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01.
Science (Express) 2026-06-18

Indium-free perovskite/silicon tandem solar cells with tin oxide recombination layer and electrodes | Science

Authors: Unknown Author

Indium-based transparent conductive oxides are widely used as electrodes and recombination layers in perovskite/silicon tandem solar cells, yet their scalability is constrained by indium scarcity and sputtering-induced damage. Here we report high efficiency and stable indium-free perovskite/silicon tandem solar cells enabled by reactive plasma deposited tin oxide (RPD-SnO x ). For RPD-SnO x as the recombination layer, a certified efficiency of 33.6% is achieved. Fully indium-free tandems that used RPD-SnO x as both recombination layer and electrodes delivering a champion PCE of 33.2% (1 cm 2 ) and a mini-module with a certified efficiency of 31.0% (207.9 cm 2 ). Dense and uniform self-assembled monolayer anchoring enabled by RPD-SnO x suppressed non-radiative recombination and reduced halide migration. Indium-free mini-modules exhibited high thermal, damp-heat, and outdoor operational stability and retained 65% of their maximum initial efficiency after 105 days of outdoor operation.

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02.
medRxiv (Medicine) 2026-06-11

Electrical signatures of divergent connectivity in the human subgenual cingulate cortex

Authors:
Qianq↗Kerezoudis↗Gregg↗Hermes↗Klassen↗B. T↗Chari↗Tisdall↗M. M↗Baker↗M. R↗Miller↗…

Background: Major depressive disorder remains a leading cause of disability. While subgenual cingulate cortex (sgCC) deep brain stimulation (DBS) shows promise for medically refractory depression, clinical outcomes have been heterogeneous, suggesting that individual differences in neural circuitry engagement may critically influence therapeutic efficacy. We aimed to define the electrophysiological signatures of sgCC efferent connectivity using single-pulse electrical stimulation (SPES) with intracranial stereo-EEG (sEEG) to inform rational targeting and physiological biomarkers for sgCC-DBS. Methods: In four patients undergoing clinically indicated sEEG for seizure mapping, SPES was delivered through sgCC pairs, while distributed brain stimulation-evoked potentials (BSEPs) were recorded across cortical and subcortical sites. Responses were characterized using Canonical Response Parameterization to extract reproducible waveforms and per-trial reliability. Results: sgCC stimulation elicited reproducible, spatially organized BSEPs across frontal, limbic, and paralimbic networks, aligning with known anatomical pathways. Frontal recruitment featured robust, lateralized orbitofrontal activation favoring the ipsilateral central, medial OFC and bilateral ventromedial prefrontal responses. Limbic effects demonstrated bilateral cingulate activation with stronger ipsilateral recruitment and lateralized amygdala and hippocampal responses. Paralimbic engagement included insular responses with subject-specific anterior predominance and bi-hemispheric temporal-polar slow-wave deflections. Conclusion: These findings provide direct electrophysiological evidence of distributed, lateralized sgCC divergent network connectivity in the human brain, offering physiologic confirmation of its role in affective circuitry. The observed topography and laterality have direct applications for sgCC-DBS targeting and implicate BSEP signatures as candidate biomarkers to guide patient-specific therapy.

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03.
arXiv (CS.CL) 2026-06-15

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

Authors:
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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04.
arXiv (CS.CV) 2026-06-24

TopoPult-SSL: Gland-Mask-Free Cross-Device Meibomian Gland Segmentation via Self-Distilled Weak Clinical Priors

Authors:
Nicol\`o Savioli↗Luca Del Tongo↗

Every new clinical imaging device creates a domain shift where dense gland masks are expensive yet cheap clinical signals – eyelid outlines, Pult grades, morphometric ratios – are routinely recorded. We present TopoPult-SSL, a two-stage framework for cross-device meibomian gland segmentation. Stage 1 adapts a source-trained model without target gland masks in the training loss, using four weak-prior anchors driven by target eyelid masks and clinical metadata only. Stage 2, when target gland masks are available, distils complementary Stage-1 teachers into a single compact student via supervised self-distillation. We develop and validate the technique on the public MGD-1k to CAMG research benchmark (1,000 to 100 images, different device), where the distilled model achieves Dice 0.716+/-0.006 (best 0.726), surpassing UA-MT (0.710) and the ensemble teacher (0.720) – with a single pass. The gland-mask-free Stage-1 variant reaches Precision 0.694 vs. 0.30-0.34 for SAM/MedSAM (p

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

Frontier: Towards Comprehensive and Accurate LLM Inference Simulation

Authors:
Yicheng Feng↗Xin Tan↗Yangtao Deng↗Yimin Jiang↗Yibo Zhu↗Hong Xu↗

arXiv:2605.21312v2 Announce Type: replace-cross Abstract: Modern LLM serving is no longer homogeneous or monolithic. Production systems now combine disaggregated execution, complex parallelism, runtime optimizations, and stateful workloads such as reasoning, agents, and RL rollouts. Simulation is attractive for exploring this growing design space, yet existing simulators lack the architectural completeness and decision-grade fidelity it demands. Their monolithic-replica abstractions are ill-suited to disaggregated serving, while average-case analytical proxies can distort SLA predictions and even reverse optimization conclusions. We present Frontier, a discrete-event simulator for modern LLM inference serving. Frontier features a disaggregated abstraction. It captures the structure and dynamics of modern serving systems by modeling co-location, Prefill-Decode Disaggregation (PDD), and Attention-FFN Disaggregation (AFD) with role-specific cluster workers, incorporating key runtime optimizations (e.g., CUDA Graphs, speculative decoding) within the scheduler-batch-engine loop, and supporting stateful requests for emerging workloads. It further provides accurate and generalizable predictions of computation, communication, and memory costs across diverse serving scenarios with complex workload compositions. On 16-H800 GPU testbed, Frontier achieves an average throughput error below 4%. Compared with state-of-the-art simulators, it reduces end-to-end latency error from 44.9% to 6.4% under co-location and from 51.7% to 2.6% under disaggregation. It scales to over 1K GPUs on commodity CPUs and enables new use cases such as SLA-dependent Pareto frontier exploration, heterogeneous disaggregated allocation, agentic reasoning scheduling validation, and RL post-training reconfiguration. We release Frontier at https://github.com/NetX-lab/Frontier.

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

RippleBench: Capturing Ripple Effects Using Existing Knowledge Repositories

Authors:
Roy Rinberg↗Usha Bhalla↗Igor Shilov↗Flavio P. Calmon↗Rohit Gandikota↗

arXiv:2512.04144v2 Announce Type: replace Abstract: Targeted interventions on language models, such as unlearning or model editing, aim to modify specific information, but their effects often propagate to related, unintended areas (e.g., removing virology content may degrade performance on allergies); these side-effects are commonly referred to as the ripple effect. We introduce RippleBench-Maker, an automatic pipeline that retrieves semantic neighbors of any source concept from a knowledge repository and generates multiple-choice questions at varying semantic distances. We instantiate this framework using WikiRAG, an open-source RAG system over English Wikipedia, to construct RippleBench-WMDP-Bio (584 seed topics, 352,961 questions), and evaluate eight unlearning methods on Llama3-8B-Instruct. All eight exhibit accuracy drops that are largest near the unlearned target and decay with semantic distance, each with a distinct propagation profile. We replicate these findings across Mistral-7B, Zephyr-7B, and Yi-34B; cross-model delta curves are nearly identical, suggesting ripple effects are a property of the unlearning method rather than the base model. We validate all major pipeline stages using a four-experiment Mechanical Turk study (5,200+ responses, 61 workers). We release all code, data, and infrastructure.

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07.
arXiv (CS.LG) 2026-06-19

Multimodal Concept Bottleneck Models

Authors:
Tongqing Shi↗Ge Yan↗Tuomas Oikarinen↗Tsui-Wei Weng↗

arXiv:2606.19882v1 Announce Type: cross Abstract: Concept Bottleneck Models (CBMs) enhance the interpretability of deep learning networks by aligning the features extracted from images with natural concepts. However, existing CBMs are constrained in their ability to generalize beyond a fixed set of predefined classes and the risk of non-concept information leakage, where predictive signals outside the intended concepts are inadvertently exploited. In this paper, we propose Multimodal Concept Bottleneck Model (MM-CBM) to address these issues and extend CBMs into CLIP. MM-CBM utilizes dual Concept Bottleneck Layers (CBLs) to align both the image and text embeddings into interpretable features. This allows us to perform new vision tasks like zero-shot classification or image retrieval in an interpretable way. Compared to existing methods, MM-CBM achieves up to 51.26% accuracy improvement on average across four standard benchmarks. Our method maintains high accuracy, staying within ~5% of black-box performance while offering greater interpretability.

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08.
arXiv (CS.CL) 2026-06-12

GENIE: A Fine-Grained Measure for Novelty

Authors:
Ramya Namuduri↗Manya Wadhwa↗Anshun Asher Zheng↗Greg Durrett↗Junyi Jessy Li↗

Large Language Models have consistently demonstrated a lack of creativity and diversity across tasks. Prior work has focused on addressing whether models are capable of generating creative outputs. Here, we aim to consider novelty and investigate what makes model-generated content novel or not novel in a task-specific manner. We propose a fine-grained evaluation metric GENIE to measure the novelty of responses along task-specific features with respect to a population of responses. We show that unlike GENIE, holistic metrics struggle to capture the high-dimensionality of novelty and do not provide insight on which properties they target. Finally, we use GENIE to measure the effectiveness of mitigation methods that address creativity to better understand where these methods can improve novelty.

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09.
PLOS Computational Biology 2026-06-22

GrassSV – hybrid method to detect structural variants in high throughput DNA-seq data

Authors:
Dominik Witczak↗

by Dominik Witczak, Krzysztof Sychla, Julia Wysocka, Artur Laskowski, Wojciech Frohmberg, Marta Glowacka, Alicja Dzik, Piotr Lukasiak, Jacek Blazewicz, Aleksandra Swiercz Genetic diversity is crucial for populations to adapt and survive in dynamic environments. This diversity arises from genetic mutations, which manifest in the genome as structural variants (SVs). Several types of SVs exist, but not all are equally easy to detect. Current SV detection tools tend to specialize in certain SV types or require the use of multiple tools to obtain a comprehensive variant profile, which increases computational cost and complexity. While some methods excel at identifying breakpoints, they often struggle with accurately classifying variant types, and their precision depends strongly on data quality and sequencing technology. At present, the majority of available genomic data originates from high-quality short reads, which remain the most affordable sequencing technology. In this manuscript, we introduce GrassSV, a novel and computationally efficient method that employs a hybrid pattern-matching approach to detect all major classes of structural variants using short-read sequencing data. GrassSV integrates depth-of-coverage analysis with contig-based pattern recognition to ensure both sensitivity and precision while minimizing false positives and runtime. Its robustness was demonstrated on the human Genome in a Bottle dataset, as well as on synthetic data derived from the yeast genome, where it achieved high accuracy across all SV types at a lower computational cost compared to existing methods. This makes GrassSV a practical alternative to multi-tool pipelines typically required for comprehensive SV detection. GrassSV is available at https://github.com/Domomod/GrassSV under GPL-3.0 license and the benchmark at: https://github.com/Domomod/GrassBenchmark.

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10.
arXiv (CS.AI) 2026-06-12

Select and Improve: Understanding the Mechanics of Post-Training for Reasoning

Authors:
Akshay Krishnamurthy↗Audrey Huang↗Nived Rajaraman↗

arXiv:2606.13125v1 Announce Type: cross Abstract: Reinforcement learning has rapidly emerged as a key component in the training of reasoning and coding models, yet it remains poorly understood from a mechanistic perspective. We study how and through what underlying processes capabilities are acquired or enhanced via reinforcement learning post-training. Our analysis, based on controlled math reasoning experiments with Qwen-2.5-1.5B, reveals two core mechanisms: strategy selection and strategy improvement. Our results highlight the role of SFT data and reinforcement learning data in activating these mechanisms, in particular showing how supervising the model on diverse reasoning strategies can enable strategy selection and how increasing difficulty in reinforcement learning data can enable strategy improvement. Taken together, our results provide mechanistic insight into RL training and suggest practical interventions to continue scaling reasoning capabilities.

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11.
arXiv (CS.AI) 2026-06-24

LaGO: Latent Action Guidance for Online Reinforcement Learning

Authors:
Kuan-Yen Liu↗Ren-Jyun Huang↗Ti-Rong Wu↗

arXiv:2606.24669v1 Announce Type: new Abstract: Large language models (LLMs) have shown strong potential for planning and sequential decision-making, but prior work often relies on using them as direct controllers, which requires precise action generation and can be unreliable in practice. This paper proposes Latent Action Guidance for Online Reinforcement Learning (LaGO), a framework that uses a pretrained LLM as a latent action prior to softly guide online policy optimization, rather than treating the LLM as an explicit planner or controller. Experiments on both a discrete-control benchmark, CLEVR-Robot, and a continuous-control benchmark, Meta-World, demonstrate that LaGO consistently improves both reward and success rate over Vanilla PPO. In particular, LaGO increases the average success rate from 15.1% to 27.2% on CLEVR-Robot and from 2.7% to 15.2% on Meta-World. Our analysis further shows that stronger pretrained LLMs provide more effective guidance, suggesting that LLM knowledge can improve planning and online decision-making.

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

Text-Vision Co-Instructed Image Editing

Authors:
Chenxi Xie↗Yuhui Wu↗Qiaosi Yi↗Lei Zhang↗

Existing image editing methods can be generally categorized into textual instruction-based and visual prompt-based ones. Textual instructions are semantically expressive, but are limited by the coarse granularity of spatial control of the editing results. In contrast, visual prompts such as drag and point can provide precise spatial guidance, but are limited by the inherent ambiguity in semantic intent. To unify the strength of textual and visual prompts, we present Text-Vision Co-Instructed Image Editing, which jointly models textual instructions as semantic intent and sparse visual instructions as spatial guidance, aiming to achieve precise and intent-faithful image manipulation. To this end, we first construct a textual-visual instruction paired dataset with more than 23K samples derived from dynamic videos, enabling aligned supervision for cross-modal instruction. We then propose TV-Edit, a Textual-Visual instruction unified Editing framework to contextualize drag or point-based visual instructions with image-text semantics and lift them into semantic-aware control representations for pretrained editing backbones. By integrating semantic intent and spatial constraints, TV-Edit leads to more precise spatial control, less instruction ambiguity, and stronger structural consistency than text-only or drag-based alternatives. Finally, we establish TV-Edit-Bench, a deliberately designed benchmark to evaluate semantic faithfulness, spatial alignment, and visual consistency with ground-truth references and controlled textual-visual variations for reliable assessment. Our experiments across multiple editing backbones demonstrate that TV-Edit consistently yields more precise and intent-faithful edits, significantly outperforming state-of-the-art instruction-based and drag-based baselines.

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13.
arXiv (quant-ph) 2026-06-12

Driven-dissipative entanglement of distant giant atoms

Authors:
Aziza Almanakly↗Ariadna Soro↗Alejandro Vivas-Via\~na↗Beatriz Yankelevich↗Caspar Groiseau↗David Pahl↗Junyoung An↗Gabriel Cutter↗Michael E. Gingras↗Bethany M. Niedzielski↗Hannah Stickler↗Ren\'ee DeP\'encier Pi\~nero↗…

arXiv:2606.13375v1 Announce Type: new Abstract: Quantum interconnects distribute entanglement via controlled light-matter interactions for quantum computing and sensing applications. Many entanglement generation schemes use coherent, reversible interactions that require precisely calibrated pulses to execute. In contrast, driven-dissipative protocols use a continuous-wave drive in the presence of correlated dissipation to stabilize entanglement in protected (dark) states. However, the same dissipation that generates the entanglement also limits its utility once the stabilization protocol ends. Here, we engineer a superconducting system of two giant artificial atoms coupled sequentially to a waveguide, with tunable individual and correlated dissipation enabled by interference between coupling points. Continuously driving the atoms through the waveguide exploits correlated dissipation to generate remote entanglement. We then tune the qubit frequencies in situ to suppress individual dissipation and thereby preserve the entanglement, achieving a Bell-state fidelity F = 0.89 +/- 0.02. This demonstration indicates that the driven dissipation of giant atoms is a viable approach for distributing entanglement across quantum networks.

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

Minim: Privacy-Aware Minimal View for Agents via Trusted Local Sanitization

Authors:
Hexuan Yu↗Chaoyu Zhang↗Heng Jin↗Shanghao Shi↗Ning Zhang↗Y. Thomas Hou↗Wenjing Lou↗

arXiv:2606.13949v1 Announce Type: new Abstract: Modern LLM-powered autonomous agents increasingly rely on rich user interface (UI) state observations to achieve reliable action grounding in complex digital environments. However, many deployments transmit the full UI state to remote inference servers even when most elements are irrelevant to the current task, which can leak sensitive but unnecessary context such as authentication codes, private notifications, and background application states. We propose MINIM, a trusted local broker that performs privacy-aware minimization on the client side before any observation leaves the device. Grounded in Contextual Integrity (CI), MINIM learns a dual-score representation for each UI element by predicting an inherent sensitivity score (s) and a task-conditioned necessity score (n). These scores drive a ternary disclosure policy that keeps essential elements, abstracts sensitive attributes when needed, and removes task-irrelevant content. We optimize a CI-aware objective that penalizes necessity errors more strongly on high-risk content, enabling aggressive pruning while preserving task-critical information. Experiments on real-world UI observations derived from WebArena show that MINIM substantially reduces task-irrelevant sensitive leakage while preserving task-critical semantic context and the interactive affordances required for reliable agent actions.

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15.
arXiv (CS.CV) 2026-06-19

ImageWAM: Do World Action Models Really Need Video Generation, or Just Image Editing?

Authors:
Yuyang Zhang↗Wenyao Zhang↗Zekun Qi↗He Zhang↗Haitao Lin↗Jingbo Zhang↗Yao Mu↗Xiaokang Yang↗Wenjun Zeng↗Xin Jin↗

World Action Models (WAMs) commonly rely on video generation to bridge visual world modeling and robot control. However, video-based WAMs face three coupled limitations: dense multi-frame future tokens make inference costly, full video prediction spends capacity on action-irrelevant temporal and appearance details, and long-horizon future imagination may introduce errors that mislead action prediction. These issues raise a simple question: Does world action model really need video generation? We propose ImageWAM, a simple WAM framework that repurposes pretrained image editing models for robot action prediction. In contrast to video generation, image editing provides a better-matched prior: it only needs to model a target-frame transformation, focuses on action-relevant current-to-target visual differences, and grounds task instructions to localized visual changes through edit pretraining. In practice, ImageWAM does not decode the target frame at inference time; instead, it conditions a flow-matching action expert on the KV caches produced by image-editing denoising, using them as a compact world-action context. ImageWAM outperforms standard VLA baselines and matching competitive WAMs without additional policy pretraining across different simulator and real-world experiments. It also reduces FLOPs to 1/6 and latency to 1/4 of video-based WAMs. Attention analysis further shows that editing caches focus on task-relevant change regions, supporting image editing as an effective alternative to video-based world-action modeling.

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

Abstracting Cross-Domain Action Sequences into Interpretable Workflows

Authors:
Gaurav Verma↗Scott Counts↗

Sequential or time-stamped interaction logs provide objective records of digital application usage, yet their granularity and noise often obscure meaningful insights into people's work. Such insights are essential for improving digital products in ways grounded in real-world user interactions. Prior research has applied deep learning models to cluster user actions into high-level activities, but these approaches are highly sensitive to noise and struggle to generalize across applications. To address this limitation, we introduce WorkflowView, a framework that uses large language models (LLMs) to abstract low-level action sequences into high-level activities. We establish the effectiveness and generality of our approach across three distinct, challenging sequential tasks and diverse domains: (a) zero-shot task description reconstruction from browser logs (achieving high semantic similarity, $\mu_{sim} = 0.91$), (b) few-shot student dropout prediction using MOOC interaction logs (reaching weighted $F_1 = 0.90$ with only five few-shot examples), and (c) anonymized, privacy-preserving analysis of AI tool integration within document workflows in Microsoft Word. Our work demonstrates that LLM-based abstraction is a robust and efficient path forward for transforming low-level behavioral data into high-level, interpretable, and actionable insights. We also discuss practical considerations for deploying LLM-based inferences within logging infrastructures, including computational efficiency and user privacy.

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

CADBench: A Multimodal Benchmark for AI-Assisted CAD Program Generation

Authors:
Anna C. Doris↗Jacob Thomas Sony↗Ghadi Nehme↗Era Syla↗Amin Heyrani Nobari↗Faez Ahmed↗

arXiv:2605.10873v2 Announce Type: replace-cross Abstract: Recovering editable CAD programs from images or 3D observations is central to AI-assisted design, but progress is difficult to measure because existing evaluations are fragmented across datasets, modalities, and metrics. We introduce CADBench, a unified benchmark for multimodal CAD program generation. CADBench contains 18,000 evaluation samples spanning six benchmark families derived from DeepCAD, Fusion 360, ABC, MCB, and Objaverse; five input modalities including clean meshes, noisy meshes, single-view renders, photorealistic renders, and multi-view renders; and six metrics covering geometric fidelity, executability, and program compactness. STEP-based families are stratified by B-rep face count and all families are diversity-sampled to support controlled analysis across complexity and object variation. We benchmark eleven CAD-specialized and general-purpose vision-language systems, generating more than 1.4 million CAD programs. Under idealized inputs, specialized mesh-to-CAD models substantially outperform code-generating VLMs, which remain far from reliable CAD program reconstruction. CADBench further reveals three recurring failure modes: reconstruction quality degrades with geometric complexity, CAD-specialized models can be brittle under modality shift, and model rankings change across metrics. Together, these results position CADBench as a diagnostic testbed for measuring progress in editable 3D reconstruction and multimodal CAD understanding. The benchmark is publicly available at https://github.com/anniedoris/CADBench.

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

Light Interaction: Training-Free Inference Acceleration for Interactive Video World Models

Authors:
Jiacheng Lu↗Haoyi Zhu↗Sipei Yi↗Enze Xie↗Yu Li↗Cheng Zhuo↗

arXiv:2605.31158v3 Announce Type: replace-cross Abstract: Interactive video world models generate video chunk by chunk in response to user-controlled camera movements, enabling applications such as real-time game simulation, virtual scene navigation, and embodied AI training. However, scaling to long interactive trajectories is prohibitively expensive due to growing context memory, quadratic attention complexity, and repeated denoising steps. We present Light Interaction, a training-free inference acceleration framework for interactive video world models. Our key insight is that interaction naturally enables trajectory-dependent adaptive computation: retrieved spatial memory can be discarded during novel exploration, temporal context can be adjusted according to local latent dynamics, and early-step model outputs can be reused when the camera revisits familiar regions. Based on this insight, Light Interaction combines adaptive context management, denoising cache acceleration, and hardware-software co-designed 3D block sparse attention with fused Triton kernels. Evaluated on HY-WorldPlay and Matrix-Game-3.0, Light Interaction achieves up to 2.59x speedup without model retraining while maintaining competitive visual quality.

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19.
bioRxiv (Bioinfo) 2026-06-18

ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets

Authors:
Lang↗O. W↗Beer↗Zhang↗LeSon↗Deen↗Pugh↗Lai↗W. K↗

Background: The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability and reproducibility. Results: We present the v1.0 release of ScriptManager, a Java-based framework for modular and reproducible analysis and visualization workflows of genomics and epigenomics data. Unlike existing tools specialized for individual assay types, ScriptManager provides a unified and extensible framework for cross-assay visualization and workflow reproducibility. The v1.0 release adds novel analytical modules, GUI session logging, automated unit and integration testing, tutorials, and expanded documentation. It also integrates with the broader reproducibility ecosystem through Singularity containers, Anaconda packaging, and Galaxy XML wrappers. We demonstrate ScriptManager's TagPileup scaling from local single-core execution to a 10,305-job analysis distributed across the Open Science Grid (OSG), with the full workload completing in

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20.
arXiv (CS.AI) 2026-06-15

CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

Authors:
Wei Zhang↗Xun Jiang↗Yuesi Xi↗Ming Tang↗

arXiv:2606.13713v1 Announce Type: cross Abstract: Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.

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21.
arXiv (CS.AI) 2026-06-17

Models Take Notes at Prefill: KV Cache Can Be Editable and Composable

Authors:
Bojie Li↗

arXiv:2606.17107v1 Announce Type: cross Abstract: Prefix caching reuses prefill only across an exactly shared prefix, so one changed field invalidates the entire downstream cache. Yet overwriting the field's own key/value vectors and reusing the rest leaves the model acting on the old value. The reason, established causally across four model families: at prefill the model has already written the field-conditioned conclusion onto downstream notes; the field's own key/value drives under 1% of the decision. Read as a notebook of memoized conclusions, two capabilities follow. (1) It is editable. A salient erratum amends the notes; and with chain-of-thought, editing the field alone recovers the decision (1.00 at 8B, ~1% compute), while without CoT it is ignored. (2) It is composable. The notes are position-portable, so a precompiled skill can be RoPE-repositioned and spliced into any context, indistinguishable from full recompute (logit cosine 0.90-0.999, twelve models) at O(L) rather than O(L^2) time-to-first-token. A unified edit+compose agent stays decision-identical to recompute at up to 14.9x lower latency. The approach applies to any per-token attention KV cache, validated across scale, quantization, Mixture-of-Experts, and multimodal caches, and extends to several attention variants through small adapters. Because the erratum is append-only, it composes with production prefix caching: in an online vLLM benchmark it keeps the prefix cache-aligned (98.5% hit-rate), cutting p90 time-to-first-token by 53-398x.

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

Probing Semantic Alignment, Lexical Invariance, and Syntactic Influence in LLM Metaphor Processing

Authors:
Fengying Ye↗Shanshan Wang↗Lidia S. Chao↗Derek F. Wong↗

Large language models (LLMs) achieve strong performance on metaphor detection and interpretation tasks, yet it remains unclear what such behavioral success reveals about metaphor processing. We present a diagnostic analysis that examines the limits of behavioral evidence by probing three complementary dimensions: semantic attribute alignment, lexical invariance, and syntactic sensitivity. Using geometric probing, we assess whether model-generated interpretations align with reference semantic attributes; through context-varying substitution, we analyze the stability of lexical associations between metaphorical and literal expressions; and via controlled syntactic perturbations, we examine sensitivity in metaphor detection. Our analysis reveals that LLM-generated interpretations can exhibit semantic drift relative to reference attributes; stable lexical anchors persist across contextual conditions, potentially supporting conventional metaphors while biasing novel metaphors requiring contextual integration; and detection performance is sensitive to syntactic irregularities. These findings suggest that strong behavioral performance may reflect heterogeneous underlying signals, highlighting the need for caution when interpreting metaphor benchmarks as evidence of robust, integrated semantic understanding.

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23.
arXiv (CS.AI) 2026-06-12

From Verdict to Process: Agentic Reinforcement Learning for Multi-Stage Fact Verification

Authors:
Rongxin Yang↗Shenghong He↗Siyuan Zhu↗Chao Yu↗

arXiv:2606.13262v1 Announce Type: new Abstract: Recent approaches combining Large Language Models (LLMs) with retrieval-augmented reasoning have shown promise for automated fact verification. To process complex claims, these verification pipelines typically execute multi-stage workflows that coordinate tightly coupled modules, including claim decomposition, evidence gathering, and verdict prediction. However, existing methods optimize individual stages in isolation or rely on fixed heuristics, which limits adaptive coordination among stages and can lead to suboptimal outcomes. In this work, we propose ProFact, an agentic reinforcement learning framework for end-to-end optimization of multi-stage fact verification trajectories. ProFact trains a unified policy to coordinate claim decomposition, evidence seeking, answer generation, and verdict prediction. To address the sparse and delayed supervision provided by final veracity labels, ProFact introduces process-aware rewards that provide stage-level learning signals throughout the verification process. Empirical evaluation shows that ProFact consistently outperforms strong baselines in both verification performance and inference efficiency. These results highlight the effectiveness of process-aware trajectory optimization for multi-stage fact verification.

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24.
arXiv (CS.LG) 2026-06-17

The Morse Transform for Discrete Shape Analysis

Authors:
Alexander M. Tanaka↗Aras T. Asaad↗Richard Cooper↗Vidit Nanda↗

arXiv:2503.04507v2 Announce Type: replace-cross Abstract: The geometry of an object plays a vital role in modulating its interactions with the physical world. It nevertheless remains difficult to describe geometric information numerically for the purposes of statistical inference or classification tasks. Here, we introduce a new topological transform which leverages directional piecewise-linear Morse theory to quantify the geometry of an embedded object by cataloguing critical points across multiple height-functions. The output of this Morse transform records both the heights and the local topological type (peak, trough or saddle) of the critical points that characterise the underlying shape, retaining finer information than the Euler characteristic transform whilst naturally prioritising a shape's outermost regions. Crucially, this output can be further compressed into a rich but compact feature vector. We benchmark the Morse feature vector as a descriptor for ligand-based virtual screening (LBVS), which intrinsically depends on the shape of molecules. Under a common gradient-boosted tree classification pipeline, Morse descriptors achieve the highest mean AUROC when compared to other topological transform descriptors and to standard shape-based LBVS descriptors.

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25.
arXiv (CS.CL) 2026-06-18

Compact Geometric Representations of Hierarchies

Authors:
Prashant Gokhale↗Piotr Indyk↗Yuhao Liu↗Sandeep Silwal↗Tony Chang Wang↗Haike Xu↗

Computing geometric representations of data is a cornerstone of modern machine learning, typically achieved by training dual encoders which map queries and documents into a shared embedding space. Recent work of You et al. [NeurIPS '25] has extended this approach to hierarchical retrieval, where relevance is determined by the ancestor-descendant relationships in a Directed Acyclic Graph (DAG). While previous work has shown that valid embeddings exist when the number of descendants is small, these bounds degrade significantly for deep hierarchies, requiring dimensions as large as the total number of nodes. In this paper, we investigate compact reachability embeddings for more general graph classes and provide theoretical guarantees for representing hierarchies using embeddings whose dimension depends on structural graph parameters. We prove that for any directed tree, there exists a reachability embedding in constant dimension 3, independent of the tree's size or depth. We generalize this result to graphs characterized by treewidth $t$, constructing embeddings of dimension $O(t \log n)$, where $n$ is the number of nodes. Complementing these upper bounds, we provide matching or near-matching lower bounds, showing that dimension $\Omega(n)$ is necessary for general DAGs and $\Omega(t/\log(n/t))$ is required for graphs of treewidth $t$. We also obtain upper and lower bounds parameterized by the number of cross-edges in the DAG. We additionally show that our embeddings can be constructed on real world datasets, and that they give much smaller dimensions in high recall regimes compared to prior embeddings with theoretical guarantees.

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