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

PASQA: Pitch-Accent-Focused Speech Quality Assessment Model Trained on Synthetic Speech with Accent Errors

Existing mean opinion score (MOS) prediction models typically predict utterance-level naturalness MOS and can be insensitive to localized pitch-accent errors. We propose Pitch-Accent-focused Speech Quality Assessment (PASQA), which explicitly targets pitch-accent correctness. To train our model, we construct a controlled Japanese accent-error dataset by changing accent patterns using an accent-controllable text-to-speech system, and compute a pseudo accent-quality score from the accent-error rate. PASQA builds on self-supervised representations and employs mora-conditioned fusion, ranking loss, an auxiliary accent-error localization task, and speaker-invariant training. Experiments show that conventional models fail to preserve the ordering by accent-error severity, whereas PASQA achieves high ordering accuracy on both seen and unseen speakers. Further, PASQA shows stronger agreement with human accent-correctness judgments. The code is available at https://github.com/lycorp-jp/PASQA.

02.
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

03.
arXiv (CS.AI) 2026-06-19

MetaResearcher: Scaling Deep Research via Self-Reflective Reinforcement Learning in Adversarial Virtual Environments

arXiv:2606.19893v1 Announce Type: new Abstract: Deep research agents have demonstrated remarkable capabilities in autonomous information gathering and synthesis, yet their training remains constrained by the static nature of simulated environments, the limits of fact-retrieval-only task designs, and the inefficiency of outcome-based reinforcement learning. In this work, we propose MetaResearcher, a novel framework that scales deep research agent training across four synergistic dimensions. First, we introduce an Evolving Virtual World that injects temporal dynamics and adversarial misinformation into the training environment, forcing agents to develop source credibility assessment and temporal conflict resolution skills. Second, we design Discovery-Oriented Tasks – including hypothesis generation and contradiction resolution – that transcend simple fact retrieval and push agents toward genuine research behaviors. Third, we propose a Self-Reflective Meta-Reward mechanism within the GRPO framework that jointly optimizes for answer correctness, search path efficiency, reflection depth, and tool call diversity, directly addressing the repetitive action loop problem observed in prior work. Fourth, we introduce a Heterogeneous Multi-Agent Swarm architecture comprising specialized Scout, Filter, and Synthesizer models that learn collaborative research strategies through coordinated reinforcement learning. Built upon the LiteResearcher infrastructure, MetaResearcher requires zero marginal API cost for training while targeting substantial improvements in both benchmark performance (GAIA, Xbench-DS) and epistemic robustness under adversarial conditions. We present the complete framework design, training methodology, and planned experimental validation.

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

VibeThinker-3B: Exploring the Frontier of Verifiable Reasoning in Small Language Models

This technical report introduces VibeThinker-3B, a compact dense model with 3B parameters developed to investigate how far verifiable reasoning can be pushed within a strictly small-model regime. Building upon the Spectrum-to-Signal post-training paradigm, we systematically enhance the model through an optimized pipeline that includes curriculum-based supervised fine-tuning, multi-domain reinforcement learning, and offline self-distillation. Experimental evaluations demonstrate that VibeThinker-3B achieves frontier-level performance on highly demanding verifiable tasks. Specifically, it attains a score of 94.3 on AIME26 (improving to 97.1 with claim-level test-time scaling), an 80.2 Pass@1 on LiveCodeBench v6, and exhibits strong out-of-distribution generalization with a 96.1\% acceptance rate on recent unseen LeetCode contests. This effectively places it in the performance band of first-tier reasoning systems, matching or exceeding flagship models that are orders of magnitude larger, such as DeepSeek V3.2, GLM-5, and Gemini 3 Pro. Furthermore, a score of 93.4 on IFEval confirms that this extreme reasoning enhancement does not compromise strict instruction controllability. Extending our previous 1.5B work, these findings motivate the Parametric Compression-Coverage Hypothesis, which views verifiable reasoning as compressible into compact reasoning cores, while open-domain knowledge and general-purpose competence require broad parameter coverage over facts, concepts, and long-tail scenarios. This perspective suggests that compact models are not merely deployment-efficient substitutes, but a complementary path toward frontier-level performance in parameter-dense capability regimes.

05.
arXiv (CS.CV) 2026-06-12

OR-Action: Multi-Role Video Understanding with Fine-Grained Actions

Fine-grained understanding of operating room (OR) activity could enable workflow-aware assistance, yet remains difficult due to clutter, occlusions, and limited sensing. The prevailing approach to model this environment is scene graphs as an interpretable representation of OR interactions. Converting their frame-wise relational predictions into temporally extended, fine-grained actions however, is challenging without explicit temporal modeling. To enable a principled temporal evaluation of current OR understanding methods, we introduce the first action-centric benchmark built on a publicly available ego-exocentric OR dataset by defining a fine-grained, multi-role action taxonomy and generating dense action segments via distillation from ground-truth scene graph state changes. Experiments on this benchmark show that current scene graph prediction methods struggle to model temporal structure, even when adding explicit modeling through Graph Neural Networks. We therefore introduce a vision-only temporal model that outperforms graph-based methods significantly when using all available egocentric video as input. Building on this model we also introduce a novel multi- to single-view feature alignment strategy that improves single-view performance on multi-role action recognition, mitigating the need for extensive egocentric video capture. Benchmark and code will be released upon acceptance.

06.
medRxiv (Medicine) 2026-06-22

Characteristics and Outcomes of Gene-Elusive Dilated Cardiomyopathy

Background and Aims Genetic testing in dilated cardiomyopathy (DCM) guides risk stratification and family screening. Likely pathogenic or pathogenic (LP/P) variants are identified in approximately one-third of patients, leaving many without a genetic diagnosis. Cohort studies suggest that "gene-elusive" patients have a lower risk of adverse events. This study aims to better characterise this group and identify factors associated with adverse outcomes. Methods Consecutive and unrelated DCM patients undergoing genetic testing and returning no LP/P variants were retrospectively recruited and compared to two control cohorts of DCM patients carrying LP/P variants in LMNA and TTN for a primary composite endpoint of end-stage heart failure (ESHF) or malignant ventricular arrhythmia (MVA). Results Among patients without prior MVA, the composite endpoint occurred in 36/423 (8.5%) gene-elusive, 14/39 (35.9%) LMNA and 11/100 (11%) TTN cardiomyopathy patients (log-rank p

07.
arXiv (quant-ph) 2026-06-16

Detecting basis-dependent hardware errors through spatio-temporal quantum steering

arXiv:2606.16451v1 Announce Type: new Abstract: Spatio-temporal quantum steering provides a framework for benchmarking the nonclassicality of general quantum state transfer processes. A central diagnostic is the no-signaling-in-time (NSIT) condition, whose violation can indicate basis-dependent hardware errors. However, finite measurement statistics may also yield apparent violations, thereby obscuring the detection of basis-dependent hardware errors. To address this, we construct a statistical hypothesis test under the null hypothesis that NSIT violations arise solely from statistical fluctuations. Combining the statistical properties of NSIT violation under the null hypothesis with Chebyshev's inequality, we obtain a distribution-free upper bound on the $p$-value without parametric assumptions. We apply this method to two examples. For a single-qubit state-transfer experiment on a superconducting processor, we observe several instances that the NSIT violation is observed and the null hypothesis is simultaneously rejected by a small $p$-value, providing statistical evidence of basis-dependent hardware errors. For a seven-qubit Hayden-Preskill teleportation protocol on IonQ devices, the null hypothesis is also rejected even when the average fidelity exceeds the classical threshold, while the associated nonclassicality measure vanishes. Our results highlight the necessity of statistical hypothesis testing for detecting basis-dependent errors in near-term quantum devices.

08.
arXiv (CS.CV) 2026-06-11

SceneMiner: Identity-Preserving Multi-Task Fine-Tuning for Unified BEV Scene Mining

Mining hard, safety-critical scenes from driving logs is bottlenecked by the absence of difficulty labels, and no single proxy, collision risk, trajectory ambiguity, or semantic rarity suffices to find such scenes on its own. We present SceneMiner, a unified, camera-only bird's-eye-view pipeline that emits complementary mining signals from a frozen vision-language backbone in a single forward pass, with no LiDAR or radar: a retrieval embedding for text-prompted scenario search, a multi-label scene-tag distribution, and a continuous physics-based risk score (a motion forecast is a byproduct, not a contribution). Building such a multi-head model exposes our central finding, a failure mode we term cross-task interference: adding or upgrading one head shifts a shared activation stream and degrades weight-frozen sibling heads, so freezing parameters alone is insufficient. Our contribution, identity-preserving multi-task fine-tuning, removes this interference by zero-initializing every new sub-module and freezing every parameter that feeds the shared stream. The mining heads are thereby preserved bit-identically while training only ~102k parameters. The tagging head reaches mAP 0.4614 (micro-F1 0.5557) on 20 scene tags by pooling each scene into 32 visual tokens, and the embedding head supports text-prompted retrieval, validated qualitatively. Code is available at: https://anonymous.4open.science/r/sceneminer_anonymous-64E5

09.
bioRxiv (Bioinfo) 2026-06-20

SAbDab2: The structural antibody database in the age of machine learning

The Structural Antibody Database (SAbDab) is a publicly available repository of experimentally determined antibody structures, first released in 2013. Explicit support for single-domain antibodies was added in 2021, with SAbDab-nano. Recently, increasing interest in antibodies has led to a proliferation of novel antibody formats, while simultaneous advances in machine learning have increased demand for standardised, high-quality structure data. Here, we present SAbDab2, re-engineered for the machine-learning age. It introduces support for a variety of new formats, and makes it easy to retrieve and compare all known structures of a given antibody. In addition, SAbDab2 provides ready access to ML-grade structures of antibody and antibody–antigen-complexes, with standardised, versioned train/test splits. These will be updated every six months going forward, and are available at https://zenodo.org/records/20083995. SAbDab2 itself is updated weekly and is freely available at https://sabdab2.opig.stats.ox.ac.uk.

10.
arXiv (quant-ph) 2026-06-17

SPICE-Q and Large-Scale Quantum Chip Production

arXiv:2606.17907v1 Announce Type: new Abstract: We propose SPICE-Q, a SPICE-inspired design-technology co-optimization framework for superconducting quantum processors. Rather than replacing tools such as HFSS, Qiskit Metal, pyEPR, SQcircuit, SQuADDS, scqubits, or QuTiP, SPICE-Q aims to connect them through a unified, traceable data chain spanning process rules, layout, electromagnetic simulation, energy-participation-ratio and circuit quantization, Hamiltonian extraction, noise analysis, cryogenic test, and manufacturing feedback. The central mapping is from process and PDK constraints to layout geometry, electromagnetic modes, equivalent circuit parameters, effective Hamiltonians, and finally metrics such as frequency, coupling, anharmonicity, decoherence, readout performance, and yield. This flow must capture Josephson-junction variability, transmon frequency allocation, resonator and Purcell constraints, coupler crosstalk, microwave routing, 3D interconnects, material/interface loss, package modes, and wafer-scale process statistics. By introducing standardized model interfaces, statistical parameter models, model cards, version governance, and closed-loop calibration from cryogenic and fabrication data, SPICE-Q frames superconducting quantum-chip design as an engineering workflow rather than a collection of isolated simulations. We argue that scalable and fault-tolerant quantum processors will require such a continuous model chain from device physics and electromagnetic fields to quantum dynamics, noise, manufacturability, and system-level yield.

11.
arXiv (quant-ph) 2026-06-19

Quantum Dynamics from Lax Pair Theory: A Reconstruction from Spectrum Preservation

arXiv:2606.19664v1 Announce Type: new Abstract: We reconstruct unitary quantum dynamics from a minimal axiomatic foundation built on Hilbert-space observables and isospectral evolution. The only dynamical assumption is that physical time evolution is a continuous one-parameter flow of Hermitian observables that preserves their spectra, i.e. the possible outcomes of measurement. We show that this assumption is already sufficient to force the Lax form of quantum dynamics. The Heisenberg equation, the time-dependent and time-independent Schrödinger equations, conservation laws, and good quantum numbers then follow as theorems rather than postulates. In this formulation, Lax pair theory supplies the missing dynamical bridge between the measurement structure of a Hilbert space and standard quantum evolution: the Hamiltonian is not assumed, but emerges as the generator required for an isospectral observable flow.

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

SciR: A Controllable Benchmark for Scientific Reasoning in LLMs

arXiv:2606.13020v1 Announce Type: new Abstract: Three paradigmatic forms of inference recur across scientific reasoning: deduction, induction, and causal abduction. Reliably evaluating LLMs on these in scientific settings is currently out of reach: scientific benchmarks built on human annotations are costly and lack mechanistic ground truth, while synthetic logical-reasoning benchmarks do not resemble real scientific documents. We introduce SciR, a benchmark that combines multi-paradigm reasoning with controllable scientific rendering, anchored on three paradigmatic scientific problems. Tasks are generated from formal objects (deduction tree, inductive rule hypothesis, causal graph) to guarantee verifiable answers, then rendered into multi-document scientific discourse via per-track domain-tuned genres. The construction lets us independently vary two difficulty axes: how hard it is to extract the key information needed for inference, and how hard the principled inference itself is. We test six models. Both axes hurt every model, and their effects compound. The rendering even hurts neurosymbolic pipelines, which hand inference to a verified solver. The two axes yield a per-model extraction-vs-inference profile: for instance, reasoning models like deepseek-r1 mostly surpass non-reasoning instruct models on the inference axis. To our knowledge, SciR is the first multi-paradigm scientific-reasoning benchmark with parametric control on both extraction and inference difficulty.

13.
arXiv (CS.CV) 2026-06-16

CT-VDETR: Semi-supervised 3D Trauma Detection in Computed Tomography (CT) scans using Dense Vertex Relative Position Encoding

Accurate detection and localization of traumatic injuries in abdominal CT remain challenging because voxel-level annotations are limited and expensive to obtain. We present a label-efficient framework for 3D abdominal trauma detection that combines self-supervised pretraining with semi-supervised transformer-based detection. First, we use Masked Image Modeling (MIM) on 1098 CT volumes to pretrain a 3D U-Net encoder for anatomical representation learning. Next, we adapt V-DETR to dense volumetric CT through a feature adapter that converts the encoder feature grid into a compact token sequence for transformer decoding. The pretrained encoder is then integrated with V-DETR and 3D Vertex Relative Position Encoding (3D V-RPE) to improve the localization of irregularly shaped injuries. Finally, semi-supervised teacher-student consistency regularization leverages 2,000 additional unlabeled volumes during detector training. To the best of our knowledge, this is the first application of a 3D DETR-style detector to the RSNA abdominal trauma detection task. On this benchmark, the proposed method achieves 31.33% test mAP@0.50 using only 78 labeled training volumes, corresponding to a 1.53x improvement over supervised-only training. These results show that combining medical-domain pretraining with semi-supervised learning is an effective strategy for label-scarce 3D medical detection.

14.
arXiv (CS.LG) 2026-06-15

Testing For Distribution Shifts with Conditional Conformal Test Martingales

arXiv:2602.13848v2 Announce Type: replace Abstract: We propose a sequential test for detecting arbitrary distribution shifts that allows conformal test martingales (CTMs) to work under a fixed, reference-conditional setting. Existing CTM detectors construct test martingales by continually growing a reference set with each incoming sample, using it to assess how atypical the new sample is relative to past observations. While this design yields anytime-valid type-I error control, it suffers from test-time contamination: after a change, post-shift observations enter the reference set and dilute the evidence for distribution shift, increasing detection delay and reducing power. In contrast, our method avoids contamination by design by comparing each new sample to a fixed null reference dataset. Our main technical contribution is a robust martingale construction that remains valid conditional on the null reference data, achieved by explicitly accounting for the estimation error in the reference distribution induced by the finite reference set. This yields anytime-valid type-I error control together with guarantees of asymptotic power one and bounded expected detection delay. Empirically, our method detects shifts faster than standard CTMs, providing a powerful and reliable distribution-shift detector.

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

The Coin Flip Judge? Reliability and Bias in LLM-as-a-Judge Evaluation

Authors:

LLM-as-a-Judge is now widely used to rank model outputs, train reward models, and populate public leaderboards, but its run-to-run reliability remains under-characterized. We study repeated identical evaluations on 29 tasks spanning 10 categories using two OpenAI judge models (GPT-4o-mini and GPT-4.1-mini), with 50 pairwise trials and 50 pointwise trials per question, supplemented by temperature and prompt-sensitivity ablations. Across judges, pairwise preferences flip on average 13.6% of the time, with 28% of questions exceeding a 20% flip rate and one question reaching 56%. GPT-4o-mini also exhibits a significant first-position bias (72% A-majority, p = 0.024). At the same time, mean pointwise score gaps are small (0.19–0.36 on a 10-point scale) and not statistically significant in aggregate, producing a pairwise–pointwise gap: judges frequently choose a winner even when their own scalar scores provide little evidence of a meaningful quality difference. Beyond within-judge instability, cross-judge agreement is only 76% ($\kappa = 0.51$), semantically equivalent prompt templates change majority outcomes in 25% of tested cases, and deterministic decoding reduces but does not eliminate inconsistency. A reliability curve analysis shows that, in our dataset, 11 repeated trials are needed for a majority vote to recover the 50-trial reference verdict with 95% probability on average, rising to 15 for high-variance questions. These findings suggest that single-trial LLM judging is often too noisy for high-stakes evaluation, and that multi-trial aggregation, position randomization, and explicit uncertainty reporting should be standard practice. Because both judges are from a single provider, cross-provider replication remains an important next step.

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

Can Post-Training Turn LLMs into Good Medical Coders? An Empirical Study of Generative ICD Coding

Automated International Classification of Diseases (ICD) coding is a core medical-coding task for billing, epidemiology, and clinical decision support. Generative large language models (LLMs) are often reported as weak medical coders, but this finding mainly comes from inference-time settings such as prompting, retrieval, reranking, or tool use, leaving the role of task-specific post-training underexplored. We present a controlled empirical study of post-training for generative ICD coding, comparing discriminative baselines with LLM coders across prompting, supervised fine-tuning, and reinforcement learning under a common protocol and metric set. To our knowledge, this is the first study to evaluate RL-based post-training for generative LLM coders in ICD coding. We further introduce PHI, a diagnostic curriculum that extends GRPO to refine missed-code cases. Our results show that prompting-only evaluation substantially underestimates the potential of LLMs for ICD coding. SFT provides the main capability jump, GRPO further improves code-set prediction beyond SFT, and PHI provides targeted gains on macro-level performance. These findings suggest that the main bottleneck is not the generative formulation alone, but how the model is adapted and optimized for full-taxonomy recall. We release our code, data splits, and checkpoints at https://github.com/AlexandreWANG915/LLM4ICD.

17.
arXiv (CS.LG) 2026-06-19

Optimal Ansatz-free Hamiltonian Learning In Situ

arXiv:2606.19486v1 Announce Type: cross Abstract: Characterizing the features of a Hamiltonian that governs a quantum system serves as a fundamental subroutine of quantum device calibration, signal sensing, and error correction. Recent works proposed protocols have achieved the optimal Heisenberg-limited scaling learning ansatz-free Hamiltonians from their real-time evolutions without fully specifying interaction structures. However, these protocols rely on both deep circuits with interleaving probes and control, and extremely short time resolution, making them difficult to implement on near- and intermediate-term in situ quantum experiments. In this work, we propose a computationally efficient, control-free, and ancilla-free algorithm that uses only Pauli product state preparation and measurement, and learns an ansatz-free Hamiltonian $H$ with $||H||\leq\Lambda$ in total evolution time of $\Theta(\frac{\Lambda}{\epsilon^2}\log(\frac{\Lambda}{\epsilon}))$. The evolution time cost of our algorithm is optimal for any control-free protocols as we further prove a lower bound of $\Omega(\frac{\Lambda}{\epsilon^2}\log(\frac{\Lambda}{\epsilon}))$. Technically, our method introduces a randomized-sampling framework that combines band-limited kernel-based time sampling with a displacement sieve for Hamiltonian structure learning. The characteristic probe time resolution depends only on $\Lambda$ instead of $\varepsilon$, which makes our protocol especially appealing in the high-precision regime for sensing and calibration applications. We also show that the algorithm maintains the same asymptotic total evolution time in the presence of state-preparation-and-measurement (SPAM) noise when the Hamiltonian is local after calibration. Our results demonstrate the fundamental cost of experimentally friendly Hamiltonian learning and provide a practical route to rigorous in situ characterization of near-term quantum platforms.

18.
arXiv (CS.CV) 2026-06-15

Explaining RhythmFormer: A Systematic XAI Analysis of Periodic Sparse Attention for Remote Photoplethysmography

Remote photoplethysmography (rPPG) transformers achieve low heart-rate error on benchmarks, yet their decisions remain opaque–a growing concern as rPPG moves toward clinical heart rate estimation. Existing rPPG XAI is dominated by qualitative heatmap inspection without quantitative faithfulness metrics or physiology-grounded validation, leaving a gap between visual plausibility and auditable evidence. We address this gap. First, we adapt four attribution methods (raw attention, rollout, flow, Beyond Intuition) to RhythmFormer's bi-level routing attention with top-$k$ selection. Second, we introduce a skin coverage metric quantifying how much attribution mass falls on skin regions. Third, we adapt the SaCo faithfulness coefficient from its original classification setting to rPPG regression by using the MAE between original and perturbed predicted rPPG waveforms as the perturbation impact. Applying these tools, we quantify a multi-hop leakage effect under sparse top-$k$ routing: attention rollout and flow almost completely restores the connections that individual refined-attention layers explicitly set to zero. Beyond Intuition mitigates this via its value-projection-weighted rollout and gradient-supported mask, attaining the highest median refined skin coverage ($0.83$ vs. $0.57$ for vanilla rollout) and faithfulness ($F=0.92$) among the evaluated methods on UBFC-rPPG. Validation across diverse datasets and model variants is needed. A case study on a low-SaCo outlier further shows all four methods recovering consistently once an artefactual region is replaced, suggesting consistent SaCo behavior across attribution families in this illustrative case. Together, these metrics move XAI for rPPG toward auditable numerical evidence about spatial alignment and perturbation faithfulness, i.e. trustworthy rPPG XAI.

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

MotionVLA: Vision-Language-Action Model for Humanoid Motion

Generating realistic humanoid motion from scene images and text involves both low-frequency pose semantics and high-frequency physical dynamics. However, many existing methods tokenize motion with a single shared codebook, forcing heterogeneous motion signals into the same quantization space. Our frequency-domain analysis of human motion data reveals a clear mismatch between single-codebook quantization and motion statistics: five DCT coefficients capture 93% of joint-position energy but only 37% of joint-velocity energy, which can bias quantization toward pose statistics and under-represent high-frequency velocity components. A second challenge lies in adapting a standard autoregressive model to effectively model high-frequency physical signals in motion sequences. Therefore, we propose DSFT, a dual-stream frequency tokenizer that separates motion into Base and physical streams and compresses them independently with DCT truncation and BPE. Furthermore, we present MotionVLA, a Qwen3.5-based model that arranges Base and physical tokens in a unified sequence, where Phys tokens are predicted after Base tokens. Experiments on HumanML3D and MBench show that, despite using a lightweight 2B backbone, MotionVLA reduces the Diversity gap to real data by over 50% on HumanML3D and improves Motion-Condition Consistency by 3.8% on MBench, supporting frequency-aware dual-stream decoupling as an effective formulation for autoregressive motion generation. Code: https://github.com/AIGeeksGroup/MotionVLA. Website: https://aigeeksgroup.github.io/MotionVLA.

20.
bioRxiv (Bioinfo) 2026-06-11

OMIO: A policy-driven Python library for reproducible microscopy image I/O

Modern fluorescence and multiphoton microscopy workflows operate within a heterogeneous ecosystem of file formats, partially overlapping metadata standards, and reader-specific conventions. In practice, this frequently leads to silent axis misinterpretations, loss or corruption of physical voxel size information, and laboratory-specific glue code that is fragile, poorly documented, and difficult to reproduce. OMIO, short for Open Microscopy Image I/O, addresses these issues by providing a lightweight, policy-driven image I/O layer for Python that enforces a canonical, OME-compatible data representation at the API boundary. The central contribution of OMIO is the explicit separation of low-level format access from semantic normalization. Existing reader libraries are used as interchangeable backends for extracting pixel data and available metadata, while OMIO enforces axis conventions, metadata interpretation, and fallback decisions in a centralized and auditable policy layer. This design allows heterogeneous microscopy inputs to be converted into a stable representation without propagating backend-specific assumptions into downstream analysis code. The core design principles of OMIO include canonical axis semantics (TZCYX), robust metadata normalization with explicit and auditable fallbacks, memory-aware operation via optional Zarr-based backends, and workflow-level semantics that extend beyond individual files to folder stacks and BIDS-like project structures. This architecture allows OMIO to orchestrate existing reader libraries into a coherent and reproducible I/O pipeline without replacing or duplicating their functionality. OMIO is implemented as an open-source and community-oriented system in which support for additional file formats and metadata conventions can be added incrementally through modular reader backends. By encouraging the contribution of example datasets, backend extensions, and feature requests, OMIO is designed to evolve alongside emerging acquisition systems while preserving strict semantic guarantees at the interface level. The resulting standardized OME-TIFF outputs are immediately suitable for downstream quantitative analysis and interactive inspection in scientific Python workflows, including workflows based on ImageJ and Napari.

21.
arXiv (CS.CV) 2026-06-16

DriveReward: A Comprehensive Dataset and Generative Vision-Language Reward Model for Autonomous Driving

Reward models play a pivotal role in reinforcement learning (RL) and multi-modal trajectory selection for autonomous driving. However, acquiring such rewards typically relies on hand-crafted rule-based objectives or perception ground truth, which hinders generalization for data-scaling. While Vision-Language Models (VLMs) have demonstrated feasibility as reward models in other domains, their effectiveness in driving tasks remains underexplored. In this work, we bridge this gap by (1) introducing DriveReward, a reasoning trajectory evaluation dataset rigorously labeled via temporally-grounded visual guidance, and augmented with counterfactual driving behaviors., (2) alongside a specialized Vision-Language Reward Model. To address the scarcity of failure cases in conventional datasets, we propose a counterfactual data annotation scheme to construct cases encompassing diverse driving styles and erroneous behaviors. Evaluations on our proposed benchmark reveal that even leading open-source and proprietary VLMs fail to excel across all tasks, highlighting significant room for improvement in existing models. Building on these findings, we subsequently tailor a specialized 1B reward model that outperforms larger VLMs on task-specific reward alignment. Finally, we validate our reward model's effectiveness by integrating it into RL finetuning and multi-modal trajectory scoring across multiple baselines, achieving performance comparable to rule-based reward calculations in both open-loop and closed-loop evaluation.

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

PatchWorld: Gradient-Free Optimization of Executable World Models

Text-agent environments are typically modeled as partially observable Markov decision processes (POMDPs), assuming that the simulator's latent state and transition dynamics are hidden from the agent. Yet little work has examined whether executable code can be induced to serve as a world model for prediction and planning under partial observability. We introduce PatchWorld, a gradient-free framework that turns offline trajectories into executable Python world models through counterexample-guided code repair. Instead of predicting the next observation with a black-box model, PatchWorld induces symbolic belief-state programs whose action updates can be inspected, replayed, and locally patched. Across seven AgentGym environments, PatchWorld-Simple achieves the highest code-based planning score among evaluated methods, reaching 76.4\% macro success in live one-step lookahead while invoking no LLM calls inside the world-model prediction module itself. We further find that a human-specified residual-memory bias improves surface observation fidelity but weakens decision utility. This exposes a tradeoff in executable world models, since improving observation fidelity can come at the expense of action-discriminative dynamics, and vice versa. Code is available at https://github.com/HKBU-KnowComp/PatchWorld.

23.
bioRxiv (Bioinfo) 2026-06-21

GENATATORs: ab initio Gene Annotation With DNA Language Models

Inference of gene structure and location from genome sequences - known as de novo gene annotation - is a fundamental task in biological research. However, sequence grammar encoding gene structure is complex and poorly understood, often requiring costly transcriptomic data for accurate gene annotation. In this work, we benchmark current solutions and develop new methods of gene annotation. We show that pretrained DNA language model (DNA LM) embeddings do not capture the features necessary for precise gene segmentation, and that task-specific fine-tuning remains essential. We comprehensively evaluate the impact of model architecture, training strategy, receptive field size, dataset composition, and data augmentations on gene segmentation performance. We revisit standard evaluation protocols, showing that commonly used per-token and per-sequence metrics fail to capture the challenges of real-world gene annotation. We introduce and theoretically justify new biologically grounded metrics, along with benchmarking datasets that better capture annotation quality. We show that fine-tuned DNA LMs outperform existing annotation tools, generalizing across species separated by hundreds of millions of years from those seen during training, and providing segmentation of previously intractable non-coding transcripts and untranslated regions of protein-coding genes. Our results thus provide a foundation for new biological applications centered on accurate gene annotation.

24.
arXiv (CS.AI) 2026-06-15

Mood-Aware Music Recommendation: Integrating User Affective Signals into Ranking Systems

arXiv:2606.13858v1 Announce Type: cross Abstract: Recommendation systems are essential in modern music streaming platforms due to the vast amount of available content. While collaborative filtering is widely used to suggest items based on the preferences of others with similar patterns, it performs poorly in domains where user-item interactions are sparse, such as music. Content-based filtering is an alternative approach that examines the qualities of the items themselves. Genre, instrumentation, and lyrics have been explored; however, relatively little attention has been given to emotion recognition. Since a user's emotional state strongly influences their music choice, incorporating mood signals offers a promising direction for personalization. In this work, we propose a mood-conditioned ranking framework that integrates user affective signals into the recommendation process via softmax-based sampling in the energy-valence space. We evaluate the approach via single-blind experiments in which participants compare recommendations from the proposed system against a baseline. The results indicate improved perceived recommendation quality, providing preliminary evidence for the effectiveness of incorporating mood-based inputs into music recommendations.

25.
arXiv (CS.CV) 2026-06-16

Understanding Cross-Modal Contributions in Continual Vision-Language Models: A Theoretical Perspective

Continual vision-language models are commonly addressed through sequential fine-tuning; however, although this paradigm enables adaptation to new environments (tasks), it inherently emphasizes the contribution of previously learned environments (tasks) at the expense of the stability required to preserve previously acquired knowledge. While existing approaches have adequately studied continual learning and catastrophic forgetting in vision-language models (VLMs), the theoretical understanding of modality-specific contributions across a sequence of environments remains largely unexplored. In this paper, we present a new theoretical perspective to understand the cross-modal (vision-language) contributions to consecutive environments. We empirically evaluate our theoretical findings on large VLMs and demonstrate their effectiveness in capturing environment-level cross-modal contributions. Our analysis provides deeper insights into continual VLMs, highlighting their contribution robustness to varying task orders and inter-task similarities, and their improved generalization performance.