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01.
arXiv (CS.CL) 2026-06-17

HistoRAG: Embedding Historical Methodology in Retrieval-Augmented Generation Through Critical Technical Practice

Retrieval-Augmented Generation (RAG) is the prevailing architecture for grounding language model outputs in external evidence, yet its dominant evaluation paradigms and default configurations remain oriented toward factual question-answering. For interpretive disciplines such as historical studies, RAG embeds assumptions that conflict with scholarly practice. We introduce HistoRAG, a framework that translates historiographical principles into concrete architectural interventions. Separated retrieval and generation decouples source discovery from interpretation, temporal windowing enforces balanced source representation across the research period as a methodological requirement of historical inquiry, and LLM-as-judge evaluation makes relevance judgments transparent and contestable. We evaluate these interventions using SPIEGELragged, applied to 102,189 articles from Der Spiegel (1950-1979). Each intervention addresses a measurable deficiency in standard RAG: era-specific vocabulary retrieves zero chunks from the 1950s when using 1970s terminology, evidence of the temporal skew that motivates windowing; vector similarity and LLM-assessed relevance correlate only weakly (Spearman rho = 0.275), motivating post-retrieval evaluation; and keyword-based and semantic retrieval surface largely disjoint source pools, motivating an architecture in which both operate as complementary retrieval layers under a shared LLM evaluation filter. We also introduce the concept of Zwischentexte (intermediate texts that function as interpretive proposals rather than findings) as a framework for responsible integration of LLM-generated text into scholarly practice. The architecture offers a model for how domain-specific epistemological commitments can be translated into RAG design decisions, and may transfer to other interpretive disciplines working with large corpora.

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

Bridging the Morphology Gap: Adapting VLA Models to Dexterous Manipulation via Intent-Conditioned Fine-Tuning

arXiv:2606.12109v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models have demonstrated remarkable zero-shot generalization in robotic manipulation, yet the vast majority of pre-trained pipelines remain strictly confined to low-DoF parallel grippers. Adapting these rich semantic priors to high-DoF dexterous hands introduces a severe morphology gap, direct end-to-end joint fine-tuning inherently causes catastrophic forgetting of spatial reasoning and acute action manifold collapse due to data scarcity. In this paper, we present InDex, a novel, data-efficient adaptation framework rooted in cross-morphology semantic inheritance. Rather than discarding the pre-trained 1-DoF parallel grasp output, we repurpose it as a continuous, macroscopic virtual grasp intent proxy to sequentialize the control topology. We implement a two-stage decoupled learning architecture: the first stage parameter-efficiently aligns the VLA backbone to predict continuous arm trajectories and the scalar grasp intent; the second stage freezes this spatial backbone and leverages an intent-conditioned denoising diffusion head to decode fine-grained joint articulations for multi-fingered end-effectors. Extensive simulation benchmarks across a suite of multi-stage, contact-rich dexterous manipulation tasks demonstrate that InDex effectively masters intricate skills with minimal demonstration data, substantially outperforming monolithic baselines while preserving the robust spatial generalizability of the original VLA prior.

03.
arXiv (quant-ph) 2026-06-16

Degeneracy Cannot Violate the Quantum Hamming Bound

arXiv:2606.15558v1 Announce Type: new Abstract: The quantum Hamming bound is the standard finite-length sphere-packing bound for exact correction of arbitrary qubit errors. Whether degeneracy can evade this bound has remained unresolved in full generality for nearly three decades: distinct correctable errors may act identically on the code space, so the usual disjoint-sphere argument breaks down. We prove that every exact binary quantum subspace code with $K>1$ obeys the bound, without assuming either nondegeneracy or additivity. Our proof turns the Li–Xing linear-programming polynomial into an exact intersection count for quaternary Hamming balls. Monotonicity in block length and in ball-center separation then reduces the problem to a local node–edge charging inequality at the shortest admissible length. Thus degeneracy can merge correctable error sectors, but cannot enlarge the finite-length binary Hamming bound.

04.
medRxiv (Medicine) 2026-06-11

Corticospinal tract risk modifies motor recovery after minimally invasive surgery for intracerebral hemorrhage: a secondary analysis of MISTIE-III

Objective: Outcome after surgical hematoma evacuation for intracerebral hemorrhage (ICH) depends on hematoma location. As corticospinal tract (CST) integrity affects motor recovery after stroke, we hypothesized that CST integrity drives heterogeneity in surgical outcomes and investigated this in a secondary analysis of MISTIE-III participants. Methods: Risk of CST injury was categorized into four levels, based on the interaction between the CST, the hematoma, and perihematomal edema (PHE) on automatically segmented stability CT: no risk, PHE infiltration, hematoma infiltration, and complete interruption of the CST. Associations with outcome were tested using multivariable linear regression for motor National Institutes of Health Stroke Scale (NIHSS) at day 180 and ordinal regression for modified Rankin Scale (mRS) at day 365, introducing an interaction term between CST risk and treatment group. Results: Day 180 motor NIHSS was significantly lower for 'no risk' ({beta}:-3.77, [95% confidence interval [CI]: -5.8 to -1.70], p=0.0003) and 'PHE infiltration' ({beta}:-2.3, [95%CI: -3.5 to -1.1]; p=0.0002) vs. 'complete interruption'. Surgery was associated with lower Day 180 motor NIHSS in participants with hematoma infiltration ({beta}:-2.07, [95%CI: -3.8 to -0.4], p=0.016). Compared to complete interruption, 'no risk' (adjusted odds ratio [aOR]:0.27, [95%CI: 0.10 to 0.74], p=0.01) and 'PHE infiltration' (aOR:0.41, [95%CI: 0.23 to 0.74]; p=0.003) were associated with lower odds of unfavorable day 365 mRS. Surgery was associated with lower mRS in participants with no risk (aOR:0.23, [95%CI: 0.05 to 0.97, p=0.045). Interpretation: Increasing CST risk is associated with worse motor recovery (day 180) and disability (day 365). CST risk modifies the effect of the MISTIE-III procedure on motor recovery and disability.

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

LIBERO-Occ: Evaluating and Improving Vision-Language-Action Models under Scene-Induced Occlusion via Viewpoint Imagination

Vision-Language-Action (VLA) models achieve strong performance on standard manipulation benchmarks, but most evaluations assume that task-relevant objects are fully visible. This assumption often fails in realistic settings, where occlusion makes manipulation partially observable. In this paper, we study scene-induced occlusion as a fundamental challenge for VLA models and introduce LIBERO-Occ, an occlusion-oriented extension of LIBERO. Experiments show that state-of-the-art VLAs suffer substantial performance degradation under occlusion. To address this issue, we propose Viewpoint Imagination (VIM), which generates a complementary view from an occluded primary observation and conditions action prediction on both observed and imagined evidence. VIM improves robustness across task suites, occlusion types, and severity levels without requiring additional cameras at deployment time, suggesting that viewpoint imagination is an promising mechanism for perception completion in partially observable manipulation. Our benchmark and corresponding code are available at: \href{https://github.com/litsh/Libero-Occ}{https://github.com/litsh/Libero-Occ}.

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

Fast Non-Episodic Finite-Horizon RL with K-Step Lookahead Thresholding

arXiv:2602.00781v2 Announce Type: replace Abstract: Online reinforcement learning in non-episodic, finite-horizon MDPs remains underexplored and is challenged by the need to estimate returns to a fixed terminal time. Existing infinite-horizon methods, which often rely on discounted contraction, do not naturally account for this fixed-horizon structure. We introduce a modified Q-function: rather than targeting the full-horizon, we learn a K-step lookahead Q-function that truncates planning to the next K steps. To further improve sample efficiency, we introduce a thresholding mechanism: actions are selected only when their estimated K-step lookahead value exceeds a time-varying threshold. We provide an efficient tabular learning algorithm for this novel objective, proving it achieves fast finite-sample convergence: it achieves minimax optimal constant regret for $K=1$ and $\mathcal{O}(\max((K-1),C_{K-1})\sqrt{SAT\log(T)})$ regret for any $K \geq 2$. We numerically evaluate the performance of our algorithm under the objective of maximizing reward. Our implementation adaptively increases K over time, balancing lookahead depth against estimation variance. Empirical results demonstrate superior cumulative rewards over state-of-the-art tabular RL methods across synthetic MDPs and RL environments: JumpRiverswim, FrozenLake and AnyTrading. Code is provided on \href{https://github.com/jamie01713/K-Step-Lookahead}{github}.

07.
arXiv (CS.CV) 2026-06-16

MVEB: Massive Video Embedding Benchmark

We introduce the Massive Video Embedding Benchmark (MVEB), a 23-task benchmark for video embeddings spanning classification, zero-shot classification, clustering, pair classification, retrieval, and video-centric question answering. We evaluate 33 models and find that no single model dominates: MLLM-based embeddings lead on classification, clustering, pair classification, and QA; multimodal binding leads on retrieval and zero-shot classification; generative MLLMs without contrastive adaptation collapse on cross-modal tasks. Paired video-only vs. audio+video evaluations show that audio's contribution depends on dataset annotation provenance: audio helps when labels were produced from both modalities and hurts when they were produced from visuals alone, a six-point gap consistent across model families. MVEB is derived from MVEB+, a 184-task pool, and is designed to maintain task diversity while reducing evaluation cost. It integrates into the MTEB ecosystem for unified evaluation across text, image, audio, and video. We release MVEB and all 184 tasks along with code and a leaderboard at https://github.com/embeddings-benchmark/mteb.

08.
arXiv (CS.AI) 2026-06-18

From Memorization to Creation: Evaluating the Cognitive Depth of LLM-Generated Educational Questions

arXiv:2606.18257v1 Announce Type: cross Abstract: While LLMs show promise in automating educational content creation, their ability to generate questions that stimulate higher-order thinking remains understudied. This work evaluates six widely-used LLMs through a Bloom's Taxonomy lens, focusing on their capacity to transcend rote memorization and achieve cognitive leaps. Using a hybrid human–AI evaluation protocol, we generate and analyze 20{,}700 questions across computer science, K–12 math, and social-science domains. Key contributions include: (1) a fine-grained prompting strategy that reduces question repetitiveness by 24.45\% for Qwen2.5-7B-Instruct, and increases the proportion of higher-order cognitive level outputs by 11.53\% for InternLM3-8B-Instruct; (2) quantitative metrics for cognitive shift intensity (CogShift) and category drift, revealing InternLM3's superior performance in multi-level transitions; (3) an interpretability analysis revealing metric-level correlations that enhance the transparency of Chain-of-Thought prompting. Our findings highlight the importance of cognitive-aware prompt design and provide benchmarks for deploying LLMs in personalized learning systems.

09.
arXiv (CS.AI) 2026-06-16

AIRMap: AI-Generated Radio Maps for Wireless Digital Twins

arXiv:2511.05522v4 Announce Type: replace-cross Abstract: Accurate, low-latency channel modeling is essential for real-time wireless network simulation and digital-twin applications. Traditional modeling methods like ray tracing are however computationally demanding and unsuited to model dynamic conditions. In this paper, we propose AIRMap, a deep-learning framework for ultra-fast radio-map estimation, along with an automated pipeline for creating the largest radio-map dataset to date. AIRMap uses a single-input U-Net autoencoder that processes only a 2D elevation map of terrain and building heights. Trained on 1.2M Boston-area samples and validated across four distinct urban and rural environments with varying terrain and building density, AIRMap predicts path gain with under 4 dB RMSE in 4 ms per inference on an NVIDIA L40S-over 100x faster than GPU-accelerated ray tracing based radio maps. A lightweight calibration using just 20% of field measurements reduces the median error to approximately 5%, significantly outperforming traditional simulators, which exceed 50% error. Integration into the Colosseum emulator and the Sionna SYS platform demonstrate near-zero error in spectral efficiency and block-error rate compared to measurement-based channels. These findings validate AIRMap's potential for scalable, accurate, and real-time radio map estimation in wireless digital twins.

10.
bioRxiv (Bioinfo) 2026-06-11

Revealing trajectories of multi-modal voxel-level changes in neurodegenerative diseases using latent event mapping

Neurodegenerative diseases are driven by pathological mechanisms that can be indirectly measured in vivo using multi-modal neuroimaging. However, current computational methods that aim to reconstruct trajectories of voxel-level changes in the brain are either not computationally scalable or fully interpretable, limiting their ability to reveal associations between disease progression and underlying mechanisms. Here we introduce Latent Event Mapping (LEMING), a generative unsupervised modelling technique that learns a latent map of disease events along a common pseudo-timeline of events. We apply LEMING to amyloid PET and structural MRI data from the Alzheimer's Disease Neuroimaging Initiative to reveal the first voxel-level trajectories of events in Alzheimer's disease. Notably, we show how LEMING can provide new insights into progression-dependent disease mechanisms. We find that acetylcholine receptor density is significantly positively associated with both late-stage amyloid and atrophy events, suggesting that either these receptors are targeted later in disease progression, or that amyloid does not play an active role. This has strong implications for therapeutics that target acetylcholine receptors, particularly for early-stage intervention strategies.

11.
arXiv (CS.CL) 2026-06-17

MemSlides: A Hierarchical Memory Driven Agent Framework for Personalized Slide Generation with Multi-turn Local Revision

Personalized presentation generation requires more than conditioning on a current prompt or template: agents must preserve stable user preferences across tasks, retain newly introduced preferences and constraints during multi-turn revision, and carry out local edits reliably. We propose MemSlides, a hierarchical memory framework for personalized presentation agents that separates long-term memory from working memory and further divides long-term memory into user profile memory and tool memory. User profile memory stores intent-conditioned profiles for round-0 personalization, working memory carries active preferences and session constraints across revision rounds, and tool memory stores reusable execution experience for reliable localized editing. MemSlides pairs this memory design with scoped slide-local revision, so targeted updates act on the smallest affected region instead of repeatedly regenerating the full deck. In controlled experiments, user profile memory improves persona-alignment judgments on a multi-persona, multi-intent profile bank, tool-memory injection improves closed-loop modify behavior in diagnostic matched-pair settings, and qualitative cases illustrate working memory's ability to carryover preferences. Taken together, these results suggest that effective personalization in presentation authoring depends on separating persistent user profiles, session-level working memory, and reusable execution experience across generation and localized revision.

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

First Proof Second Batch

arXiv:2606.18119v1 Announce Type: new Abstract: To assess the ability of current AI systems to correctly solve research-level mathematics problems, we tested several AI systems on a set of ten problems in a broad range of mathematical fields; these problems arose naturally in the research process of the contributors. This document includes the problems, our methodology, and the results of our testing. We provide links to supplementary documents including the human solutions, the AI-generated solutions, and the referee reports and logs for the AI-generated solutions. The ten problems were contributed by the following mathematicians: (1) Dariusz Kaloci\'nski and Theodore A. Slaman, (2) Richard Schwartz, (3) Aleksa Milojevic and Benny Sudakov, (4) Larry Guth, (5) Oleg Butkovsky, Jonathan Mattingly, and Lorenzo Zambotti, (6) Joshua Evan Greene and Duncan McCoy, (7) Sucharit Sarkar, (8) Sam Payne and Jidong (Jayden) Wang, (9) Sylvie Corteel and John Lentfer, (10) Srivatsav Kunnawalkam Elayavalli.

13.
arXiv (CS.CV) 2026-06-15

Schrödinger's Navigator: Imagining an Ensemble of Futures for Zero-Shot Object Navigation

Zero-shot object navigation (ZSON) requires robots to find target objects in unseen environments without task-specific fine-tuning or pre-built maps, a key capability for general-purpose service robots. Yet methods that perform well in simulation often degrade in cluttered real-world scenes with severe occlusion and latent hazards, where large unseen regions make single-scene inference brittle and unsafe. We propose Schrödinger's Navigator, a belief-aware framework that reasons at inference time over multiple trajectory-conditioned imagined 3D futures. Given candidate paths, a trajectory-conditioned 3D world model predicts hypothetical observations and maintains a superposition of plausible scene realizations rather than committing to one map. An adaptive occluder-aware sampler directs imagination to uncertainty-critical regions, while a Future-Aware Value Map (FAVM) aggregates imagined futures for robust, proactive action selection. Experiments in simulation and on a physical Go2 quadruped show that Schrödinger's Navigator outperforms strong ZSON baselines, improving hidden-target discovery and risk-aware waypoint selection in occlusion-heavy navigation scenarios. These results highlight imagined 3D futures as a scalable and generalizable strategy for zero-shot navigation in uncertain real-world environments.

14.
arXiv (CS.AI) 2026-06-19

ITNet: A Learnable Integral Transform That Subsumes Convolution, Attention, and Recurrence

arXiv:2606.19538v1 Announce Type: new Abstract: Convolutional networks, recurrent networks, and transformers each encode different inductive biases – locality, sequential memory, and content-dependent pairwise interaction – and have remained mathematically distinct since their inception. We show that this fragmentation reflects not a fundamental diversity in how signals should be processed, but rather incomplete views of a single underlying mathematical object: a learnable integral transform. We introduce the Integral Transform Network (ITNet), a unified architecture built around a learnable kernel that depends jointly on positions and features. This kernel is implemented as a small neural network, specifically an MLP, that models pairwise interactions, enabling the model to adapt its behavior from data. We show that convolution, self-attention (including multi-head), and autoregressive recurrence (including LSTM, GRU, S4, and Mamba) arise as special cases under appropriate parameterizations, and that ITNet is a universal approximator of continuous operators. To make this practical, we develop tiled kernel fusion, importance-weighted Monte Carlo integration, and learned low-rank factorization, enabling efficient and scalable computation. A single ITNet architecture with a shared operator and lightweight modality-specific encoders matches or exceeds specialized baselines on ImageNet-1K , GLUE, ModelNet40, VQA\,v2 and NLVR2. The results demonstrate that a single learned interaction mechanism can recover the behavior of all three architectural families from data.

15.
arXiv (CS.AI) 2026-06-12

Representing Time Series as Structured Programs for LLM Reasoning

arXiv:2606.12481v1 Announce Type: cross Abstract: Large language models (LLMs) have demonstrated strong reasoning and instruction-following capabilities, making them potentially powerful tools for time-series analysis. However, time series lie outside their native textual modality, raising a fundamental question: how should time series be represented so that LLMs can reason about them effectively? Existing work typically serializes raw numerical sequences or fine-tunes pre-trained LLMs on time-series data. These approaches place the burden of extracting temporal structure directly on the LLM, creating a modality mismatch that often degrades performance on long sequences and introduces substantial computational overhead. In this work, we introduce Time-Series-to-Structured-Program representation (T2SP), a deterministic, training-free method that represents a time series as a structured symbolic program. T2SP decomposes time series into trends, periods, and salient events, expressing them in a program-friendly format aligned with the textual and code-like modalities on which LLMs are natively trained. By shifting temporal-structure extraction from the model to the representation itself, T2SP enables off-the-shelf LLMs to leverage their existing reasoning capabilities for time-series understanding. We evaluate T2SP on three reasoning tasks – editing, captioning, and question answering – where it consistently improves performance, reduces reasoning time, and lowers failure rates compared with raw-string representations. Our results demonstrate that T2SP provides an effective interface between time series and LLMs.

16.
arXiv (CS.AI) 2026-06-17

Unlocking LLM Code Correction with Iterative Feedback Loops

arXiv:2606.17514v1 Announce Type: cross Abstract: Large Language Models have shown remarkable capabilities in code generation. However, most existing evaluations focus only on single-attempt accuracy and overlook the iterative refinement process that is central to real-world programming. This study presents a systematic investigation of LLMs' ability to rectify their own code through execution feedback. Using real-world programming problems across four models and two major programming languages, this study evaluates performance using iterative refinement framework where LLMs receive compiler error messages and testcase feedback after each attempt. This study introduces metrics to evaluate code failures, analyze rectification patterns, and compare the effectiveness of reasoning and non-reasoning models, offering actionable insights into both the understanding and practical application of feedback loops in LLM-driven code generation systems. Results show that reasoning models consistently improve over iterations, substantially outperforming non-reasoning models in leveraging feedback, while syntactic and runtime errors are far more tractable than logical or algorithmic failures.

17.
arXiv (CS.AI) 2026-06-16

Running hardware-aware neural architecture search on embedded devices under 512MB of RAM

arXiv:2606.14824v1 Announce Type: cross Abstract: This document proposes a novel approach to hardware-aware neural architecture search (HW NAS) that considers the resources available on the computing platform running it, enabling its execution on various embedded devices. The presented HW NAS produces tiny convolutional neural networks (CNNs) targeting low-end microcontroller units (MCUs), typically involved in the Internet of Things (IoT) or wearable robotics, opening new use cases. A gateway could run it to tailor CNNs' architecture on the acquired data without using external servers, ensuring privacy. The proposed technique achieves state-of-the-art results in the human-recognition tasks on the Visual Wake Word dataset, a standard TinyML benchmark, on several embedded devices.

18.
bioRxiv (Bioinfo) 2026-06-11

TMO: ASYMMETRIC CROSS-MODAL ATTENTION FOR LEARNINGCELL-STATE-DEPENDENT REGULATORY LAGS FROM SINGLE-CELL MULTIOMIC DATA

Abstract Background: Single-cell multi-omics technologies simultaneously measure chromatin accessibility (ATAC) and gene expression (RNA), providing a unique window into the temporal ordering of regulatory events during differentiation. However, most computational models treat the two modalities symmetrically, ignoring the directional relationship between chromatin and transcription, and existing lag-aware methods estimate a single global lag per gene, failing to capture cell-state-dependent dynamics. Methods and Results: We introduce Temporal Multi-Omics (TMO), a deep learning framework that learns signed, cell-state-conditional regulatory lags ({Delta}{tau}) using asymmetric cross-modal attention. TMO projects RNA and ATAC into 50 latent components each, tokenises each cell as a sequence of 100 tokens, and uses a two-pass transformer in which a data-driven lag prior - derived from a sliding-window cross-correlation function - directly biases attention asymmetrically. On four independent 10x Multiome datasets (mouse brain, human brain, mouse kidney, human PBMC), the asymmetric model achieves Lag Concordance Scores (LCS) of 0.988-0.999, compared to 0.048-0.108 for an architecturally identical symmetric baseline. A stratified 80/20 held-out experiment confirms that the learned component-lag ordering generalises to unseen cells (held-out LCS 0.85-0.99). Clustered {Delta}{tau} heatmaps show positive {Delta}{tau} (ATAC-led priming) in early pseudotime and negative {Delta}{tau} (RNA-led, activity-dependent regulation) in late pseudotime; the ATAC-RNA correlation heatmap exhibits a U-shaped pattern indicative of developmental decoupling. Components with the most positive {Delta}{tau} are enriched for chromatin organization and stem cell differentiation (FDR < 0.05), while those with the most negative {Delta}{tau} are enriched for synaptic signalling and immune activation. Ablating the cell-state information from the lag predictor reduces the LCS and collapses per-component temporal dynamics (KS p [&le;] 0.039 in all four tissues), proving that TMOs dynamic lag patterns depend on cell-state conditioning. Independent ChIP-seq validation for four transcription factors (PAX5, Pax6, ASCL1, Hnf4) confirms highly significant separation between target genes and expression-matched background (p < 10-4 in all cases). Two Multiome Perturb-seq screens provide causal validation: SMARCB1 knockout shows a directional trend (1.5-fold target shift, p = 0.056, n = 147 perturbed cells), and SMARCE1 knockout reaches statistical significance (p = 0.0089, n = 3,394 perturbed cells). Gene-level cross-correlation independently validates that the regulatory lag signal is present in the raw data, and TMO further identifies rare, statistically significant biphasic gene programs where the regulatory direction reverses across pseudotime. Conclusions: TMO is the first method to make regulatory lag a learnable, cell-state-conditional, and architecturally encoded parameter. It is scalable, interpretable, and open-source, providing a powerful tool for studying regulatory timing in development, disease, and perturbation screens.

19.
arXiv (CS.LG) 2026-06-18

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning

arXiv:2604.14906v3 Announce Type: replace-cross Abstract: The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through $-$1 programmed ribosomal frameshifting ($-1$ PRF), a mechanism that allows the virus to generate both structural and non-structural proteins from overlapping reading frames. This pseudoknot exhibits both threaded and unthreaded long-lived topologies. The influence of ligand binding on its folding is a process critical for the development of $-$1 PRF small-molecule inhibitors. Understanding this process through unbiased molecular dynamics (MD) simulations can be facilitated by introducing collective variables (CVs) that capture the corresponding slowest dynamical modes. Here, we use spectral map (SM), a thermodynamics-driven machine learning technique, to learn such CVs directly from all-atom MD trajectories of the SARS-CoV-2 RNA pseudoknot in complex with the $-$1 PRF inhibitor merafloxacin and its two structural analogs in neutral and ionized forms. Free-energy landscapes (FELs) derived from the learned CVs indicate that ligand-induced destabilization is topology-selective. In the threaded pseudoknot, the inhibitors destabilize the S2 stem, while in the unthreaded pseudoknot, destabilization occurs in the S1 and S3 stems. Furthermore, the extent to which each ligand reshapes the FEL matches experimentally reported antiviral potency, whereas the protonation state qualitatively alters dynamics within the same RNA topology. Overall, our results show how pseudoknot topology, ligand type, and protonation state collectively influence the slow conformational dynamics of viral RNA and establish physiological protonation as a critical factor for modeling RNA-targeted drug action.

20.
arXiv (CS.AI) 2026-06-11

FreeBridge: Variational Schrödinger Bridges for Cellular Transition Dynamics

arXiv:2606.11286v1 Announce Type: cross Abstract: High-content imaging assays quantify cellular responses to chemical and genetic perturbations, yet continuous trajectories of individual cells are unobservable because cells are chemically fixed at acquisition. Perturbation modeling therefore reduces to inferring stochastic transport between control and treated populations observed only as separate marginals. While recent generative models achieve strong end-point alignment, boundary consistency does not determine intermediate evolution: multiple stochastic processes may connect identical marginals while traversing regions unsupported by observed single-cell morphologies. We introduce FreeBridge, a Schrödinger Bridge formulation for single-cell transition modeling under endpoint-only supervision. FreeBridge defines atomic states as instance-segmented single-cell representations, establishing a fixed cellular manifold, and learns stochastic transport constrained within this geometry via empirical latent support regularization. Across BBBC021, RxRx1, and JUMP, FreeBridge maintains competitive or improved endpoint fidelity and mechanism-of-action retention under a unified evaluation protocol; on BBBC021, it further reduces intermediate support violations. These findings highlight the importance of geometric grounding for biologically interpretable perturbation dynamics. Project page: https://y-research-sbu.github.io/FreeBridge/.

21.
arXiv (CS.CV) 2026-06-11

SpikeTAD: Spiking Neural Networks for End-to-End Temporal Action Detection

Video understanding is a crucial part of computer vision, with numerous application scenarios. With the increasing popularity of mobile devices, an increasing number of efforts are trying to deploy video understanding models on them. However, existing video understanding models are difficult to deploy due to their large size and prohibitive power consumption. Spiking Neural Networks (SNNs) have shown bioplausibility and low power advantages over Artificial Neural Networks (ANNs), especially on neuromorphic chips which are regarded as essential components of future mobile devices. However, excessively long conversion time-steps and severe performance degradation problems limit their application. To solve the problems above, we explore the application of SNNs on temporal action detection (TAD), which is an important task in video understanding, and propose the first SNN-based end-to-end TAD architecture coined as SpikeTAD. While maintaining extremely low power consumption, SpikeTAD achieves an average mAP of 67.2% in THUMOS14 and 37.42% in ActivityNet-1.3, demonstrating the feasibility of a low-power TAD model. Our code is available at https://github.com/MCG-NJU/SpikeTAD.

22.
arXiv (CS.AI) 2026-06-18

ProfiLLM: Utility-Aligned Agentic User Profiling for Industrial Ride-Hailing Dispatch

arXiv:2606.18803v1 Announce Type: new Abstract: Bringing Large Language Models (LLMs) into industrial ride-hailing dispatch as semantic feature extractors over platform-scale behavioral logs is a compelling but under-explored data systems problem. Production matching pipelines remain dominated by structured numerical features, yet decisive behavioral signals (e.g., a driver's habitual aversion to certain regions) are inherently contextual and naturally expressible as LLM-generated user profiles. However, scaling such profiling to a live, millisecond-latency dispatcher faces three intertwined constraints rarely addressed together: on a platform with millions of daily orders, logs exceed any LLM's context window by orders of magnitude; most users are long-tail, with too few interactions for per-user profiling; and surface-fluent profiles do not necessarily improve downstream prediction utility. We present ProfiLLM, an agentic LLM data pipeline that operationalizes utility-aligned user profiling for production matching systems through two modules. (1) Tool-Augmented Global Knowledge Mining equips an LLM agent with 27 analytical tools to mine platform-scale data, producing reusable global knowledge, adaptive user clustering rules, and region-level supply-demand priors. (2) Utility-Aligned Profile Exploration generates multiple candidate profiles per cluster, evaluates them via a lightweight downstream utility proxy, iteratively refines the best candidates and constructs preference pairs for DPO fine-tuning. Deployed on DiDi's production dispatcher, ProfiLLM achieves up to +6.14% relative AUC improvement in outcome prediction, up to +4.35% GMV gain in dispatching simulation, and consistent improvements in a 14-day online A/B test including +0.47% GMV, +0.33% Completion Rate, and -0.82% Cancel-Before-Accept rate.

23.
arXiv (CS.CL) 2026-06-11

AI4SLT: Empirical Processes in Lean 4 for Formal Statistical Learning Theory

We present the first comprehensive Lean 4 formalization of statistical learning theory (SLT) grounded in empirical process theory. Our en-to-end formal infrastructure implement the missing contents in latest Lean library, including a complete development of Gaussian Lipschitz concentration, Dudley's entropy integral theorem for sub-Gaussian processes, and an application to least-squares (sparse) regression with a sharp rate. The project was carried out using a human-AI collaborative workflow, in which humans design proof strategies and AI agents execute tactical proof construction, leading to the human-verified Lean 4 toolbox for SLT. Beyond implementation, the formalization process exposes and resolves implicit assumptions and missing details in standard SLT textbooks, enforcing a granular, line-by-line understanding of the theory. This work establishes a reusable formal foundation and opens the door for future developments in machine learning theory. The code is provided in https://github.com/YuanheZ/lean-stat-learning-theory.

24.
arXiv (quant-ph) 2026-06-19

A Quantum Encoding of Traveling Salesperson Tours via Route Generation, Cost Phases, and a Reversible Valid-Permutation Oracle

arXiv:2603.21283v3 Announce Type: replace Abstract: For a traveling salesperson problem (TSP) of n cities, we present a compact quantum encoding based on a time-register representation of tours. A candidate route is represented as a sequence of n-1 city labels over discrete time steps, with one fixed start city and the remaining cities encoded in binary registers. We describe three ingredients of the construction: uniform route generation over the route register, a reversible validity oracle, and a phase oracle that encodes the total tour cost. The validity oracle checks both that the non-start city labels form a permutation and, for incomplete graphs, that every directed edge used by the route exists. The cost oracle then accumulates the start-edge, intermediate-transition, and return-edge costs into a tour-dependent phase for valid routes. This yields a coherent superposition of candidate routes with feasibility and tour-length information embedded directly in the quantum state. The complete construction uses O(n log n) qubits, while a naive implementation has worst-case elementary-gate complexity O(n^3 log n). The encoding is compatible with amplitude amplification or spectral filtering techniques such as the quantum singular value transform (QSVT) or Grover's algorithm. However, due to the exponentially small fraction of valid tours, the overall complexity remains exponential even when combined with amplitude amplification.

25.
arXiv (CS.CL) 2026-06-11

CRANE: Constrained Reasoning Injection for Code Agents via Nullspace Editing

Code agents must both reason over long-horizon repository state and obey strict tool-use protocols. In paired Instruct/Thinking checkpoints, these capabilities are complementary but misaligned. The Instruct model is concise and tool-disciplined, whereas the Thinking model offers stronger planning and recovery behavior but often over-deliberates and degrades agent performance. We present CRANE (Constrained Reasoning Injection for Code Agents via Nullspace Editing), a training-free parameter-editing method that treats the Thinking-Instruct delta as a directional pool of candidate reasoning edits for the Instruct backbone. CRANE combines magnitude thresholding to denoise the delta, a Conservative Taylor Gate to retain edits that are jointly beneficial for reasoning transfer and tool-use preservation, and Graduated Sigmoidal Projection to suppress format-critical update directions. By merging paired Instruct and Thinking checkpoints, CRANE delivers strong gains over either individual model while preserving Instruct-level efficiency: on Roo-Eval it achieves pass1 of 66.2% (+19.5%) for Qwen3-30B-A3B and 81.5% (+8.7%) for Qwen3-Next-80B-A3B; on SWE-bench-Verified it resolves up to 14 additional instances at both scales (122/500 and 180/500); and on Terminal-Bench v2 it improves pass1/pass5 by up to 2.3%/7.8%, reaching 7.6%/17.9% and 14.8%/30.3%, respectively, consistently outperforming alternative merging strategies across all three benchmarks.