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01.
arXiv (CS.AI) 2026-06-19

Multi-LCB: Extending LiveCodeBench to Multiple Programming Languages

arXiv:2606.20517v1 Announce Type: new Abstract: LiveCodeBench (LCB) has recently become a widely adopted benchmark for evaluating large language models (LLMs) on code-generation tasks. By curating competitive programming problems, constantly adding fresh problems to the set, and filtering them by release dates, LCB provides contamination-aware evaluation and offers a holistic view of coding capability. However, LCB remains restricted to Python, leaving open the question of whether LLMs can generalize across the diverse programming languages required in real-world software engineering. We introduce Multi-LCB, a benchmark for evaluating LLMs across twelve programming languages, including Python. Multi-LCB transforms Python tasks from the LCB dataset into equivalent tasks in other languages while preserving LCB's contamination controls and evaluation protocol. Because it is fully compatible with the original LCB format, Multi-LCB will automatically track future LCB updates, enabling systematic assessment of cross-language code generation competence and requiring models to sustain performance well beyond Python. We evaluated 24 LLMs for instruction and reasoning on Multi-LCB, uncovering evidence of Python overfitting, language-specific contamination, and substantial disparities in multilingual performance. Our results establish Multi-LCB as a rigorous new benchmark for multi-programming-language code evaluation, directly addressing LCB's primary limitation and exposing critical gaps in current LLM capabilities.

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

Single-Round Clustered Federated Learning via Data Collaboration Analysis for Non-IID Data

arXiv:2601.09304v2 Announce Type: replace Abstract: Federated Learning (FL) enables distributed learning across multiple clients without sharing raw data. When statistical heterogeneity across clients is severe, Clustered Federated Learning (CFL) can im-prove performance by grouping similar clients and training cluster-wise models. However, most CFL approaches rely on multiple communication rounds for cluster estimation and model updates, which limits their practicality under tight constraints on communication rounds. We propose Data Collaboration-based Clustered Federated Learning (DC-CFL), a single-round framework that completes both client clustering and cluster-wise learning, using only the information shared in DC analysis. DC-CFL quantifies inter-client similarity via total variation distance between label distributions, estimates clusters using hierarchical clustering, and performs cluster-wise learning via DC analysis. Experiments on multiple open datasets under representative non-IID conditions show that DC-CFL achieves accuracy comparable to multi-round baselines while requiring only one communication round. These results indicate that DC-CFL is a practical alternative for collaborative AI model development when multiple communication rounds are impractical. Our source code is publicly available at https://github.com/souta-suga/DC-CFL.

03.
bioRxiv (Bioinfo) 2026-06-11

OCOO-T : A SIMPLE AND SCALABLE VIRTUAL CELL MODEL FOR TRANSCRIPTIONAL PERTURBATION RESPONSE PREDICTION

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

04.
arXiv (CS.CL) 2026-06-12

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback

Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent's behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host-guest binding free-energy benchmarks, MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder. Our data and code are available at https://github.com/Zehong-Wang/MDForge.

05.
arXiv (quant-ph) 2026-06-11

Lowest order Carleman linearization for low Reynolds long-term behaviour of fluid flow simulations

arXiv:2605.23380v2 Announce Type: replace Abstract: It is shown that the lowest (second) order truncation of the Carleman linearization of the fluid equations (C2) recovers the late stage of the evolution, namely the steady-state solution, although to a decreasing degree of accuracy at increasing Reynolds number. This asymptotic property is first proved analytically for the decaying logistic with external forcing and then shown to hold to a significant degree of accuracy also for the more complex case of two-dimensional Kolmogorov-like fluid flow at low Reynolds numbers, below $Re \sim 10$. This time-asymptotic property may open interesting prospects for the quantum simulation of low-Reynolds steady-state fluid flows.

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

Cordyceps: Covert Control Attacks on LLMs via Data Poisoning

arXiv:2605.26595v2 Announce Type: replace-cross Abstract: Large language models (LLMs) are often fine-tuned on uncurated text datasets that adversaries can poison. Existing poisoning attacks primarily rely on fixed trigger phrases that defenses such as outlier detection, clean-data regularization, or online monitoring can neutralize. In this paper, we propose a data poisoning method that teaches an LLM an information hiding scheme reliably and stealthily through semantic associations between shared knowledge such as facts or concepts and attacker-chosen phrases. The induced hiding scheme can encode and decode arbitrary malicious instructions, thus revealing a new and subtle poisoning-induced vulnerability: covert control attacks. We precisely characterize covert control attacks and evaluate them across $5$ LLMs, $3$ backdoor defenses, and $4$ prompt injection defenses. With a small poisoned fraction, covert control attacks outperform heuristic-based prompt injection attacks in average attack success rate by about $40\%$ relative to clean fine-tuned models. They also circumvent defenses based on detection and fine-tuning, maintaining up to $93\%$ attack success rate after backdoor defenses and up to $98\%$ after prompt injection defenses.

07.
arXiv (CS.LG) 2026-06-18

Hierarchical Attention via Domain Decomposition

arXiv:2606.18525v1 Announce Type: new Abstract: We propose a hierarchical attention mechanism based on two-level overlapping Schwarz domain decomposition. The method is motivated by the observation that two-level Schwarz domain decomposition methods combine local subdomain corrections with a coarse level that communicates global, long-range information. We test its usefulness in the context of finite-dimensional operator learning using a simple, one-dimensional diffusion problem with homogeneous Dirichlet boundary conditions. Although elementary, this problem provides a controlled sequence-to-sequence setting in which the exact nonlocal solution operator is known. After discretization, learning the solution operator amounts to approximating the inverse of a symmetric positive definite matrix. As a baseline, we use a global softmax-free low-rank attention operator of the form $QK^T$. The proposed construction replaces this dense global factorization by a two-level additive structure: local low-rank attention blocks on overlapping subdomains are combined with a coarse attention block. The resulting operator has the form $$M_{\theta}^{-1} = \Phi Q_0 K_0^T \Phi^T + \sum_{i=1}^{N} R_i^T D_i^{1/2} Q_i K_i^T D_i^{1/2} R_i.$$ Here $R_i$ restricts to an overlapping subdomain, $D_i$ is a partition-of-unity weight, and $\Phi$ is a coarse interpolation (or prolongation) matrix. Numerical experiments for synthetic Fourier right-hand sides indicate that the domain-decomposition attention operator is able to train faster and can give more accurate approximations than a global low-rank attention baseline while using significantly fewer parameters.

08.
medRxiv (Medicine) 2026-06-18

Cost-effectiveness of a virtual fracture clinic versus traditional in-person fracture clinic care for adults with acute simple fractures: a protocol for a health economic evaluation within the RECITAL trial

ABSTRACT Introduction Traditional in-person fracture clinics are often overcrowded and inconvenient for patients. Virtual fracture clinics aim to address some of these concerns by improving the efficiency of the orthopaedic service and reducing unnecessary interventions while maintaining safety and quality of care. The RECITAL trial is a non-inferiority randomised controlled trial comparing follow-up care provided at a virtual fracture clinic for people with acute simple fractures to follow-up care provided at an in-person fracture clinic. This study describes the protocol for an economic evaluation of RECITAL where the primary aim is to investigate the cost-effectiveness of a virtual fracture clinic compared with traditional in-person fracture clinic care from a health system perspective. Methods and analysis The RECITAL trial recruited 312 participants with acute simple fractures and randomised them to receive follow-up care provided at a virtual fracture clinic or follow-up care provided at an in-person fracture clinic. We will conduct a within-trial analysis from a health system perspective (primary analysis), as well as a health service, patient and societal perspective. The economic evaluation will estimate the difference in the cost of resource inputs on an intention to treat basis used by participants in the two arms of the trial, allowing comparisons to be made between the in-person and virtual fracture clinics. Data for intervention costs and healthcare utilisation will be collected from trial records, hospital electronic medical records and district performance units. The results of the economic evaluation will be expressed in terms of incremental cost per utility weight gained at 12 weeks and will be plotted on a cost-effectiveness plane. Bootstrapping by resampling will be used to estimate 95% confidence intervals around costs and outcomes, and to calculate the confidence intervals around the incremental cost-effectiveness ratio. A cost-effectiveness acceptability curve (CEAC) will be plotted, which will provide information about the probability that an intervention is cost-effective, given the level of a decision makers willingness to pay for each additional outcome. Ethics and Dissemination The trail was approved by the SLHD Ethics Review Committee (RPAH Zone) (X23-0200 and 2023/ETH01038). The findings will be disseminated through a peer-reviewed journal and conference presentations. Trial registration number The trial was prospectively registered on the Australian New Zealand Clinical Trials Registry (ANZCTR; 12623000934640)

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

Central Limit Theorems for Stochastic Gradient Descent Quantile Estimators

arXiv:2503.02178v3 Announce Type: replace-cross Abstract: This paper develops asymptotic theory for quantile estimation via stochastic gradient descent (SGD) with a constant learning rate. The quantile loss function is neither smooth nor strongly convex. Beyond conventional perspectives and techniques, we view quantile SGD iteration as an irreducible, periodic, and positive recurrent Markov chain, which cyclically converges to its unique stationary distribution regardless of the arbitrarily fixed initialization. To derive the exact form of the stationary distribution, we analyze the structure of its characteristic function by exploiting the stationary equation. We also derive tight bounds for its moment generating function (MGF) and tail probabilities. Synthesizing the aforementioned approaches, we prove that the centered and standardized stationary distribution converges to a Gaussian distribution as the learning rate $\eta\rightarrow0$. This finding provides the first central limit theorem (CLT)-type theoretical guarantees for the quantile SGD estimator with constant learning rates. We further propose a recursive algorithm to construct confidence intervals of the estimators with statistical guarantees. Numerical studies demonstrate the effective finite-sample performance of the online estimator and inference procedure. The theoretical tools developed in this study are of independent interest for investigating general SGD algorithms formulated as Markov chains, particularly in non-strongly convex and non-smooth settings.

10.
arXiv (CS.AI) 2026-06-16

An Empirical Investigation of Pre-Trained Deep Learning Model Reuse in the Scientific Process

arXiv:2603.13584v2 Announce Type: replace-cross Abstract: Deep learning has achieved recognition for its impact within natural sciences, yet the prohibitive financial and technical cost of training models from scratch inhibit adoption. Following software engineering community guidance, natural scientists are reusing pre-trained deep learning models (PTMs) to amortize these costs. While prior works recommend PTM reuse patterns, we present the first empirical study of PTM reuse patterns in the natural sciences, quantifying the utilization and impact of PTM reuse within the scientific process across 17,718 peer reviewed, open access papers. Our results show that "Biochemistry, Genetics and Molecular Biology" has outpaced other natural scientific fields in PTM reuse, "adaptation" reuse is the most prevalent PTM reuse pattern identified across all natural science fields, and the "testing" stage of the scientific process has been most impacted by PTM integration.

11.
bioRxiv (Bioinfo) 2026-06-16

scIsoAgent enables autonomous isoform-resolved characterization and sequence-informed interpretation of long-read single-cell transcriptomes

Alternative isoform usage can alter gene function independently of total gene expression, creating a need to resolve transcript isoforms at single-cell resolution. Long-read single-cell RNA sequencing meets this need by linking cellular identity to transcript isoforms and sequence-level features. Realizing its full biological value requires reproducible workflows that connect specialized long-read analysis with biological interpretation. Existing large language model (LLM)-based biomedical agents support general omics analysis, but are not designed for isoform-resolved long-read single-cell workflows. Here, we present scIsoAgent, an autonomous LLM-powered scientific agent for long-read single-cell RNA-seq analysis. scIsoAgent turns heterogeneous long-read single-cell inputs into traceable isoform-resolved workflows, using stage-aware planning and persistent computational context to support both execution and interpretation. Across complementary evaluations, this design improved the continuity from analysis planning to executable, interactive workflows compared with general-purpose LLM baselines. In real-data reanalysis, scIsoAgent recovered major findings from published long-read single-cell resources and extended a representative differential transcript usage event into a sequence-informed functional hypothesis. By linking full-length isoform sequences with model-inferred transcript properties, scIsoAgent connects observed isoform usage with potential sequence-level functional consequences. These results demonstrate that autonomous scientific agents can transform fragmented long-read single-cell analysis into coherent, reproducible workflows for isoform-resolved discovery and biological interpretation.

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

Trust-Aware Multi-Agent Traceability: Confidence-Calibrated Knowledge Graphs for Consistent Software Artifact Management

arXiv:2606.17203v1 Announce Type: cross Abstract: Multi-agent AI systems are increasingly used to automate software engineering tasks including requirements analysis, architecture design, test generation, and traceability linking. When these agents operate as a sequential pipeline over shared software artifacts, errors and low-confidence decisions made by upstream agents propagate to downstream stages, producing orphaned requirements, contradictory links, and compliance gaps that pose significant risks in safety-critical domains. We propose a trust-aware coordination framework where a shared knowledge graph serves as both centralized semantic memory and a coordination surface through which agents assess and build upon each other's contributions using calibrated confidence scores. Our approach introduces a two-stage traceability link prediction pipeline combining embedding-based retrieval with LLM-based multi-criteria analysis, a traceability seeding mechanism that enables comparison between derivation-time and validation-time confidence, and a consistency protocol governing pipeline interactions through confidence threshold gating, confidence divergence detection, and conflict resolution. We evaluate on an automotive software engineering case study measuring link prediction calibration, protocol effectiveness, threshold sensitivity, and the impact of traceability seeding. Ablation studies confirm that confidence calibration is essential for effective pipeline coordination.

13.
arXiv (CS.LG) 2026-06-18

Hierarchical Planning with Latent World Models

arXiv:2604.03208v2 Announce Type: replace Abstract: World models are a promising path to zero-shot embodied control through planning. However, existing world model planners struggle on long-horizon, multi-stage tasks: prediction errors compound and naive search is exponential in the planning horizon. Hierarchy mitigates both by decomposing tasks into shorter, tractable subproblems; yet prior hierarchical approaches either amortize control into task-specific policies (hierarchical RL) or assume low-dimensional states and known dynamics (classical hierarchical MPC). We present Hierarchical Planning with Latent World Models (HWM), an architecture and planning paradigm for hierarchical model predictive control (MPC) directly on visual world models trained solely via next-latent prediction. HWM learns world models at multiple temporal scales within a shared latent space, so predictions from the long-horizon model serve as subgoals for the short-horizon model via latent matching, without task-specific rewards, skill learning, or hierarchical policies. To keep long-horizon search tractable, HWM learns an action encoder that compresses primitive action chunks into latent macro-actions. On real-world Franka manipulation, HWM solves pick-and-place from a single goal image at 70% success vs. 0% for single-level planning. Across simulated push manipulation and maze navigation, HWM consistently improves performance on long-horizon tasks while requiring up to 3x less planning compute.

14.
arXiv (quant-ph) 2026-06-19

Distinguishing quantum processes with bounded coherent memory

arXiv:2606.19511v1 Announce Type: new Abstract: Distinguishing multi-time quantum processes is a fundamental task underlying the diagnosis, benchmarking, and learning of temporally correlated quantum dynamics. The standard benchmark for distinguishing two processes is the strategy-norm distance, which optimizes over arbitrary adaptive probing strategies but can require large coherent memory and time-dependent control. We introduce machines for autonomous distinction~($\mathsf{MAD}$s): probing strategies that apply the same quantum instrument at each time step, retain the full classical outcome record, and carry a coherent memory of dimension $d_A$. Optimizing over these strategies defines a memory-parametrized distinguishability measure, $d^{(N)}_{\mathsf{MAD}}(\mathbf{P}^N,\mathbf{Q}^N;d_A)$. We show that the resulting hierarchy is monotone in coherent memory and complete at finite times. Specifically, any admissible $N$-step probing strategy can be compiled into a single $\mathsf{MAD}$ with an internal counter and sufficiently large coherent memory, so the hierarchy saturates the strategy-norm benchmark. For recurrent processes generated by repeated system–environment interactions, we derive a single-step description that separates the generation of new distinguishing information from the propagation and decay of information generated at earlier times. Numerical results in a repeated-interaction model show that increasing coherent memory systematically improves the $\mathsf{MAD}$ success probability and closes the gap to the strategy-norm distance while remaining substantially more tractable to evaluate. $\mathsf{MAD}$ distinguishability therefore provides an operational and scalable framework for quantifying what can be learned about genuinely multi-time quantum processes with bounded coherent memory.

15.
arXiv (CS.LG) 2026-06-16

Pushing the Boundaries of Natural Reasoning: Interleaved Bonus from Formal-Logic Verification

arXiv:2601.22642v2 Announce Type: replace Abstract: Large Language Models (LLMs) show remarkable capabilities, yet their stochastic next-token prediction creates logical inconsistencies and reward hacking that formal symbolic systems avoid. To bridge this gap, we introduce a formal logic verification-guided framework that dynamically interleaves formal symbolic verification with the natural language generation process, providing real-time feedback to detect and rectify errors as they occur. Distinguished from previous neuro-symbolic methods limited by passive post-hoc validation, our approach actively penalizes intermediate fallacies during the reasoning chain. We operationalize this framework via a novel two-stage training pipeline that synergizes formal logic verification-guided supervised fine-tuning and policy optimization. Extensive evaluation on six benchmarks spanning mathematical, logical, and general reasoning demonstrates that our 7B and 14B models outperform state-of-the-art baselines by average margins of 10.4% and 14.2%, respectively. These results validate that formal verification can serve as a scalable mechanism to significantly push the performance boundaries of advanced LLM reasoning.

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

DeXposure-Claw: An Agentic System for DeFi Risk Supervision

Decentralized finance exposes supervisors to fast-moving, networked credit risks. General-purpose LLM agents fit this setting poorly: they over-read weak evidence and recommend high-stakes interventions, while existing evaluations offer no regulator-aligned way to measure the resulting false alarms. We introduce DeXposure-Claw, a forecast-grounded agentic supervision system that routes LLM decisions through structured evidence: (1) DeXposure-FM, a graph time-series foundation model, forecasts future exposure networks; (2) deterministic monitors and stress scenarios then turn those forecasts into typed alerts, attribution signals, and scenario evidence; and (3) data-health and confidence gates constrain escalation before DeXposure-Claw emits auditable supervisory tickets with rationales. We further develop DeXposure-Bench, a six-axis evaluation harness, whose decision axis scores tickets against a regulator-aligned absolute-loss ground truth and an explicit false-intervention rate. Experiments on five years of weekly real data fully support our system. Code is at https://github.com/EVIEHub/DeXposure-Claw.

17.
arXiv (CS.CV) 2026-06-18

Improving Visual Token Reduction via Rectifying Distortions for Efficient Multimodal LLM Inference

Recent advancements in Multimodal Large Language Models (MLLMs) have achieved remarkable success in vision-language tasks, yet the quadratic computational complexity arising from the vast number of visual tokens incurs significant memory and latency bottlenecks. While visual token reduction (VTR) strategies have been explored to mitigate this burden, existing methods overlook the positional and attentional consistency between the full and reduced sequences, resulting in a distorted representation. To this end, we propose RESTORE, a novel VTR framework that rectifies the positional and attentional distortions while maintaining efficiency. Specifically, we present a simple yet effective calibration method that restores lost visual attention by augmenting attention weights based on relative distances. We also introduce a distinctive anchor selection for token merging to mitigate information loss during feature averaging. Experimental results on multiple benchmarks demonstrate that our method consistently improves the accuracy of various reduction methods, achieving state-of-the-art performance while maintaining computational efficiency. Project page is available at https://cvlab.yonsei.ac.kr/projects/RESTORE

18.
arXiv (CS.LG) 2026-06-17

On the Memorization Behavior of LLMs in Generative Recommendation: Observations, Implications, and Training Strategies

arXiv:2606.17276v1 Announce Type: cross Abstract: Generative recommendation (GR) has emerged as a promising direction for recommender systems. Recently, large language models (LLMs) have been increasingly adopted for GR, as their rich pretrained knowledge is expected to help them generalize beyond common user behavior patterns that traditional memorization-oriented baselines can capture. However, existing LLM-based GR works largely ignore LLMs' well-known tendency to memorize, which, if present in LLMs fine-tuned for GR, would restrict their utilization of pretrained knowledge. In this work, we investigate this concern by examining one-hop memorization, where a model recommends items that are direct successors of items in the training data. We show that LLMs do this more than non-LLM-based GR models-in fact, the vast majority of their gains over GR baselines are actually on users whose target items can be predicted through one-hop memorization. We intuit that improving performance on the remaining users requires LLMs to learn richer item-item relations beyond one-hop transitions. To achieve this, we propose IIRG, a novel training strategy that teaches LLMs to capture: (1) collaborative relations derived from item co-occurrences across multiple hops in user sequences, and (2) semantic relations among items with similar themes, both of which can serve as useful recommendation signals. We show that IIRG significantly improves over LLMs trained solely with standard next-item prediction, with especially large gains for users whose test items are not covered by train-time one-hop transitions.

19.
arXiv (CS.CL) 2026-06-12

SkMTEB: Slovak Massive Text Embedding Benchmark and Model Adaptation

We introduce SkMTEB, the first comprehensive MTEB-style text embedding benchmark for Slovak, a low-resource West Slavic language, comprising 31 datasets across 7 task types – nearly 4$\times$ the depth of existing multilingual benchmark coverage for Slovak. Our evaluation of 31 embedding models reveals that large instruction-tuned multilingual models achieve the strongest performance, while existing Slovak-specific models trained for NLU tasks transfer poorly to embedding tasks. To address the need for efficient, locally-deployable Slovak embeddings, we develop \texttt{e5-sk-small} (45M parameters) and \texttt{e5-sk-large} (365M) by applying vocabulary trimming and fine-tuning to Multilingual E5 models. Despite size reductions of up to 62\%, our open-source models achieve competitive performance with proprietary APIs while remaining locally deployable for semantic search and retrieval-augmented generation (RAG). We release the benchmark, models, datasets, and code openly, hoping our approach offers a replicable path for other under-resourced languages.

20.
arXiv (math.PR) 2026-06-16

Sharp One-Dimensional Sub-Gaussian Comparison in Convex Order

作者:

arXiv:2604.26819v2 Announce Type: replace Abstract: We prove that any random variable $X$ whose moment generating function is point-wise upper bounded by that of $ G \sim \mathcal{N}(0,1) $ must be dominated by $ G/\mathbb{E}[|G|] $ in convex order, meaning $ \mathbb{E}[f(X)] \le \mathbb{E}[f(G/\mathbb{E}[|G|])] $ for all convex $f$. This is sharp as witnessed by $ X \sim \mathrm{Unif}(\{-1,1\}) $ and $ f(x) = |x| $.

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 (CS.CV) 2026-06-16

Deep Residual Injection for Full-Spectrum Forensic Signal Perception in Multimodal Large Language Models

Multimodal large language models (MLLMs) have been increasingly adopted in forensics for their robust semantic understanding. As AI-generated images become realistic, semantic-level inconsistencies alone are often insufficient for reliable detection. This motivates a critical question: whether MLLMs can achieve full-spectrum forensic signal perception, i.e., capturing low-level generator artifacts without sacrificing pre-trained semantic knowledge. We further perform a layer-wise analysis of forensic signal perception in MLLMs, showing that semantic information is primarily formed in the early-to-middle layers, whereas direct fine-tuning for artifact learning disrupts these semantic representations. Based on this insight, we propose Deep Visual Residual MLLM (Deep-VRM) to preserve early semantic processing while injecting artifact-specific visual signals as a residual path into an intermediate layer, where they are fused with semantic token representations and propagated through subsequent trainable layers. This enables later layers to jointly model semantic reasoning and signal-level forensic cues, and surprisingly, the model learns to adaptively leverage different levels of forensic signals depending on the input, achieving robust and generalizable detection performance. Extensive experiments show that our method achieves state-of-the-art across most benchmarks. The code and data are available at https://github.com/KQL11/Deep-VRM.

23.
arXiv (quant-ph) 2026-06-16

Initiation of Superradiance from Different Collective Spin States

arXiv:2606.14949v1 Announce Type: new Abstract: Superradiance is an extensive cooperative spontaneous emission phenomenon. Some atomic collective spin states exhibit it. However, distinct initial states differ in their decay dynamics. Dicke states with different numbers of excitations have their peak emission intensity shifted in time depending on the number of excitations. Emission intensity in atomic coherent states depends on their polarization. Some specific states undergo a squeezing controlled crossover, making the emission character dependent on the amount of squeezing in the state. We present detailed results on the superradiant dynamics of a representative selection of Dicke states. For large N, we are able to predict fairly accurately the pulse profile in each case using the mean field approximation, an approach based on the Fokker Planck Equation. We also present results on the intensity correlation function of the emission.

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

Toward Calibrated Mixture-of-Experts Under Distribution Shift

arXiv:2606.20544v1 Announce Type: new Abstract: Calibration aligns a model's predictive uncertainty with the frequencies of its empirical outcomes and is important for understanding and trusting reported probabilities. Recent work shows that enforcing calibration at the level of individual predictors can improve ensemble accuracy and calibration, with mixture-of-experts (MoE) models showing strong empirical improvements in particular; however, the conditions under which calibration helps MoE are not well understood. In this work, we study how MoE models behave under distribution shift, focusing on how routing mechanisms interact with expert-level calibration. We show that expert calibration is sufficient to ensure calibration of the overall model under a broad class of distribution shifts in hard-routed models, but is insufficient for calibrating soft-routed models. To address this, we propose an adversarial reweighting that penalizes calibration errors of the routed aggregate under distribution shift, and we demonstrate that it improves the accuracy-calibration tradeoff both on average and on difficult subsets of the data, across model classes, prediction tasks, and distribution shifts.

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

Beyond Dark Knowledge: Mixup-Based Distillation for Reliable Predictions

Knowledge Distillation (KD) and mixup have proven effective at inducing smoothness in class boundaries; KD captures inherent class relationships in probability distributions, and mixup enforces them through convex combinations of inputs. Their interaction, however, remains poorly understood, particularly when mixup is applied only during student training. In this setting, the teacher is queried on inputs drawn from a vicinal distribution it never saw during training, a controlled mismatch whose effect on knowledge transfer has not been characterised. We show that this mismatch causes the teacher's supervisory signal to be dominated by distributional confusion rather than inter-class structure. Despite it, the student does not merely imitate the teacher: it independently acquires greater linearity in the vicinal region, a structural property that the teacher lacks, and goes beyond dark-knowledge transfer. KD with mixup consistently improves student accuracy and reduces overconfidence by an order of magnitude relative to the baseline, across CIFAR and ImageNet with varying-capacity teachers. Crucially, calibration propagates from teacher to student independently of accuracy transfer, and temperature scaling governs a measurable accuracy-calibration trade-off that becomes more pronounced under vicinal training. These results reframe mixup distillation not as a degraded version of standard KD, but as a richer transfer channel that simultaneously shapes discriminative performance, uncertainty estimation, and representational geometry.