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

MoECa: Aligning Feature Reuse with Expert Decomposition in Diffusion Transformers

Diffusion Transformers with Mixture-of-Experts (DiT-MoE) improve model capacity under sparse activation, but diffusion inference is still bottlenecked by redundant computation across timesteps. Existing caching methods mainly operate at the token level, which becomes suboptimal in DiT-MoE because each token update is internally decomposed into multiple routed expert branches. Our analysis shows that cross-timestep redundancy in DiT-MoE is better characterized at the expert-branch level than at the whole-token level. Based on this observation, we propose MoECa, a fine-grained caching framework that performs branch-level feature reuse across timesteps. MoECa further introduces expert-aware adaptive control and synchronized cache updates across MoE and attention paths to maintain stable intermediate states. Experiments on multiple DiT-MoE models show that MoECa consistently achieves a better speed-quality trade-off than prior caching methods, with up to 2.83$\times$ inference speedup and minimal quality degradation.

02.
arXiv (CS.CV) 2026-06-16

MamBOA: State-Space Architecture for Video Recognition

Fine-grained action recognition demands temporal reasoning that general-purpose architectures address through different cost-accuracy tradeoffs: 3D dense operators couple computation to the input volume, while difference-based methods approximate motion through rigid, hand-crafted subtraction of uncontextualized features - each reflecting a deliberate design choice with corresponding limitations in expressiveness or flexibility. We present MamBOA, a backbone-agnostic temporal framework built upon a novel interleaved scan structure that recasts the selective state-space recurrence (S6) as a native motion synthesizer. By interleaving consecutive feature representations extracted from a pretrained backbone into a single alternating sequence, the proposed scan structurally drives the recurrence to encode both temporal observations of each position within a shared hidden state, separated by only a single decay step - rendering the inter-frame transition an intrinsic component of the state dynamics rather than an externally computed quantity. A cascade of dedicated alignment and decoding operations then distills this joint encoding into an explicit motion representation, which a dual-path pooling mechanism adaptively aggregates by balancing attention-driven selection with uniform temporal coverage. The framework interfaces seamlessly with CNN, Transformer, and Mamba backbone families, adding only ~2.1 GFLOPs per feature pair. On Diving48, MamBOA achieves 85.02% Top-1 accuracy with an image-pretrained backbone and 86.24% with a video-pretrained backbone processing the entire video in a single forward pass - demonstrating that structurally induced state-space dynamics constitute a principled and general foundation for motion modeling.

03.
arXiv (CS.LG) 2026-06-16

Diffusion Flow Matching: Dimension-Improved KL Bounds and Wasserstein Guarantees

arXiv:2606.16610v1 Announce Type: cross Abstract: Diffusion Flow Matching (DFM) has recently emerged as a versatile framework for generative modeling, yet its theoretical convergence properties remain only partially understood. In this work, we provide refined and novel convergence guarantees for Brownian motion based DFMs, focusing on the discretization error. Our analysis is conducted under the Kullback-Leibler (KL) divergence and the 2-Wasserstein distance. Under finite-moment conditions and a mild score integrability assumption, we derive KL convergence bounds with improved dimensional dependence compared to prior work, achieving, up to our knowledge, state-of-the-art scaling under minimal conditions. We further extend the analysis to the 2-Wasserstein distance: under an additional first-order score integrability assumption and a weak log-concavity condition, we obtain convergence guarantees with dimensional dependence consistent with the KL case.

04.
arXiv (CS.AI) 2026-06-15

An Agentic Retrieval Framework for Autonomous Context-Aware Data Quality Assessment

arXiv:2606.13692v1 Announce Type: cross Abstract: Data quality assessment is a critical prerequisite for effective data analytics and data-driven decision-making, yet it remains a challenging task due to the inherently context-dependent nature of data quality. Existing approaches often rely on static rules or manual assessment strategies, limiting their adaptability to diverse usage scenarios and constraining automation at scale. Recent advances in artificial intelligence, particularly large language models, offer new opportunities for automating data quality assessment, but raise concerns related to reliability, grounding, and execution safety. In this paper, we propose a unified agentic-retrieval framework for autonomous context-aware data quality assessment. The framework interprets natural-language descriptions of intended data usage, derives context-aware assessment strategies, and generates executable validation logic through a multi-agent workflow. To ensure operational reliability, the framework introduces a feasibility validation stage that evaluates the realism and executability of generated assessment specifications before execution, enabling iterative refinement when necessary. Accepted validation logic is executed deterministically to guarantee reproducible and auditable results. We implement the proposed framework as an end-to-end prototype and evaluate it across multiple usage scenarios applied to the same dataset. The results demonstrate that assessment outcomes adapt meaningfully to different intended uses, while feasibility-gated execution reduces unrealistic or non-executable rule generation. The proposed approach provides a practical foundation for deploying autonomous yet controlled data quality assessment in modern data-driven environments.

05.
arXiv (CS.CL) 2026-06-19

Quantifying Aleatoric Uncertainty of In-Context Learning for Robust Measure of LLM Prediction Confidence

In-Context Learning (ICL) allows LLMs to adapt to new tasks from a few demonstrations, but its reliability remains a concern: predictions are highly sensitive to both prompt design and the model's ability to understand the context, obscuring whether failures arise from data properties or model limitations. Uncertainty decomposition-separating aleatoric from epistemic sources-is particularly crucial in this setting, yet existing methods, designed for standard generation tasks, fail to capture the unique dynamics of ICL. To address this, we introduce a concept of self-function vectors, built upon Bayesian views and the mechanistic interpretability of ICL. These vectors leverage internal model representations to model the latent concept learned during in-context prompting, thereby enabling a direct estimation of aleatoric uncertainty within a Bayesian framework and circumventing the reliance on brittle input or decoding manipulations. Given the lack of established benchmarks and suitable evaluation protocols, we also propose the first and rigorous evaluation protocol, in which data is manipulated in controlled ways so as to quantify aleatoric uncertainty precisely and separately from epistemic uncertainty. With this new evaluation framework, initially grounded in synthetic tasks for conceptual development and subsequently extended to real-world datasets, we show that our proposed methodology can measure uncertainty of LLM predictions made under ICL more reliably than existing alternative methods. Moreover, we show it can be used as a practical tool for trustworthy-related applications, such as hallucination detection. Our findings pave a new direction for connecting the quantitative view of uncertainty with the mechanistic understanding of model behavior.

06.
arXiv (CS.CL) 2026-06-15

GitOfThoughts: Version-Controlled Reasoning and Agent Memory You Can Replay, Diff, and Merge

Large language model (LLM) reasoning is ephemeral: chains of thought vanish with the context window, pruned search branches leave no record, and memory buffers cannot be diffed, merged, or audited. Every other complex software process (code, infrastructure, data, experiments) is version-controlled; reasoning is not. We introduce GitOfThoughts, which stores an agent's reasoning tree as a git repository: every scored thought is a commit, scores are notes, outcomes are tags, and retrieval is "git log" over the agent's own history. This makes reasoning replayable, auditable, and mergeable across agents at near-zero engineering cost. We then ask the harder question: does memory, in any substrate, actually improve accuracy? Across five substrates (none, markdown, vector, graph, git), two benchmarks, two model scales, and pre-registered replications, the answer for novel problems is no. No memory format reliably helps, and a promising early result collapsed under its own pre-registered replication. Memory pays only above what we call the copyability threshold: when the retrieved case is a near-duplicate of the current problem (similarity >~ 0.8), accuracy jumps sharply; below it, nothing. The gain is answer retrieval, not method transfer: a 4.5x larger model doubles the near-duplicate payoff yet still cannot extract a transferable method from a worked example. The only general lever we find is test-time sampling. The case for git-as-substrate is therefore auditability, provenance, and mergeability at accuracy parity. We document a retracted result and a refuted hypothesis to model the evaluation standard we hold ourselves to.

07.
medRxiv (Medicine) 2026-06-11

Allostatic Load in Endometrial Cancer Disparities

Background: Endometrial cancer incidence and mortality are increasing, particularly among Black women and for aggressive subtypes. Allostatic load (AL), a composite measure of physiologic dysregulation across metabolic, cardiovascular, and immune systems, varies by racial category and tumor subtype in other cancers. Endometrial cancer is strongly associated with obesity, and it is unknown whether AL scores maintain sufficient heterogeneity to evaluate differences across subgroups or with clinical outcomes. Objective: To describe the performance of AL scoring in endometrial cancer patients and examine associations with tumor characteristics (grade/histology) and survival outcomes. Methods: We evaluated AL among 398 participants newly diagnosed with endometrial cancer. AL score was calculated by assigning 1 point for each ''high-risk'' value (by clinical reference range or distribution-based) for 15 biologic variables for vital signs, anthropometrics, blood-based biomarkers, and medical comorbidities. Results: Distribution-based thresholds for variables were used to preserve heterogeneity in this obesity-dominant context. Overall, 68.7% of Black women had high AL compared to White (56.7%), Hispanic (56.7%), and other race (32.3%) women. Decision tree analyses revealed grade-dependent associations between AL and survival. For women with low-grade tumors, higher AL was associated with poorer overall survival. For high-grade tumors, intermediate AL ([≥]4,

08.
arXiv (CS.AI) 2026-06-17

RLRC: Reinforcement Learning-based Recovery for Compressed Vision-Language-Action Models

arXiv:2506.17639v2 Announce Type: replace-cross Abstract: Vision-Language-Action models (VLA) have demonstrated remarkable capabilities and strong potential in complex robotic manipulation. However, their large parameter sizes and high inference latency hinder real-world deployment, especially on resource-constrained platforms. To address this, we conduct a systematic empirical study of model compression for VLAs. Building on these insights, we present RLRC, a three-stage compression and recovery pipeline consisting of structured pruning, performance recovery via SFT and RL, and subsequent quantization. The RL stage incorporates a critic warm-up strategy and BC loss regularization to stabilize training and preserve policy behavior. RLRC achieves up to an 8 times memory reduction and 2.3 times inference speedup while maintaining the original task success rate. Extensive experiments across multiple VLA backbones show that RLRC consistently outperforms existing compression baselines, highlighting its effectiveness for on-device deployment. Project website: https://rlrc-vla.github.io

09.
arXiv (CS.AI) 2026-06-17

LoopCoder-v2: Only Loop Once for Efficient Test-Time Computation Scaling

arXiv:2606.18023v1 Announce Type: cross Abstract: Looped Transformers scale latent computation by repeatedly applying shared blocks, but sequential looping increases latency and KV-cache memory with the loop count. Parallel loop Transformers (PLT) alleviate this cost through cross-loop position offsets (CLP) and shared-KV gated sliding-window attention, making loop count a practical design choice. We therefore study PLT loop-count selection through a gain–cost view: an extra loop may refine representations, but CLP also introduces a positional mismatch at each loop boundary. We instantiate this study by training LoopCoder-v2, a family of 7B PLT coders with different loop counts, from scratch on 18T tokens, followed by matched instruction tuning and evaluation. Empirically, the two-loop variant delivers broad gains over the non-looped baseline across code generation, code reasoning, agentic software engineering, and tool-use benchmarks, improving SWE-bench Verified from 43.0 to 64.4 points and Multi-SWE from 14.0 to 31.0 points. In contrast, variants with three or more loops regress, revealing a strongly non-monotonic loop-count effect. Our diagnostics show that loop 2 provides the main productive refinement, while later loops yield diminishing, oscillatory updates and reduced representational diversity. Because the CLP-induced mismatch remains roughly fixed as refinement gains shrink, the offset cost increasingly dominates. This gain–cost trade-off explains PLT's saturation at two loops and provides diagnostics for loop-count selection.

10.
arXiv (CS.LG) 2026-06-17

Loss Landscape Poisoning: Targeted Extraction of Unseen Training Data from LLMs

arXiv:2606.17110v1 Announce Type: cross Abstract: Large Language Models are increasingly trained on proprietary or sensitive data, from private healthcare and financial records to user conversations containing secrets. Ensuring the privacy of such data against extraction attacks has become a central concern. In this paper, we ask whether an attacker who can poison a portion of the training data can facilitate the leakage of a separate target record they have no access to. We answer in the affirmative and show that such leakage can be induced by a poisoning mechanism that reshapes the model's local loss landscape around the target completion. Our key insight is that poisoning to create a sharp loss minimum at the target, surrounded by elevated loss on nearby alternatives, forces the model to memorize the target as the unique low-loss solution in its neighborhood. The attack requires no architectural changes, and generalizes across centralized and federated learning settings. We demonstrate that the attack amplifies privacy leakage across language (up to 100% successful extraction), and vision-language models (up 90% successful extraction). We show that the attack is thwarted when the model is trained to be differentially private. However, we introduce a new attack that directly probes the loss landscape bypassing even differential privacy defenses.

11.
bioRxiv (Bioinfo) 2026-06-18

Predicting optimal growth temperatures of bacteria using learned structural information from a single protein

Temperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species are most likely to thrive. Although the OGTs for most bacteria remain unknown, the increasing availability of genomes from uncultivated and cultivated taxa has made it advantageous to build genomic, cultivation-independent models to infer OGT. However, pre-existing genomic models often lack the generalizability and mechanistic grounding required for robust inferences of OGT. We propose a novel framework for predicting bacterial OGT which uses learned protein structural signatures of thermal adaptation. We hypothesize that biophysical tradeoffs which dictate enzymatic functions across variable temperatures provide a more robust empirical basis for OGT prediction than broad genomic features. Our OGT-predicting model, ROSEATE, is based on a single gene, adenylate kinase (ADK), that encodes for a ubiquitous enzyme essential for energy homeostasis. ROSEATE uses high-dimensional latent space encoding via MSA Transformer, a protein language model which embeds ADKs in a manner which preserves biophysical information about embedded proteins. We show that the accuracy of the ROSEATE model is on par with other genome-based models, has a high degree of phylogenetic generalizability, and the ESM embeddings effectively capture key temperature-adaptive enzyme characteristics derived from AlphaFold structures. Because ROSEATE is based on analyses of a single ubiquitous protein, it can be used with metagenomic data to infer the community-level variation in bacterial OGTs. We demonstrate this feature of ROSEATE by reconstructing ADK sequences from over 500 environmental and host-associated metagenomes, successfully distinguishing community-wide thermal preferences across diverse habitats, from polar oceans to mammalian guts. By transitioning from genomic proxies to informationally dense protein structural features, this work provides an efficient, interpretable tool for predicting bacterial OGTs across taxa and whole communities.

12.
arXiv (CS.AI) 2026-06-16

The Reservoir Attention Network: Cross-Pass State in Pretrained Transformers via Content-Addressable Reservoir Injection

arXiv:2606.15678v1 Announce Type: cross Abstract: A feasibility and dynamics study of the Reservoir Attention Network (RAN), an architecture that injects a fixed, randomly-initialized reservoir into the mid-layer attention of a pretrained transformer to carry state across forward passes. Experiments span GPT-2 (124M, 355M) to Qwen2.5 (0.5B, 1.5B) on a single consumer GPU. The tasks are minimal probes chosen to isolate individual mechanisms; the broader always-alive agent vision is treated throughout as compute-limited future work, not a claim of this paper. The reservoir is left untrained (fixed random) by design: this isolates whether untrained recurrent dynamics alone suffice to carry usable cross-pass state, leaving trained recurrence as a complementary, more expensive direction.

13.
arXiv (math.PR) 2026-06-12

Voronoi Percolation: Topological Stability and Giant Cycles

arXiv:2601.00793v2 Announce Type: replace Abstract: We study the topological stability of Voronoi percolation in higher dimensions. We show that slightly increasing p allows a discretization that preserves increasing topological properties with high probability. This strengthens a theorem of Bollobás and Riordan and generalizes it to higher dimensions. As a consequence, we prove a sharp phase transition for the emergence of i-dimensional giant cycles in Voronoi percolation on the 2i-dimensional torus.

14.
arXiv (CS.LG) 2026-06-11

Momentum LMS Theory beyond Stationarity: Stability, Tracking, and Regret

arXiv:2602.11995v2 Announce Type: replace Abstract: In large-scale data processing scenarios, data often arrive in sequential streams generated by complex systems that exhibit drifting distributions and time-varying system parameters. This nonstationarity challenges theoretical analysis, as it violates classical assumptions of i.i.d. (independent and identically distributed) samples, necessitating algorithms capable of real-time updates without expensive retraining. An effective approach should process each sample in a single pass, while maintaining computational and memory complexities independent of the data stream length. Motivated by these challenges, this paper investigates the Momentum Least Mean Squares (MLMS) algorithm as an adaptive identification tool, leveraging its computational simplicity and online processing capabilities. Theoretically, we derive tracking performance and regret bounds for the MLMS in time-varying stochastic linear systems under various practical conditions. Unlike classical LMS, whose stability can be characterized by first-order random vector difference equations, MLMS introduces an additional dynamical state due to momentum, leading to second-order time-varying random vector difference equations whose stability analysis hinges on more complicated products of random matrices, which poses a substantially challenging problem to resolve. Experiments on synthetic and real-world data streams demonstrate that MLMS achieves rapid adaptation and robust tracking, in agreement with our theoretical results especially in nonstationary settings, highlighting its promise for modern streaming and online learning applications.

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

Two Wrongs, No Right: Auditing Social-Desirability Bias in LLM Annotators for Computational Social Science

作者:

LLM annotators are increasingly used in computational social science (CSS), but it is unclear whether their alignment-shaped errors preserve the empirical conclusions a researcher would report. We audit three open-source 7B instruction-tuned models (Zephyr, Mistral-Instruct, Qwen2.5-Instruct) across six TweetEval tasks under four prompt conditions (72 cells) and find that social-desirability failures do not run in a single direction. Zephyr exhibits leniency bias, systematically under-applying harmful labels (offensive language: false benign rate 0.729, false alarm rate 0.031). Mistral and Qwen exhibit overcorrection, over-applying the same labels (Mistral hate-speech FAR = 0.604). All three models exhibit neutrality bias on abortion stance, underestimating opposition prevalence by 24 to 40 percentage points and inflating the neutral label. None of the four prompting interventions we test (neutral, safety framing, depersonalized, chain-of-thought) corrects these failures across models; safety framing can worsen stance distortion. Strikingly, Zephyr's hate-speech prevalence estimate matches the gold rate exactly while its class-conditional errors are large in both directions, an accidental cancellation that misleads aggregate validation. We translate these patterns into a three-part taxonomy with diagnostic FBR/FAR signatures and a lightweight gold-sample validation protocol. The headline for trustworthy CSS: a model that looks calibrated on aggregate metrics can still flip the substantive empirical conclusion a researcher would report.

16.
arXiv (CS.CV) 2026-06-12

Mana: Dexterous Manipulation of Articulated Tools

Articulated tool manipulation remains a major challenge in dexterous robotics due to the need to coordinate internal degrees of freedom and contact-rich interactions. While prior work has largely focused on rigid objects, articulated tool use remains underexplored because of its physical complexity and the difficulty of learning functional grasping and manipulation policies. We present Mana (Manipulation Animator), a general sim-to-real framework that reinterprets dexterous manipulation as an animation problem. Inspired by computer animation, Mana employs a coarse-to-fine pipeline that transforms procedurally-generated grasp keyframes into manipulation trajectories through motion planning and reinforcement learning. The data generation process is largely automatic, requiring only a few mouse clicks to specify functional affordances (

17.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

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

Giskard : Byzantine Robust and Confidential Aggregation for Large-Scale Decentralized Learning

arXiv:2606.19129v1 Announce Type: cross Abstract: Dealing simultaneously with confidentiality and Byzantine behaviors in decentralized learning is a challenging problem. Indeed, in decentralized learning, clients train a machine learning model while keeping their data locally and share their model parameters or gradients with a set of neighbors. While enforcing confidentiality calls for hiding the exchanged model parameters/gradients (e.g., by using cryptographic techniques), dealing with Byzantine contributions often requires inspecting the latter. Hence, most research works address these objectives separately. A recent line of work proposes to employ secure multi-party computation (MPC) to implement robust aggregators against model poisoning, thereby enforcing both confidentiality and Byzantine resilience. However, these solutions scale badly: they either require all-to-all communication between participants or delegate the entire computation to a small subset, whose computational and communication load grows proportionally with the size of the network. In this paper, we present Giskard, a protocol for confidential and Byzantine-robust decentralized aggregation. Giskard organizes $n$ parties into a tree of committees of size $O(\log n)$ and evaluates a coordinate-wise approximate median via a committee-adapted distributed binary search over the value domain, using BGW-style MPC within each committee. We assess Giskard both theoretically by proving its security and confidentiality properties and experimentally through extensive experiments involving up to one million participants. Compared to its closest competitors, Giskard reduces per-party communication complexity asymptotically while exhibiting comparable model utility under up to $n/4$ Byzantine parties.

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

DreamReg: Belief-Driven World Model for 2D-3D Ultrasound Registration

Ultrasound (US) is widely used for surgical navigation, yet real-time registration between intraoperative 2D slices and preoperative 3D volumes remains challenging due to partial observability, speckle noise, and the action-dependent US acquisition. Existing methods are one-shot or short-horizon, making it hard for them to gather evidence over time or capture how surgeons adjust probe motion based on on-screen feedback. We propose DreamReg, a belief-driven world-model framework that formulates 2D-3D registration as belief updating over rigid transformations. DreamReg maintains a latent belief state that summarizes past observations and poses information, and continuously refines the transformation through learned dynamics as new slices arrive. During training, DreamReg is exposed to probe-motion trajectories that mimic clinical scanning behavior and learns to update its belief by conditioning pose refinement on the current US observation. During inference, DreamReg refines registration via internal imagination: it rolls out the learned world model to simulate candidate probe motions and their predicted observations, and integrates these imagined outcomes to converge to an accurate rigid transformation. Experiments on CAMUS and u-RegPro datasets demonstrate improved robustness and competitive registration accuracy for real-time guidance compared with state-of-the-art methods.

20.
arXiv (CS.CL) 2026-06-16

Understanding LLM Reasoning for Abstractive Summarization

Reasoning has substantially improved Large Language Models (LLMs) on analytical tasks such as mathematics and code generation, but its value for abstractive summarization remains unclear. To address this gap, we adapt general reasoning strategies to the summarization setting and conduct a large-scale comparative study of 8 reasoning strategies and 3 Large Reasoning Models (LRMs) across 8 diverse datasets, evaluating both summary quality and factual faithfulness. Our results show that reasoning is not a universal solution and its effectiveness depends strongly on the strategy and the summarization setting. In particular, we find a trade-off between summary quality and factual faithfulness. Explicit reasoning strategies often improve reference-based quality, but may weaken factual grounding, whereas implicit reasoning in LRMs shows the opposite tendency. We further find that increasing an LRM's internal reasoning budget does not reliably improve summarization and can even reduce factual consistency. These findings suggest that, for summarization, more reasoning is not always better. Effective reasoning should preserve faithful compression rather than induce over-elaboration. Our source code is publicly available.

21.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.

22.
arXiv (quant-ph) 2026-06-15

Spin-orbit coupling by design in quantum state engineering of atomically defined quantum dots

arXiv:2606.14487v1 Announce Type: cross Abstract: Tuning spin-orbit coupling is essential in controlling both spin and charge in confined semiconductor nanostructures, yet it is rarely a truly controllable parameter. Here, we show control over the spin-orbit Hamiltonian in quantum dots and the resulting quantum states by tailoring the confinement potential with atomic-scale precision. Using scanning tunnelling microscopy and spectroscopy, we pattern individual Cs ions into designer quantum dot structures on the surface of indium antimonide, in which electrons from a two-dimensional electron gas are confined with chosen in-plane electric-field gradients. We then quantify the atomic level structure, both spatially resolving the orbital character of the electronic states and their magnetic-field evolution. We demonstrate that the level structure, including the induced zero-field splitting, can be tailored by the designed geometry of the local electric fields. These effects can be described using a Hamiltonian that allows consistent treatment of the confinement-induced spin-orbit coupling beyond the conventional Bychkov-Rashba description. This Hamiltonian is derived from a multiband k.p model and takes the energy dependence of the relevant physical parameters into account. Such precise control of spin-orbit coupling in semiconductor quantum dots is relevant to quantum and spintronic technologies.

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

Automated Scoring of Arabic Text Using Large Language Models: A Literature Review

In modern educational systems, Automatic Text Scoring (ATS) plays a central role by enabling scalable and consistent evaluation of learner responses without human intervention. Recently, the increased accessibility of LLMs and Arabic-specific datasets has sparked renewed interest in this area. In this work, we investigate LLM-Based approaches for the automated evaluation of Arabic texts, focusing on both short answer grading (ASAG) and essay scoring (AES). We further introduce a structured taxonomy comprising five dimensions: application domain, feedback generation capability, LLM architecture deployed, alignment with competency referential frameworks, and prompt engineering strategy. By applying this taxonomy, we conduct a comparative analysis of existing studies, examining their methodological approaches, datasets, evaluation metrics, and reported performance. The findings highlight the need for sustained and pedagogically grounded research efforts in Arabic ATS, given its significance for improving educational quality across Arabic-speaking communities.

24.
arXiv (CS.CL) 2026-06-19

Token-Operations-Oriented Inference Optimization Techniques for Large Models

Large model inference optimization serves as a key foundation for supporting the scalable, low-cost, and highly stable operation of large model services. Centered on token-oriented inference optimization technology, this paper proposes for the first time a four-layer technical architecture consisting of Multi-model Fusion, Model Optimization, Compute-Model Fusion, and Compute-Network-Model Fusion. It systematically reviews the key technologies and current industry status across these four levels and analyzes the application value of related technologies in real-world business scenarios. This paper provides a practical technical path for reducing token production costs, improving token service efficiency, ensuring the stability of token supply, and driving the transition of large model services from being merely callable to being operable.

25.
arXiv (CS.CL) 2026-06-17

EngTrace: A Symbolic Benchmark for Verifiable Process Supervision of Engineering Reasoning

Large Language Models (LLMs) are increasingly entering specialized, safety-critical engineering workflows governed by strict quantitative standards and immutable physical laws, making rigorous evaluation of their reasoning capabilities imperative. However, existing benchmarks such as MMLU, MATH, and HumanEval assess isolated cognitive skills, failing to capture the physically grounded reasoning central to engineering, where scientific principles, quantitative modeling, and practical constraints must converge. To enable verifiable process supervision in engineering, we introduce EngTrace, a symbolic benchmark built on 90 parameterized templates, each generating unique, contamination-resistant problem instances, spanning three major engineering branches, nine core domains, and 20 distinct areas, yielding 1,350 test cases that stress-test generalization across diverse physical scenarios. Moving beyond outcome matching, we introduce a verifiable two-stage evaluation framework that uses a tiered protocol to validate intermediate reasoning traces alongside final answers through automated procedural checks and a heterogeneous AI Tribunal. Our evaluation of 27 leading LLMs reveals a distinct trade-off between numeric precision and trace fidelity, identifying a complexity cliff where abstract mathematical pre-training fails to translate into the integrative reasoning required for advanced engineering tasks.