F-ALF, an ALF-mutated contamination-sensitive benchmark on which every evaluated model loses accuracy; here our 32B remains strongest and our 4B matches the prior state of the art, Goedel-Prover-V2-32B.

19.
arXiv (CS.CL) 2026-06-16

Contrastive-Difference CKA Reveals Concept-Specific Structural Alignment Across Language Model Architectures

作者:

Do different LLM architectures encode high-level concepts in structurally compatible ways? We systematically characterize a geometric-functional universality dissociation: across multiple concept domains and architectural families, moderate geometric convergence coexists with near-perfect functional transfer. Using contrastive-difference CKA (CKA_Delta), a training-free diagnostic that computes kernel alignment on per-sample contrastive differences, we isolate concept-specific convergence from generic similarity – achieving significant discrimination where standard CKA cannot. The dissociation replicates across all six concept domains we test (five with p =70B models. We position CKA_Delta as a practical regime classifier and architectural outlier detector (Gemma: d = 1.08, AUC = 0.79) rather than an absolute transfer-accuracy predictor, providing a training-free diagnostic for cross-architecture concept monitoring.

20.
arXiv (CS.CV) 2026-06-18

Rethinking the Pointer Loss in Table Structure Recognition: Geometry-Aware Pointer Loss for Spatial Locality

Table Structure Recognition (TSR) using a pointer network achieves impressive results by predicting HTML sequences while aligning tags to detected text (or cell) regions. However, our analysis reveals that when pointer networks fail, 79.6% of errors occur between spatially adjacent cells (Manhattan distance

21.
medRxiv (Medicine) 2026-06-22

Paired plasma and EV-enriched plasma proteomics reveal nonredundant sepsis-associated host-response signatures in critical illness

Background: Plasma proteomics may identify host-response signatures in sepsis, but it is unclear whether extracellular vesicle (EV)-enriched plasma provides distinct or redundant information compared with plasma. We compared paired plasma and EV-enriched plasma proteomes in critically ill patients with sepsis and critically ill non-sepsis controls (CINS). Methods: In this prospective observational study, paired plasma and EV-enriched plasma samples were analyzed from 56 critically ill adults, including 40 patients with sepsis and 16 CINS patients. Protein abundance was quantified using liquid chromatography-tandem mass spectrometry. Analyses compared proteomic depth, protein overlap, global concordance between compartments, and differential protein abundance between CINS and sepsis. Exploratory Gene Ontology enrichment was performed as a supplementary analysis. Results: EV-enriched plasma expanded proteomic detection, identifying 2,476 filtered proteins compared with 506 in plasma. Only 386 proteins were detected in both compartments, while 2,090 were unique to EV-enriched plasma and 120 were unique to plasma. Among shared proteins, plasma and EV-enriched plasma showed modest global concordance across critically ill patients (Spearman coeff = 0.322, p = 9.19 x 10^-11), with similar findings in sepsis alone. Differential abundance analysis identified 11 sepsis-associated proteins in plasma and 22 in EV-enriched plasma. Only SAA1, SAA2, and IGFBP6 were significant in both compartments. Exploratory pathway analysis supported acute-phase and inflammatory enrichment in plasma sepsis-associated proteins, while EV-enriched signals were directionally plausible but did not meet prespecified FDR thresholds. Conclusion: Plasma and EV-enriched plasma proteomics capture related but nonredundant sepsis-associated host-response information in critically ill patients.

22.
bioRxiv (Bioinfo) 2026-06-14

Cellfm-datasets: A Unified Data Infrastructure for Single-Cell and Spatial Transcriptomics Foundation Model Pretraining

Large-scale cell foundation models are increasingly limited not only by model architecture, but also by the data infrastructure required to repeatedly sample sparse transcriptomic profiles from out-of-core cohorts. AnnData/H5AD has become a standard exchange format for single-cell and spatial omics analysis, yet its HDF5-backed layout is not designed for high-frequency random mini-batch loading under multi-worker and distributed pretraining. We present Cellfm-datasets, a data infrastructure artifact that converts H5AD cohorts into a self-describing compressed sparse row (CSR) memmap layout and exposes the resulting corpus through Hugging Face Dataset and IterableDataset interfaces. The artifact stores a shared gene vocabulary, per-sample metadata, optional spatial coordinates, observation metadata, manifests, and checksums, and reconstructs sparse cell or group records at runtime without dense expansion. A unified sampling abstraction supports random-cell groups, manifest-defined biological regions, and coordinate-based spatial blocks, with deterministic sharding across distributed ranks and data-loader workers. Spatial demonstrations on P14 mouse brain transcriptomics sections illustrate region- and block-level sampling over real anatomical structures. In controlled benchmarks on a public heterogeneous ModelScope scRNA-seq subset, Cellfm-datasets reached 60,571 +/- 1,734 samples/s in single-core random loading, scaled to approximately 160,000 samples/s with eight workers, and maintained near-constant process-private memory while reading up to one million cells. By moving sparse single-cell and spatial corpora from model-specific loader code into reusable, validated, and framework-native dataset artifacts, this design may reduce the engineering burden of reproducible cell foundation model pretraining and make repeated training runs, model comparisons, and mixed-modality data reuse easier to standardize.

23.
arXiv (CS.AI) 2026-06-12

Transformer Field Theory: A Response-Theoretic Approach to Mechanistic Interpretability

arXiv:2605.25225v2 Announce Type: replace-cross Abstract: Mechanistic interpretability often studies Transformer behavior by intervening on internal activations through activation patching, causal tracing, path patching, and steering directions. This paper develops Transformer Field Theory: a response-theoretic framework in which the residual stream of a fixed forward pass is treated as a Transformer field over layer depth and token position. In this formulation, patching becomes a localized source insertion into the Transformer field, first-order sensitivity fields predict patch effects, Green functions describe downstream propagation, and patch selection is posed as an adjoint inverse problem. Empirically, we test the theory's forward response objects in GPT-2-style autoregressive Transformers. Localized Transformer-field interventions exhibit a bounded local linear regime; first-order sensitivities predict patch effects across layer-token sites; localized sources generate structured anisotropic Transformer-field propagation; high-sensitivity sites and sliced Green operators provide reduced response descriptions; and prompt-induced Transformer-field displacements partially transfer answer behavior. These results establish sensitivities, Transformer-field responses, and sliced Green operators as practical objects for organizing patching experiments, while providing the forward mathematical basis for patch-site inference and cross-scale response transfer.

24.
arXiv (math.PR) 2026-06-16

Risk-averse mean field games: exploitability and non-asymptotic analysis

arXiv:2301.06930v5 Announce Type: replace-cross Abstract: In this paper, we use mean field games (MFGs) to investigate approximations of $N$-player games ($N$pGs) with uniformly symmetrically continuous heterogeneous closed-loop actions. To incorporate agents' risk aversion (beyond the classical expected utility of total costs), we use an abstract evaluation functional for their performance criteria. Centered around the notion of exploitability, we conduct non-asymptotic analysis on the approximation capability of MFGs from the perspective of state-action distributions without requiring the uniqueness of equilibria. Under suitable assumptions, we first show that scenarios in the $N$pGs with large $N$ and small average exploitabilities can be well approximated by approximate solutions of MFGs with relatively small exploitabilities. We then show that $\delta$-mean field equilibria can be used to construct $\varepsilon$-equilibria in $N$pGs. Furthermore, in this general setting, we prove the existence of mean field equilibria. This proof reveals a possible avenue for incorporating penalization for randomized action into MFGs.

25.
arXiv (quant-ph) 2026-06-15

Quantum Simulation of Spin-Dependent Electron Transfer in a Synthetic Chiral Lattice with a Trapped Ion

arXiv:2606.13930v1 Announce Type: new Abstract: Electron transfer through chiral structures can exhibit spin asymmetry, known as the chiral-induced spin selectivity effect, whose microscopic origin remains an open question. While path-interference within the chiral moiety has been proposed as a key mechanism, its experimental validation requires precise and versatile tunability of system parameters. Here we implement a programmable quantum simulation of spin-dependent electron transfer in a donor–chiral-bridge–acceptor model using a trapped ion. The bridge is encoded in internal states of the ion with tunable nearest- and next-nearest-neighbor couplings, while donor and acceptor states are coupled via a spectator bosonic motional mode. We observe spin-dependent interference within the bridge, and further reveal spin-dependence in donor-to-acceptor transfer dynamics, controlled by amplitude and phase of the coupling parameter. Our results identify interference among spin-dependent pathways as a microscopic origin of spin-dependent transfer, and open a route toward quantum simulations of complex chiral lattices with multi-level and bosonic degrees of freedom.