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01.

Nature (Science) 2026-06-10 DOI: HASH:a8b3e22c4e143693890f90f12cc4cd1c

Confirmation that bryozoan animals were present during the Cambrian explosion

作者: 未知作者

Bryozoans are marine invertebrates that live in colonies and have long been considered absent from the Cambrian explosion — a rapid evolutionary event that began around 538 million years ago. Newly discovered fossils from the Cambrian period reveal that the bryozoan phylum had already diversified by this time. Fossils of two forms of bryozoans show evidence of soft tissue still preserved inside their mineralized skeletons.

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02.

arXiv (CS.CV) 2026-06-19 DOI: arXiv:2606.19874

MMD-SLAM: Structure-Enhanced Multi-Meta Gaussian Distribution-Guided Visual SLAM

作者:

Fan Zhu↗Ziyu Chen↗Peichen Liu↗Yifan Zhao↗Zhisong Xu↗Hui Zhu↗Hongxing Zhou↗Sixun Liu↗Chunmao Jiang↗

3D Gaussian Splatting (3DGS) has significantly boosted novel view synthesis and high-fidelity scene reconstruction, expanding the potential of 3DGS-based Visual Simultaneous Localization and Mapping (SLAM) methods. However, most existing systems fail to fully exploit the underlying structural information, which limits rendering quality and often leads to inconsistent maps. To address these limitations, we propose MMD-SLAM, a structure-enhanced Visual SLAM framework that leverages the Atlanta World (AW) assumption to guide a Multi-Meta Gaussian representation for photorealistic mapping. First, we introduce a point-line fusion strategy for pose optimization, where 3D line segments are incorporated to improve tracking robustness and provide additional constraints for mapping. Second, we design a Multi-Meta Gaussian representation with dominant directions, explicitly encoding structural priors from the AW hypothesis. Finally, we propose a Gaussian evolution strategy that adapts to scene geometry and incorporates structural cues into global optimization. Extensive experiments demonstrate that these innovations enable MMD-SLAM to achieve state-of-the-art performance in both tracking accuracy and mapping quality. e.g., our method achieves a 48.56% reduction in ATE RMSE on ScanNet and a 5.71% improvement in PSNR on Replica, compared with MonoGS.

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03.

arXiv (CS.LG) 2026-06-12 DOI: arXiv:2509.07150

PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design

作者:

Andy Xu↗Rohan Desai↗Larry Wang↗Ethan Ritz↗Gabriel Hope↗

arXiv:2509.07150v4 Announce Type: replace Abstract: Reinforcement Learning from Verifiable Rewards (RLVR) has emerged as a promising approach to improve correctness in LLMs, however, in many scientific problems, the objective is not necessarily to produce the correct answer, but instead to produce a diverse array of candidates which satisfy a set of constraints. We study this challenge in the context of materials generation. To this end, we introduce PLaID++, an LLM post-trained for stable and property-guided crystal generation. We find that performance hinges on our crystallographic representation and reward formulation. First, we introduce a compact, symmetry-informed Wyckoff text representation which improves computational efficiency and encourages generalization from physical priors. Second, we demonstrate that temperature scaling acts as an entropy regularizer which counteracts mode collapse and encourages exploration. By encoding symmetry constraints directly into text and guiding model outputs towards desirable chemical space, PLaID++ generates structures that are thermodynamically stable, unique, and novel at a $\sim$50\% greater rate than prior methods and conditionally generates structures with desired space group properties. Our work demonstrates the potential of adapting post-training techniques from natural language processing to materials design, paving the way for targeted and efficient discovery of novel materials.

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04.

arXiv (CS.CV) 2026-06-19 DOI: arXiv:2606.20449

InfantFace: Detecting infant faces in neonatal clinical environments

作者:

Abdullah Bin-Obaid↗Maria M. Cobo↗Rebeccah Slater↗Lionel Tarassenko↗Mauricio Villarroel↗

Reliable localisation of the neonatal face is the first step for several video-camera based non-contact assessments such as pain and distress related facial expression analysis, pain scoring, cardiorespiratory signal extraction and cessation of breathing alerts. However, major challenges persist in neonatal clinical environments. Cluttered backgrounds, illumination changes and poor lighting conditions can reduce the accuracy of face detection models. Clinical interventions, monitoring equipment and, in some cases, medical devices can obstruct the face, making visual assessment difficult. We propose a one-stage YOLOv11m-based model tailored for face detection of infants in neonatal clinical environments. We combined multiple publicly available datasets (VGGFace2, CelebA, FDDB, WIDER FACE) to train and evaluate our proposed model. We then fine-tuned our model on a neonatal research dataset involving 228 videos from 114 recording sessions of 113 independent infants. Before fine-tuning, our model achieved an AP50 of 0.87, surpassing the performance of three state-of-the-art general face detectors. Performance improved further to an AP50 of 0.96 after clinical-domain adaptation. Evaluating face detection performance across different datasets remains a challenge due to the lack of publicly available neonatal datasets. Prioritising the creation of such datasets, while upholding appropriate privacy safeguards and ethical standards in their creation and use, would greatly support further progress in this field.

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05.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2606.13400

PolyFlow: Safe and Efficient Polytope-Constrained Flow Matching with Constraint Embedding and Projection-free Update

作者:

Jianming Ma↗Qiyue Yang↗Yang Zhang↗Liyun Yan↗Zhanxiang Cao↗Yazhou Zhang↗Yue Gao↗

arXiv:2606.13400v1 Announce Type: cross Abstract: While flow-based generative models have demonstrated strong performance across a wide range of domains, deploying them in safety-critical physical systems remains challenging due to strict constraint requirements. Existing approaches typically enforce safety through post-hoc corrections, which incur substantial computational overhead and may distort the learned distribution. We propose PolyFlow, a polytope-constrained flow matching framework that embeds constraints directly into the model and flow dynamics. PolyFlow introduces a discrete-time flow formulation and a projection-free architecture, which eliminate the discretization error and guarantee strict satisfaction of arbitrary polyhedral constraints, without the need for expensive iterative solvers. Experimental results show that PolyFlow achieves zero constraint violation while maintaining high distributional fidelity across a range of planning and control tasks. Compared to state-of-the-art constrained generation baselines, PolyFlow significantly reduces inference latency and demonstrates a favorable trade-off between safety, efficiency, and generative quality. Code is available on https://github.com/MJianM/PolyFlow.

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06.

PLOS Computational Biology 2026-06-12 DOI: HASH:5c8c918a8a7100b969116a452c936bdc

Ten simple rules for executing an inherited research plan in computational biology

作者:

Sahar Javaheri Tehrani↗

by Sahar Javaheri Tehrani, Toni Ingolf Gossmann Trainees in computational biology frequently inherit research plans whose aims, datasets, analytical strategies, and technical constraints were defined before their arrival. These plans often emerge from grants, collaborations, legacy codebases, shared high-performance computing environments, or partially completed analyses. While such plans provide a useful scaffold, they rarely specify all implementation details, prior assumptions, evaluation criteria, or dependencies needed for reliable execution. The transition from inheriting a partially articulated plan to producing reproducible results therefore creates an execution gap: a phase in which trainees must reconstruct what the project is, which elements are fixed, which remain negotiable, and which technical or organizational assumptions need to be tested before full-scale analysis begins. In this Ten Simple Rules article, we provide a practice-oriented framework for stabilizing inherited computational biology projects before workflows, benchmarks, and decision paths become entrenched. We do not claim that the individual practices described here are novel in isolation. Rather, our contribution is to organize familiar practices into a sequenced framework for a recurrent but under-articulated phase of computational research: inherited-plan execution. Computational biology makes this phase especially important because projects often combine heterogeneous datasets, fragile software environments, undocumented preprocessing choices, benchmarking assumptions, distributed collaborators, and asymmetrical access to contextual knowledge. By making this transition visible and operational, the rules aim to help trainees, supervisors, and collaborators reduce ambiguity, test feasibility, document decisions, and support reproducible and equitable project execution under real-world constraints.

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07.

arXiv (CS.CV) 2026-06-17 DOI: arXiv:2606.17246

GeoDisaster: Benchmarking Orchestrated Agents for Operational Disaster Geo-Intelligence

作者:

Maram Hasan↗Aman Verma↗Savitra Roy↗Hariseetharam Gunduboina↗Daksh Jain↗Muhammad Haris Khan↗Subhasis Chaudhuri↗Biplab Banerjee↗

Remote-sensing vision-language models (RS-VLMs) have advanced Earth-observation analysis toward visual interpretation and instruction-following, yet fall short of operational geo-intelligence, which demands tool-grounded spatial reasoning and structured, evidence-backed decisions. We introduce GeoDisaster, an operational geospatial disaster reasoning benchmark with 2,921 verified instances across 43 question types and five task families: deforestation monitoring, multi-hazard analysis, building-damage assessment, flood-safe routing, and Sentinel-1 SAR flood monitoring. Instances integrate heterogeneous EO/GIS evidence-optical and SAR imagery, raster masks, vector geometries, road networks, and exposure layers-spanning hazard detection, damage assessment, exposure estimation, and diagnostic report generation. Ground-truth answers are grounded in executable geospatial workflows and deterministic consistency checks, removing the need for language-model annotation. We further propose an orchestrated multi-agent framework with 18 disaster-oriented tools, where role-specialized agents coordinate through explicit execution contracts, aligned via Role-Contract Expectation Alignment (RCEA): failure-aware supervised fine-tuning combined with contract-grounded reinforcement learning over dense step-level signals. Experiments show that GeoDisaster challenges existing RS-VLMs and agentic systems, while RCEA improves tool use, evidence grounding, state consistency, and decision generation.

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08.

bioRxiv (Bioinfo) 2026-06-12 DOI: HASH:6aefb1ea75208f2e67494db444e15e7a

Deciphering cross-omics complexity of tissues via diagonal integration of unpaired spatial multi-omics data

作者:

Zhou↗Kangning↗Xiao↗Chen↗Zhang↗

Recent spatial multi-omics technologies enable the simultaneous in situ profiling of multiple omics modalities on the same tissue section; however, they face challenges in experimental complexity and high costs. This technical limitation can be circumvented by diagonal integration methods, which integrate omics data from different modalities. However, existing single-cell diagonal integration approaches overlook spatial information, causing unreliable anchoring across omics layers. Here, we introduce STAMO, a graph attention neural network model for spatially aware integration of unpaired spatial slices from different omics. Systematic benchmarking on spatial epigenome-transcriptome slices proves that STAMO outperforms the state-of-the-art methods in generating aligned embeddings and identifying consensus spatial domains across omics. We apply STAMO to integrate unpaired data from diverse spatial omics types (transcripts, epigenetics, DNA, and proteins), including slices from spatial RNA and four different epigenomic modalities, spatial ATAC and RNA slices across embryonic stages, spatial protein and RNA slices, and spatial DNA and RNA slices. In addition, the integration capability of STAMO can be further used to achieve cross-omics generation, offering a solution for exploring spatial region-specific gene regulatory mechanisms.

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09.

arXiv (CS.CL) 2026-06-12 DOI: arXiv:2606.13171

NTS-CoT: Mitigating Hallucinations in LLM-based News Timeline Summarization with Chain-of-Thought Reasoning

作者:

Feng Lyu↗Huiqin Yan↗Sijing Duan↗Hao Wu↗Shuang Gu↗Xue Qiao↗Weixu Zhang↗Haolun Wu↗

The rapid updates of online news make tracking event developments challenging, highlighting the need for timeline summarization (TLS). Hallucinations, where LLM-generated content deviates from source news, still remain a critical issue in LLM-based TLS and are not well studied in existing works. To bridge this gap, we identify two primary types of hallucinations: unfaithful content during news summarization and information omission in date-event summarization. Then, we propose NTS-CoT, a novel framework that leverages Chain-of-Thought (CoT) reasoning to mitigate hallucinations in TLS. The framework consists of three key modules: i) Element-CoT to capture essential news elements for faithful summarization, ii) Date Selection to combine temporal saliency and event prominence for timestamp selection, and iii) Causal-CoT to infer causal relationships and reduce omissions in date-event summarization. Extensive experiments, including quantitative analysis on three TLS benchmarks and human evaluation, demonstrate that NTS-CoT outperforms state-of-the-art baselines, effectively mitigating hallucinations and improving LLM-based TLS performance. Our source code is available at https://anonymous.4open.science/r/NTS-CoT .

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10.

arXiv (CS.CL) 2026-06-18 DOI: arXiv:2506.12311

Phonikud: Overcoming Phonetic Underspecification for Hebrew Text-To-Speech

作者:

Yakov Kolani↗Maxim Melichov↗Cobi Calev↗Morris Alper↗

Text-to-speech (TTS) for Modern Hebrew is challenged by the language's orthographic complexity, with existing solutions ignoring underspecified phonetic features such as stress. We present a framework for more phonetically accurate Hebrew TTS with four contributions: (1) Phonikud, an open-source Hebrew grapheme-to-phoneme (G2P) system that outputs fully-specified International Phonetic Alphabet (IPA) transcriptions, designed by augmenting a base diacritizer. (2) The ILSpeech corpus of paired Hebrew audio, text, and expert IPA annotations. (3) A benchmark for the previously unmeasured task of Hebrew G2P conversion. (4) Hebrew audio-to-IPA models capturing previously disregarded phonetic details for automatic TTS evaluation. Our results show that Phonikud more accurately predicts Hebrew phonemes than prior methods, and that small, local TTS models with phonetic input from Phonikud approach large proprietary systems. We release our code, data, and models at https://phonikud.github.io.

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11.

arXiv (CS.CL) 2026-06-18 DOI: arXiv:2606.19266

Trade-offs in Medical LLM Adaptation: An Empirical Study in French QA

作者:

Ikram Belmadani↗Oumaima El Khettari↗Carlos Ramisch↗Frederic Bechet↗Richard Dufour↗Benoit Favre↗

The development of large language models (LLMs) has led to an increased focus on their adaptation to specialized domains and languages, yet the effectiveness of domain adaptation strategies remains unclear. We present a study of medical domain adaptation using French medical question-answering (QA) as a case study. We compare continual pretraining (CPT), supervised fine-tuning (SFT), and their combination across three model families, multiple sizes, and three initialization types, explicitly disentangling adaptation effects from base model choice. We evaluate both multiple-choice (MCQA) and open-ended QA (OEQA) under greedy and constrained decoding using automatic metrics and LLM-as-a-Judge evaluation. For MCQA, CPT+SFT most often achieves the best scores, but gains over SFT are small and frequently not statistically significant, making SFT a strong and cost-effective default. For OEQA, CPT consistently improves overlap-based metrics, while SFT often degrades generation quality; instruction tuning and CPT+SFT are preferred by LLM-based evaluation. Cross-lingual experiments further show effective transfer from French adaptation to English benchmarks. Overall, we provide practical guidelines for selecting adaptation strategies under computational constraints.

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12.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2606.17851

A homotopy-type-theoretic generalization of neurosymbolic inference

作者:

Fernando Zhapa-Camacho↗Robert Hoehndorf↗

arXiv:2606.17851v1 Announce Type: new Abstract: A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $\sigma$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $\sigma$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Replacing the underlying sets by types, in the sense of homotopy type theory, preserves this information, and turns this functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.

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13.

bioRxiv (Bioinfo) 2026-06-11 DOI: HASH:1ed1599b2761a2f1a327d9d2779cbcf3

Tumour evolution as ground truth for cancer whole-genome sequencing

作者:

Valeriani↗Gandolfi↗Buscaroli↗Davydzenka↗Santacatterina↗Antonello↗Sadr↗A. H↗Gazziero↗V. A↗Milite↗Rivaroli↗…

Cancer genomes are shaped by evolutionary processes that couple mutagenesis, clonal selection, chromosomal instability, spatial growth and treatment response into structured genomic patterns, yet current benchmarking strategies largely ignore this evolutionary dependency. Here, we present SCOUT, a large-scale synthetic whole-genome sequencing resource of over 200 samples, designed for systematic benchmarking of tumour genomic analysis and evolutionary inference under controlled evolutionary ground truth. Unlike conventional task-specific simulations, SCOUT models tumour evolution as a latent generative process that simultaneously shapes mutations, copy-number alterations, variant allele frequencies, mutational signatures and clonal architectures. SCOUT recapitulates key features of solid and haematological malignancies, including driver mutations, chromosomal instability, intratumour heterogeneity, spatial sampling and treatment-associated evolutionary dynamics in tumour and matched-normal longitudinal and multi-region sequencing designs. Using SCOUT, we benchmarked widely used methods for somatic variant detection, copy-number analysis, mutational signature inference and tumour evolutionary reconstruction. Across analytical tasks, performance deteriorated in low-purity, highly subclonal and structurally complex tumours, while spatial sampling bias and hypermutation generated spurious evolutionary signals that confounded tumour interpretation across multiple inference layers. Evolutionary simulations further distinguished lineage-restricted genetic bottlenecks from multi-lineage resistance dynamics associated with tumour plasticity. Tumour purity consistently exerted a stronger effect on inference accuracy than sequencing depth. Together, our results establish evolutionary ground truth as a prerequisite for reproducible benchmarking and biologically interpretable analysis of cancer whole-genome sequencing data.

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14.

arXiv (CS.CV) 2026-06-19 DOI: arXiv:2606.20233

Cinematic Compositing Using Character-Environment-Harmonized Video Generation Models

作者:

Tianyi Xiang↗Mingming He↗Li Ma↗Jing Liao↗

Cinematic compositing aims to integrate green-screen characters into novel environments while maintaining physical and photometric realism. Previous methods often fail to capture the complex bidirectional interactions between characters and their surroundings, which we characterize as Character-to-Environment (C2E) physical interaction and Environment-to-Character (E2C) lighting harmonization. To address this, we propose an end-to-end video diffusion framework that jointly models C2E and E2C interactions, specifically handling the challenges of interactive props. Our approach introduces a tri-mask-guided architecture with RGB-D joint denoising to ensure physically consistent interactions among the character, props, and environment. We further develop an efficient prior-driven data curation pipeline to construct high-quality relighting pairs without expensive rendering. Finally, a reference-conditioned mechanism enables controllable environment synthesis and precise prop replacement. Extensive experiments demonstrate that our framework significantly outperforms existing methods in cinematic-quality dynamic video compositing.

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15.

arXiv (CS.CL) 2026-06-11 DOI: arXiv:2606.11709

RLCSD: Reinforcement Learning with Contrastive On-Policy Self-Distillation

作者:

Leyi Pan↗Shuchang Tao↗Yunpeng Zhai↗Lingzhe Zhang↗Zhaoyang Liu↗Bolin Ding↗Aiwei Liu↗Lijie Wen↗

On-policy self-distillation (OPSD) provides dense, token-level supervision for reasoning models by aligning a model's own distribution with the distribution it produces under privileged context, typically a verified solution. However, we show that the learning signal drawn from this distributional gap concentrates on style tokens rather than task-bearing ones, as the hinted model tends to produce more direct, shorter outputs. We term this pathology privilege-induced style drift, which destabilizes training or causes response length to shrink. To address this, we propose RLCSD (Reinforcement Learning with Contrastive on-policy Self-Distillation), which mitigates this drift by contrasting the teacher-student gap under a correct hint against that under a wrong hint, suppressing the style shift that conditioning on a hint tends to induce regardless of correctness, and yielding a signal that is more concentrated on task-bearing tokens. Experiments on Qwen3 (1.7B/4B/8B) and Olmo-3-7B-Think across mathematical and logical reasoning show that RLCSD consistently outperforms GRPO and prior OPSD methods. We further show that the contrastive principle is general: it plugs into existing OPSD methods to improve them, and its underlying insight extends to the broader cross-model on-policy distillation setting.

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16.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.16802

LabOSBench: Benchmarking Computer Use Agents for Scientific Instrument Control

作者:

Anqi Zou↗Han Deng↗Chengyu Zhang↗Junquan Hu↗Yu Wang↗Yuxiang Xing↗Aokai Zhang↗Hanling Zhang↗Zhaoyang Liu↗Ben Fei↗Zhihui Wang↗Wanli Ouyang↗…

arXiv:2606.16802v1 Announce Type: new Abstract: Current computer-use benchmarks primarily focus on software operation tasks in virtualized systems, whereas scientific instrumentation scenarios require coordinated control over complex interfaces, and feedback-driven parameter adjustment. However, directly evaluating agents on physical high-precision instruments is impractical due to high cost, safety risks, limited accessibility, and difficulty in ensuring reproducible evaluation. This motivates the need for a simulated yet realistic testbed that preserves the operational challenges of scientific instruments while enabling scalable and safe benchmarking. To this end, we introduce LabOSBench, a challenging benchmark for multimodal GUI agents built on a suite of web-based scientific-instrument simulators. Operating directly via a browser, LabOSBench avoids resource-heavy OS virtualization while supporting flexible task configuration and execution-based evaluation. Specifically, LabOSBench constructs 96 subtasks across eight instrument simulators, covering workflows from sample loading, alignment, parameter tuning, and data acquisition to result inspection. We evaluate general-purpose vision-language models, specialized GUI agent models, and advanced agentic frameworks at both subtask and end-to-end levels. Our experiments reveal that while existing agents can complete many structured GUI subtasks, they still struggle with feedback-driven operations and long-horizon workflow execution. Overall, LabOSBench provides a reproducible, low-cost testbed for advancing computer-using agents toward scientific-instrument control.

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17.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.15370

MNet++: Extended 2D/3D Networks for Anisotropic Medical Image Segmentation

作者:

Kirsten Odendaal↗Rade Bajic↗

This work demonstrates a full reproduction and extension of MNet, a hybrid 2D/3D convolutional network designed for anisotropic medical image segmentation. The original architecture was re-implemented within the nnU-Net framework to verify its reported performance and robustness to variable voxel spacing, known as anisotropy. Experiments were conducted on PROMISE prostate MRI and a controlled subset of LiTS liver CT under matched preprocessing and compute constraints. The reproduced MNet achieved a Dice similarity coefficient (DSC) of 89.0 +/- 0.9% on PROMISE, within 0.8% of the published result, and 94.3 +/- 1.9% / 54.6 +/- 3.1% for liver and tumor segmentation on LiTS, respectively. Two lightweight extensions were further introduced: (1) a learned Fusion Gating mechanism enabling adaptive 2D-3D feature blending, and (2) a VMamba state-space module for efficient long-range depth modelling. The Spatial Gating variant improved DSC by +0.8% with less than 3% inference overhead, while VMamba improved performance consistency, reducing PROMISE Dice variation to +/- 0.7% and achieving the strongest LiTS liver performance at 95.8% Dice. Both extensions preserved MNet robustness to anisotropy, with delta Dice = 1.5% across 1-4 mm voxel spacing. Overall, the study confirms MNet reproducibility and demonstrates that adaptive fusion and state-space modelling have the potential to further strengthen segmentation reliability under anisotropic conditions. However, further tests are required to provide definitive conclusions.

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18.

medRxiv (Medicine) 2026-06-18 DOI: HASH:044dfcf5f9e63b0a9fde64b658f103ac

MOSAIC: Methylation-Oriented Site Analysis and Information Classifier for Robust Epigenomic Classification of Acute Leukemia in Clinical Cohorts with Variable Tumor Purity

作者:

Shah↗Green↗Wainmann↗Karrs↗

DNA methylation-based classification offers a rapid diagnostic complement to conventional molecular workflows in acute leukemia. Existing classifiers are trained on array-derived reference cohorts whose construction favors specimens with adequate tumor content, leaving clinically relevant low-purity specimens underrepresented and classifier robustness in this regime uncharacterized. On held-out low-purity specimens, existing classifiers were concordant with expert pathology in only 7 of 10 (MARLIN) and 5 of 10 (ALMA) cases, motivating a classifier built to maintain accuracy at low tumor purity. We developed MOSAIC (Methylation-Oriented Site Analysis and Information Classifier), a neural network classifier built to maintain accuracy across the full range of tumor purities encountered in clinical practice. MOSAIC is a neural network trained on publicly available array-based methylation data augmented with native methylation calls from Oxford Nanopore sequencing. MOSAIC was evaluated on low-purity specimens held out entirely from training. On these held-out low-blast leukemia specimens, all below 25% blasts and including a case at 1.4%, MOSAIC was concordant with expert pathology in every case, recovering the correct subtype where diluted disease signal would otherwise be mistaken for normal or unrelated tissue. Gradient-based saliency analysis showed that the network relies on a partially distinct set of discriminative CpG probes when classifying low-blast specimens. MOSAIC demonstrates that augmenting training with clinically representative clinical specimens yields methylation-based leukemia classification that maintains effectiveness under the variable tumor purity of real clinical cohorts.

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19.

arXiv (CS.CL) 2026-06-15 DOI: arXiv:2606.13685

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

作者:

Abel Yagubyan↗

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.

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20.

arXiv (CS.CL) 2026-06-12 DOI: arXiv:2606.13649

Operadic consistency: a label-free signal for compositional reasoning failures in LLMs

作者:

Nathaniel Bottman↗Yinhong Liu↗Kyle Richardson↗

Detecting LLM reasoning failures at inference time without ground-truth labels has motivated a wide range of confidence baselines, including self-consistency, semantic entropy, and P(True), built on within-question sampling and self-evaluation. Operad theory, the formalism for systems built by iterated substitution, suggests a complementary diagnostic: a model's direct answer to a compositional query should agree with the answer it produces by composing a stated decomposition of the same query. We instantiate this idea as operadic consistency (OC), a per-question signal. Across twelve instruction-tuned LLMs (4B to 671B parameters, open-weights and closed-source) on four multi-hop QA datasets, OC is strongly correlated with accuracy on every dataset (Pearson $r \in [0.86, 0.94]$, all $p \leq 0.0004$), and is the only signal we evaluate with $r \geq 0.85$ uniformly across all four datasets. Chain-of-thought self-consistency (CoT-SC; Wang et al., 2023) matches OC on HotpotQA and DROP ($r = 0.93, 0.87$) but drops to $r \approx 0.45$ on MuSiQue and StrategyQA. At the per-question level, OC contributes information beyond CoT-SC and semantic entropy on every dataset (cluster-robust $p \leq 10^{-16}$ for the OC coefficient), and the conclusion is robust to additionally controlling for constructed decomposition-aware baselines ($p \leq 10^{-13}$). The same signal yields selective-prediction improvements (accuracy at fixed coverage) over a tuned CoT-SC baseline at the equal-cost $K = 3$ budget (AUARC lifts of +0.086 to +0.096 and AUROC lifts of +0.092 to +0.164; 95% CIs exclude zero on every cell). On five frontier thinking models, where the decomposition is extracted from the model's own chain of thought, the same equal-cost comparison gives positive selective-prediction point-estimate lift on all 16 (dataset, budget, metric) cells tested, with 95% CIs excluding zero on 12 of the 16.

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21.

arXiv (CS.CL) 2026-06-11 DOI: arXiv:2606.11875

I Understand How You Feel: Enhancing Deeper Emotional Support Through Multilingual Emotional Validation in Dialogue System

作者:

Zi Haur Pang↗Yahui Fu↗Koji Inoue↗Tatsuya Kawahara↗

Emotional validation - explicitly acknowledging that a user's feelings make sense - has proven therapeutic value but has received little computational attention. Emotional validation in dialogue systems can be decomposed into (i) validating response identification, (ii) validation timing detection, and (iii) validating response generation. To support research on all three subtasks, we release M-EDESConv, a 120k English-Japanese multilingual corpus created through hybrid manual and automatic annotation, and M-TESC, a multilingual spoken-dialogue test set. For timing detection, we propose MEGUMI, a Multilingual Emotion-aware Gated Unit for Mutual Integration, that fuses frozen XLM-RoBERTa semantics with language-specific emotion encoders via cross-modal attention and gated fusion. MEGUMI shows superior performance on both the M-EDESConv and M-TESC datasets, both objectively and subjectively. Finally, our EmoValidBench benchmarks of GPT-4.1 Nano and Llama-3.1 8B indicate that current LLMs generate contextually similar and diverse validating responses, but emotional understanding remains a major area for improvement. Project page: https://github.com/zihaurpang/Multilingual-Emotional-Validation

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22.

arXiv (CS.LG) 2026-06-15 DOI: arXiv:2606.14169

Machine Learning for Biomedical Raman Spectroscopy: From Spectral Acquisition to Clinical Translation

作者:

Bogdan Oancea↗Ana Maria Seciu-Grama↗Nicoleta Siminea↗Laura Mihaela Stefan↗Alice Stoica↗Joel Sjoberg↗Marian Necula↗Ana-Maria Prelipcean↗Corneliu Ovidiu Vrancianu↗Eduard Milea↗Andrei P\u{a}un↗Ion Petre↗…

arXiv:2606.14169v1 Announce Type: new Abstract: Raman spectroscopy provides label-free, chemically specific characterization of biological systems and has become an important tool for cancer diagnosis, molecular subtyping, microbiological identification, and intraoperative decision support. Biomedical Raman spectra are, however, high-dimensional, noisy, and affected by fluorescence background, acquisition variability, and biological heterogeneity, making robust computational analysis essential. This review examines the role of machine learning across the biomedical Raman spectroscopy pipeline, from preprocessing and signal correction to unsupervised structure discovery, supervised diagnosis and molecular stratification, representation and transfer learning, explainability, biomarker discovery, and multimodal integration with imaging, pathology, and molecular profiling. Emphasis is placed on the use of machine learning not only for diagnostic classification, but also for biologically interpretable and clinically actionable analysis. We also discuss the main barriers to clinical translation, including limited dataset sizes, inter-instrument variability, inconsistent preprocessing, insufficient external validation, reproducibility concerns, and limited sharing of software, data, and metadata. We argue that progress will require methodological advances together with standardization, robust validation, explainability, and deployment-ready analytical frameworks. By integrating methodological, biomedical, and translational perspectives, this review outlines key directions for developing reliable and clinically deployable Raman-AI systems.

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23.

arXiv (CS.LG) 2026-06-17 DOI: arXiv:2505.17740

A tensor network approach for chaotic time series prediction

作者:

Rodrigo Mart\'inez-Pe\~na↗Rom\'an Or\'us↗

arXiv:2505.17740v2 Announce Type: replace Abstract: Making accurate predictions of chaotic time series is a complex challenge. Reservoir computing, a neuromorphic-inspired approach, has emerged as a powerful tool for this task. It exploits the memory and nonlinearity of dynamical systems without requiring extensive parameter tuning. However, selecting and optimizing reservoir architectures remains an open problem. Next-generation reservoir computing simplifies this problem by employing nonlinear vector autoregression based on truncated Volterra series, thereby reducing hyperparameter complexity. Nevertheless, the latter suffers from exponential parameter growth in terms of the maximum monomial degree. Tensor networks offer a promising solution to this issue by decomposing multidimensional arrays into low-dimensional structures, thus mitigating the curse of dimensionality. This paper explores the application of a previously proposed tensor network model for predicting chaotic time series, demonstrating its advantages in terms of accuracy and computational efficiency compared to conventional echo state networks. Using a state-of-the-art tensor network approach enables us to bridge the gap between the tensor network and reservoir computing communities, fostering advances in both fields.

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24.

arXiv (CS.CL) 2026-06-19 DOI: arXiv:2606.20527

StylisticBias: A Few Human Visual Cues Drive Most Social Biases in MLLMs

作者:

Shaghayegh Kolli↗Timo Cavelius↗Nafiseh Nikeghbal↗Samantha Dalal↗Jana Diesner↗

Multimodal large language models (MLLMs) are increasingly deployed in personally and societally consequential settings, yet the visual cues that shape how these models judge people remain poorly understood. Prior work often compares different (groups of) individuals, making it difficult to separate appearance effects from identity differences. We introduce StylisticBias, a controlled benchmark for evaluating attribute-level social bias in MLLMs. We generate 500 photorealistic base faces and create about 50 single-attribute variations per face, producing about 25K images. This design keeps identity fixed and changes one visual attribute at a time. It lets us measure how specific cues shift model judgments. We evaluate six MLLMs across 25 binary social judgment scenarios. We find that age and body type dominate identity-level effects, while fashion style and other visual cues drive the largest attribute-level shifts. We further find that about 15 attributes account for nearly 80\% of the total variation, showing that bias is concentrated in a small set of visual cues. Sensitivity is strongest in judgments that are semantically aligned with appearance, especially socioeconomic and style-related judgments. We release StylisticBias as a benchmark for fine-grained bias evaluation in multimodal models. Code and dataset: https://github.com/timo-cavelius/StylisticBias and https://hf.co/datasets/shaghayegh/stylistic-bias-dataset.

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25.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2602.03846

PLATE: Plasticity-Tunable Efficient Adapters for Geometry-Aware Continual Learning

作者:

Romain Cosentino↗

arXiv:2602.03846v2 Announce Type: replace-cross Abstract: We develop a continual learning method for pretrained models that requires no access to old-task data, addressing a practical barrier in foundation model adaptation where pretraining distributions are often unavailable. Our key observation is that pretrained networks exhibit substantial geometric redundancy, and that this redundancy can be exploited in two complementary ways. First, redundant neurons provide a proxy for dominant pretraining-era feature directions, enabling the construction of approximately protected update subspaces directly from pretrained weights. Second, redundancy offers a natural bias for where to place plasticity: by restricting updates to a subset of redundant neurons and constraining the remaining degrees of freedom, we obtain update families with reduced functional drift on the old-data distribution and improved worst-case retention guarantees. These insights lead to \textsc{PLATE} (Plasticity-Tunable Efficient Adapters), a continual learning method requiring no past-task data that provides explicit control over the plasticity-retention trade-off. PLATE parameterizes each layer with a structured low-rank update $\Delta W = B A Q^\top$, where $B$ and $Q$ are computed once from pretrained weights and kept frozen, and only $A$ is trained on the new task. The code is available at https://github.com/SalesforceAIResearch/PLATE.

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