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01.
arXiv (CS.CV) 2026-06-15

Conditioning Matters: Stabilizing Inversion and Attention in Diffusion Image Editing

Inversion-based image editing offers flexible and training-free control but still struggles with inversion accuracy and the trade-off between editing fidelity and background preservation. While recent methods improve inversion formulations or attention interactions, the role of textual conditioning in shaping diffusion dynamics and editing behavior remains underexplored. We show both empirically and theoretically that the precision of textual conditioning influences inversion stability by modulating the geometry of the diffusion velocity field, while also affecting the consistency of cross-branch attention during editing. These effects directly impact background preservation and semantic fidelity. Building on this analysis, we propose SimEdit, a conditioning-aware framework with two complementary components: (a) conditioning refinement, which constructs conditioning signals with improved semantic precision and structural alignment to facilitate stable inversion and consistent attention manipulation, and (b) token-wise cross-branch attention control, which separates edit-relevant and structure-preserving components and modulates them asymmetrically during attention manipulation. Extensive experiments on PIE-Bench demonstrate that SimEdit consistently improves both inversion reconstruction quality and editing performance over previous attention-manipulation approaches. Our code is available at https://github.com/zju-pi/SimEdit.

02.
arXiv (CS.AI) 2026-06-12

TerraBench: Can Agents Reason Over Heterogeneous Earth-System Data?

arXiv:2606.13148v1 Announce Type: new Abstract: Climate and environmental decision-making increasingly requires reasoning across heterogeneous inputs, including gridded physical data, satellite imagery, geospatial context, and simulator outputs. Weather and climate foundation models can forecast well, but do not reason interactively in language, while large language models (LLMs) reason in language but cannot operate directly on high-dimensional Earth-system data. As a result, real scientific workflows in Earth-science remain underserved. We introduce TerraBench, a benchmark for grounded Earth-science reasoning, built on TerraAgent, a ReAct-style executable framework that interleaves reasoning, tool calls, and observations to couple LLM planning with scientific tools for environmental retrieval, geospatial processing, simulation, and artifact-backed computation. TerraBench unifies analysis of Earth observation imagery, gridded data, GIS reasoning and simulation in a single executable interface, whereas prior benchmarks isolate these capabilities into narrow individual tasks. It is also the first in this space to pair process-level tool-use metrics with tolerance-aware numeric scoring. The benchmark comprises 403 extensive agentic tasks across three tracks (Fundamentals, Simulator-Grounded, and Document-Grounded Verification) and eight application domains with 24,500 verified execution steps. These results indicate that reliable Earth-science agents must go beyond tool access to coordinate heterogeneous workflows, parameterize tools precisely, and preserve artifact provenance.

03.
arXiv (CS.CV) 2026-06-17

Plug-and-Adapt: Multimodal Coreference Resolution at First Sight with a Pretrained Alignment Model

Visual information helps resolve ambiguity in coreference resolution, leading to notable performance gains. However, existing Multi-modal Coreference Resolution (MCR) methods require training with (partially) annotated data from the target dataset before they can be applied, preventing their direct usability and raising concerns about generalization. While Vision-Language Large Models (VLLMs) with billions of parameters offer promising zero-shot capabilities, they remain largely inaccessible. Their massive size limits deployability, and many are only accessible through paid APIs. In this paper, we propose a plug-and-adapt method that strategically adapts a carefully pre-trained alignment model for immediate use in MCR tasks, designed to eliminate the need for training on scarce benchmark datasets or relying on resource-intensive VLLMs. Specifically, we first pre-train a fine-grained alignment model between textual and visual contextual information using vision-language alignment datasets. We then repurpose the alignment model to MCR through similarity aggregation by fusing visual and categorical cues with evidence theory, thereby enhancing effectiveness. Experiments on the Coreference Image Narratives (CIN) benchmark dataset demonstrate the effectiveness of our method, achieving a 5.31\% and 2.12\% improvement in CoNLL F1 over SOTA dedicated methods and popular VLLMs, respectively. We further evaluate our method on a masked CIN dataset for robustness testing and on a specially constructed VCR-MCR dataset for generalization assessment, with results confirming both capabilities.

04.
medRxiv (Medicine) 2026-06-22

Impact of Antidiabetic Medications on IgG and Plasma Protein N-Glycosylation in Type 2 Diabetes Patients

Introduction. Diabetes is a growing global health challenge, necessitating effective management strategies. Glycosylation, a highly regulated post-translational protein modification, has emerged as a pivotal factor in diabetes pathophysiology. However, the modulation of protein glycosylation by antidiabetic treatment is still largely unknown. This study explored the longitudinal effects of four distinct antidiabetic therapies - metformin, insulin, sodium-glucose cotransporter-2 (SGLT2) inhibitors, and glucagon-like peptide-1 receptor agonists (GLP-1RA) - on plasma protein and immunoglobulin G (IgG) glycosylation in patients with type 2 diabetes (T2D). Research Design and Methods. Plasma protein and IgG N-glycans were enzymatically released, purified and chromatographically profiled in a cohort of 124 patients, examined at four time points, to assess therapy-induced glycan alterations. Linear mixed models adjusting for covariates and multiple testing (FDR

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

Pantheon360: Taming Digital Twin Generation via 3D-Aware 360{\deg} Video Diffusion

Generating complete digital twins from videos requires precise camera control, global scene coverage, and strict spatial-temporal consistency constraints that remain challenging for perspective video generators due to their limited field of view (FoV). Their narrow FoV forces long or multi-view trajectories, amplifying cross-view inconsistency and temporal drift. We argue that 360{\deg} video generation offers a natural solution: panoramic coverage simplifies trajectory design and provides a strong global context for maintaining coherence. We introduce Pantheon360: Taming Digital Twin Generation via 3D-Aware 360{\deg} Video Diffusion, a controllable 360{\deg} video generation framework that synthesizes high-fidelity videos from sparse 360{\deg} inputs. The key idea is an explicit 3D Cache, reconstructed from the input, which serves as a geometric scaffold for any user-defined camera path. This allows the diffusion model to focus on photorealistic texture refinement while the 3D Cache enforces global geometric consistency. Experiments show that Pantheon360 achieves superior visual quality and unmatched geometric coherence, enabling reliable and flexible 360{\deg} scene generation for downstream simulation and digital-twin applications.

06.
PLOS Medicine 2026-05-14

Antibody fine specificity correlates with protection from malaria for the RTS,S vaccine in young African children: A post hoc analysis of a phase IIb randomised controlled trial

作者:

by Alessia Hysa, D. Herbert Opi, Joshua Waterhouse, Sandra Chishimba, Jessica L. Horton, Natalie Kingston, Hans J. Netter, David Wetzel, Michael Piontek, Gaoqian Feng, Jahit Sacarlal, Carlota Dobaño, Liriye Kurtovic, James G. Beeson Background The RTS,S/AS01 malaria vaccine was recently approved for implementation in children, but only provides modest and short-lived efficacy against malaria. RTS,S targets a portion of the Plasmodium falciparum (Pf) circumsporozoite protein (CSP), comprising the central NANP-repeat region and C-terminal domain. Mechanisms of immunity and correlates of protection for the RTS,S vaccine are not well defined, hindering progress towards generating highly effective CSP-based vaccines. Methods and findings We investigated epitope specificity and cross-reactivity of vaccine-induced antibodies to six peptides representing CSP epitopes in the N-terminal and central NANP-repeat region. We evaluated antibody reactivity in preclinical mouse vaccine studies, among CSP-specific monoclonal antibodies (mAbs), and in a large RTS,S phase IIb clinical trial in young children 1–4 years old (n = 735).The preclinical mouse vaccine studies and CSP-specific mAbs were used to initially evaluate IgG responses to the six peptides. Mice immunised with the central NANP-repeat region had IgG with cross-reactivity to an epitope in the N-terminal region. Additionally, we demonstrated that a single CSP-specific mAb could display cross-reactivity to several CSP epitopes. Through post hoc quantification and analysis of antibody responses in the RTS,S phase IIb clinical trial, we found that a subset of children generated IgG with specificity for a short NANP-repeat epitope (NANP2; amino acid sequence: NANPNANP) and cross-reactivity to an N-terminal epitope (J1; amino acid sequence: KQPADGNPDPNANPN). Notably, children with high IgG responses to NANP2 and J1 had a significantly reduced risk of clinical malaria, compared to children with low responses (IgG to NANP2 (aHR: 0.838 (95% CI [0.716, 0.981]; p = 0.028)) and J1 (aHR: 0.718 (95% CI [0.611, 0.844]; p 

07.
Nature (Science) 2026-06-22

Why heritage sites are at risk in a warming world — and how to save them

As rising seas and intensifying disasters threaten historic sites worldwide, new ways to understand, preserve and adapt these places are needed urgently. As rising seas and intensifying disasters threaten historic sites worldwide, new ways to understand, preserve and adapt these places are needed urgently.

08.
arXiv (CS.CL) 2026-06-19

When Does Streaming Tool Use Help? Characterizing Tool-Intent Stabilization in Streaming Retrieval-Augmented Generation

Streaming Retrieval-Augmented Generation (Streaming RAG) reduces user-perceived latency by issuing tool queries in parallel with ongoing user input, before the utterance is complete. Reported gains are aggregate, yet the mechanism's benefit is fundamentally query-intrinsic: speculation can only help when the correct tool query becomes determinable before the user stops speaking or typing. We isolate and measure this property – tool-intent stabilization, the point in the input stream at which a speculative query's retrieval converges to the answer-bearing result. On the CRAG benchmark (1371 validation questions) we (i) measure the distribution of stabilization, (ii) derive a model-agnostic bound H on the portion of tool latency that can be hidden behind the user's remaining input, as a function of tool latency L and input cadence {\delta}, (iii) validate against a working streaming pipeline that realized savings meet or exceed this bound, and (iv) identify which query properties predict early versus late stabilization. The study requires no model training and runs on commodity CPU hardware. We find that at a realistic operating point (L=600ms, {\delta}=3w/s, {\theta}=0.8), 73.9% of queries across the full benchmark admit substantial latency hiding – a blended figure that mixes sufficiency stabilization on the 21.3% of questions where gold evidence is verbatim-present and BM25-retrievable (95.2% streamable on this favorable slice) with a grounding-free top-1-settling fallback on the remainder. On the favorable slice, {\phi}_suf is bracketed to [0.26, 0.281] by exact and relaxed grounding – both early. Question type produces a significant but coarse early/late split (Kruskal-Wallis p=0.017, epsilon^2=0.04), directly informing when a learned speculative trigger is worth its cost.

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

Neuro-Symbolic Agents for Regulated Process Automation: Challenges and Research Agenda

arXiv:2606.13405v1 Announce Type: new Abstract: LLM-based agents are entering regulated industries where they automate judgment intensive quality management processes. We argue that symbolic structures already embedded in these domains, including regulations, typed process models, and compliance constraints, should be treated not merely as external monitoring mechanisms but as core architectural components that shape the agent's decision-making and behavior. We propose compliance-by-construction as a complementary paradigm to guardrail-based monitoring: a structural foundation that prevents control-flow violations, while guardrails remain essential for catching semantic errors. We identify a structured set of neuro-symbolic research challenges on foundational and capability level and show that addressing them jointly enables compliance-by-construction. We call on the neuro-symbolic community to engage with regulated process automation as a high impact research domain.

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

Remote sensing data imputation using deep learning for multispectral imagery

Remote sensing techniques have been increasingly utilised in aquatic applications in recent years. A common challenge in using optical satellite data is the presence of missing observations due to cloud cover. These data gaps can lead to missed detection of critical events, such as algal blooms, in lakes of high interest to water authorities. As a result, enhancing the completeness of optical satellite datasets is crucial for improving the monitoring and prediction of algal blooms. In this study, we compared a traditional data imputation method (i.e., linear interpolation) with deep learning models for reconstructing missing spectral bands across four lakes with historical records of algal blooms. The deep learning models adopted include CNN-based architectures (i.e., CNN, Inception Resnet, and Autoencoder) and CNN-LSTM-based architectures (i.e., CNN-LSTM, Resnet-LSTM, and Autoencoder-LSTM). Our results demonstrated that deep learning models substantially outperformed the baseline linear interpolation method in imputing spectral band values within artificially masked regions. Among these models, CNN delivered the best performance across most lakes. Furthermore, we evaluated the performance of algal bloom indices (i.e., Green/Red and NDCI) derived from the imputed imagery by comparing them with the observed data. Our results demonstrate that deep learning models are effective for imputing missing data in PlanetScope SuperDove imagery, enabling more reliable applications in water monitoring.

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

Unstable Features, Reproducible Subspaces: Understanding Seed Dependence in Sparse Autoencoders

Sparse autoencoders (SAEs) are widely used to interpret neural network representations, but their utility depends on whether the learned features are reproducible across training runs. We study this question through feature stability: for each SAE feature, we estimate the probability that a similar feature reappears in an independently trained SAE. This yields a scalable per-feature signal that separates stable from unstable features. In a large-scale study across seeds, models, layers, dictionary sizes, and SAE variants, we find a pronounced functional asymmetry: stable features carry most of the reconstruction- and prediction-relevant signal, while unstable features have weak marginal impact and are dominated by low-frequency surface-form triggers in both activation statistics and automatic explanations. Geometrically, unstable features are individually non-reproducible but concentrate in reproducible lower-rank subspaces, suggesting that seed dependence often reflects basis ambiguity within a shared region of activation space rather than pure noise. A controlled synthetic model makes this mechanism explicit, showing that low-rank ground-truth features can be recovered at the subspace level while remaining non-identifiable as individual SAE latents across seeds. Finally, by pooling unique cross-seed features, we construct more stable SAEs while preserving explained variance in this setting. Together, these results show that unstable features are not merely failed or noisy latents: they have weak individual functional impact, but reflect reproducible low-dimensional structure that standard SAEs resolve differently across seeds.

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

Telenor Nordics Customer Service self-help corpus

作者:

This paper presents a multilingual customer service self-help corpus comprising 1,122 manually validated documents in Finnish, Danish, Norwegian, and Swedish, totaling 274,599 words and 1,884,833 characters. The documents have been sourced from the public self-help pages of four Nordic telecommunications operators and subsequently filtered for person-identifiable information and relevance through a combined LLM and human annotation pipeline. Domain-specific datasets for Nordic languages remain scarce, particularly in customer service: a domain of growing importance for retrieval-augmented generation, cross-lingual transfer learning, and emerging agent-based service architectures. An analysis of the corpus reveals substantial variation in document length and structure across operators, reflecting distinct editorial strategies, as well as broad topical coverage spanning network hardware, mobile services, TV and streaming, billing, and account management. The dataset is publicly available under a CC-BY-NC-SA-4.0 license at https://zenodo.org/records/20732652, intended to support reproducible research in Nordic NLP and information retrieval.

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

Vernier: Probing Representational Misalignment Behind Lexical Gaps in Causal Reasoning

作者:

Instruction-tuned language models can answer the same causal-reasoning question differently after its English variable names are replaced by type-preserving placeholders, although the structural causal model and the gold answer are unchanged. We ask whether this lexical gap reflects information loss in the placeholder view or a misaligned read-out from a representation that still carries answer-relevant content. Vernier uses a paired-view weight update as an instrument and then inspects the mechanism left after the gap closes. In the working regimes, the evidence favours representational misalignment. A variable-name probe becomes more accurate on the placeholder view, and activation patching on Qwen-7B, Qwen-14B, and Llama-3.1-8B shows that the decision-token representation can transfer answer identity between views. The update that realigns the views is counterfactual augmentation over original and placeholder prompts, while the answer-subspace KL mainly sharpens intermediate answer-belief agreement. Success is bounded by model family, scale, and task. CRASS transfer is reliable across Qwen scales and Llama, e-CARE remains weak, and preliminary non-causal rename tasks show a similar qualitative pattern.

14.
arXiv (CS.LG) 2026-06-19

Unsupervised Causal Abstractions Discovery

arXiv:2606.19594v1 Announce Type: new Abstract: Causal abstractions formalize when a high-level structural causal model (SCM) captures the interventional behavior of a lower-level SCM. Existing applications of this notion largely follow a hypothesis-testing paradigm: an expert proposes a candidate high-level model and then evaluates if the low-level system implements it. We study the complementary problem of learning a high-level model directly from low-level measurements. Our contributions leverage hypotheses from low-rank causal discovery, and can be summarized as follows: (1) we show that observations generated by a low-rank graph induce latents that form a causal abstraction, (2) we provide identifiability results about these latents, and (3) we propose a practical objective to learn this high-level SCM.

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

WAM4D: Fast 4D World Action Model via Spatial Register Tokens

World action models (WAMs) have recently shown promise in jointly modeling future observations and executable robot actions. However, most existing WAMs still operate in 2D video or latent spaces, where visually plausible rollouts miss the 3D spatial constraints and occluded contact geometry required for precise manipulation. While geometric foundation models offer strong priors for recovering dense 3D structure and motion from visual observations, forcing WAMs to predict the dense 4D representation introduces costly geometric decoding and slows down causal action generation. To address the trade-off, we present WAM4D, a fast 4D world action model that uses lightweight spatial register tokens as training-time future-depth readouts to transfer pretrained geometric priors into a causal video-action transformer, then removes the register branch for lightweight action inference. To prevent non-causal shortcuts, we further design causal mixture attention for the Mixture-of-Transformers (MoT) WAM backbone, defining modality-specific visibility among video, action, and geometry tokens. Comprehensive experiments on RoboTwin 2.0 and challenging real-world manipulation tasks show that WAM4D improves spatial consistency and achieves competitive action prediction while maintaining efficient inference.

16.
arXiv (quant-ph) 2026-06-11

Quantum iterative approach to the Traveling Salesman Problem

arXiv:2606.11843v1 Announce Type: new Abstract: The Traveling Salesman Problem (TSP) is a classical NP-hard problem in combinatorial optimization, where determining the shortest route among a set of cities becomes computationally prohibitive as the problem size increases. This work explores quantum computing as an alternative approach to address this complexity. Unlike existing methods that primarily rely on quantum annealing, we propose a quantum iterative framework integrating Quantum Phase Estimation (QPE) and Grover's search algorithm. Route costs are encoded as quantum phases, enabling QPE to efficiently evaluate them, while Amplitude Amplification, implemented via the Grover-Long algorithm, iteratively refines the solution space toward the optimal route. A proof-of-concept case study on a small-scale TSP instance demonstrates the feasibility of this approach and its potential for scaling to larger optimization problems. Furthermore, under an expectation-based analysis, the algorithm exhibits an expected computational complexity of $O(\frac{m^2\log_2(m)\log_2(1/\epsilon)}{\sqrt{\epsilon}})$ which depends on the error tolerance parameter $\epsilon$. This estimation omits the initialization term, which we expect future refinements to render subdominant to Phase Estimation.

17.
arXiv (CS.CL) 2026-06-11

Lius: Translation Model Based Instructional Lingustic Using Continual Instruction Tuning In Kupang Malay

Large Language Models (LLMs) offer new potential for translation tasks but often experience performance degradation when handling low-resource languages. To address this limitation, we propose an approach for fine-tuning LLMs on a low-resource language, Kupang Malay. Our approach involves designing a set of instructions by leveraging explicit lexical and semantic features from a bilingual dictionary, and introducing Continual Instruction Tuning (CIT), a training paradigm that enables iterative instruction-based training. Experimental results demonstrate that our model, named Lius, yields notable improvements over standard instruction-tuned models by outperforming 4-6 points, and surpassing both Neural Machine Translation (NMT) and Multilingual LLM models by 10-13 points on several evaluation metrics. These findings highlight the potential of our approach to mitigate the reliance on large-scale parallel data in low-resource language translation.

18.
arXiv (CS.AI) 2026-06-11

When Poison Fails After Retrieval: Revisiting Corpus Poisoning under Chunking and Reranking Pipelines

arXiv:2606.11265v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) systems are vulnerable to corpus poisoning attacks that manipulate downstream model outputs through malicious knowledge injection. Existing studies mainly evaluate poisoning under simplified retrieval settings, overlooking practical RAG pipelines involving document chunking, dense retrieval, reranking, and grounded generation. In this paper, we revisit corpus poisoning under realistic multi-stage retrieval pipelines and show that many existing attacks substantially degrade after reranking despite achieving high retrieval-stage relevance. We identify retrieval granularity mismatch as a key reason for this failure: document-level adversarial signals are often fragmented during chunking, while rerankers favor locally coherent and answer-bearing passages rather than globally optimized semantic similarity. Based on this observation, we propose Chunk-aware and Rerank-Consistent Poisoning (CRCP), a poisoning framework that jointly optimizes retrieval relevance, reranker consistency, and chunk-boundary robustness. CRCP explicitly models chunking transformations during optimization to generate locally self-contained adversarial passages that remain effective under varying chunking configurations. Experiments on standard RAG benchmarks with multiple retrievers and rerankers show that existing poisoning methods are highly sensitive to chunk size and reranking strategies, whereas CRCP achieves substantially higher attack success rates and stronger robustness across realistic retrieval pipelines. Our findings highlight an important realism gap in current RAG security evaluation and suggest that poisoning in modern RAG systems should be studied as a multi-stage retrieval consistency problem rather than a retrieval-only problem.

19.
medRxiv (Medicine) 2026-06-17

Identifying anaphylaxis using weakly-supervised prediction models and natural language processing

Objectives Scalable computable phenotyping algorithms are critical for conducting high-throughput disease-outcome research in large, distributed-data electronic health record (EHR) and claims data settings. We developed and evaluated a claims- and EHR-based computable phenotyping algorithm for anaphylaxis, a rare acute condition that is challenging to accurately identify using claims data alone. Materials and Methods Potential anaphylaxis events came from two healthcare systems (Kaiser Permanente Washington [KPWA] and Vanderbilt University Medical Center [VUMC]). We engineered features from clinical text using automated natural language processing (NLP) methods. We then developed a phenotyping algorithm using four NLP- and diagnosis code-based silver labels (proxies for the gold-standard labels). Gold-standard abstracted outcomes were used to evaluate algorithm performance. Results The largest area under the receiver operating characteristic curve (AUC) was 0.931 for an NLP-based silver-label model at KPWA. Depending on the model and healthcare system site, positive predictive value (PPV) and sensitivity at the threshold of predicted probability that maximized F1 score ranged from 0.52 to 0.77 (PPV) and 0.78 to 1 (sensitivity). Discussion NLP-based silver-label models had large AUC at KPWA but not at VUMC. This may be because clinical text at KPWA is only available for outpatient encounters and secure messaging. High sensitivity for identifying anaphylaxis can be obtained using our best-performing models. Conclusion The best-performing models had better PPV and sensitivity tradeoffs than prior bespoke anaphylaxis models with costly, manually curated features. The simplicity of the approach compared to traditional phenotyping methods allows it to be deployed easily at multiple health care systems.

20.
arXiv (quant-ph) 2026-06-17

Hamiltonian description of nonreciprocal interactions

arXiv:2505.05246v5 Announce Type: replace-cross Abstract: In a vast class of systems, which includes members as diverse as sedimenting particles and bird flocks, interactions do not stem from a potential, and are in general nonreciprocal. Thus, it is not possible to define a conventional energy function, nor to use analytical or numerical tools that rely on it. Here, we overcome these limitations by constructing a Hamiltonian that includes auxiliary degrees of freedom; when subject to a constraint, this Hamiltonian yields the original nonreciprocal dynamics. We show that Glauber dynamics based on the constrained Hamiltonian reproduce both stationary and nonstationary states of the original Langevin dynamics, as we explicitly illustrate for dissipative XY spins with vision-cone interactions. Further, the symplectic structure inherent to our construction enables us to apply the well-developed notions of Hamiltonian engineering, which we demonstrate by varying the amplitude of a periodic drive to tune the spin interactions between those of a square and a chain lattice geometry. Overall, our framework for generic nonreciprocal pairwise interactions paves the way for bringing to bear the full conceptual and methodological power of conventional statistical mechanics and Hamiltonian dynamics to nonreciprocal systems.

21.
medRxiv (Medicine) 2026-06-12

Deconvolution-based cell-type specific DNA methylation-wide and transcriptome-wide association studies identify risk CpG sites and genes associated with colorectal cancer risk

Bulk tissue-based DNA methylation-wide (MWAS) and transcriptome-wide association studies (TWAS) have identified CpG sites and genes associated with colorectal cancer (CRC) risk, but do not account for cellular heterogeneity. To address this, we developed a deconvolution-informed framework to infer cell-type specific DNA methylation and gene expression profiles from bulk normal colon tissues using reference single-cell epigenomic and transcriptomic datasets. We performed cell-type specific MWAS (ctMWAS) using deconvoluted DNA methylation data from 293 normal colon samples and conducted cell-type specific TWAS (ctTWAS) using deconvoluted gene expression data from 707 normal colon samples. Genetically predicted methylation and expression models were integrated with CRC GWAS summary statistics (78,473 cases and 107,143 controls) to identify risk-associated CpG sites and genes. Through ctMWAS, ctTWAS, and colocalization analyses, we identified 178 significant cell-type-specific CpG sites in 106 loci and 68 risk genes in 40 loci, including 26 previously unreported loci. Through additional integrative methylation-gene analysis, we prioritized 132 candidate risk genes, the majority of which were supported by multi-omics evidence and stage-specific dysregulation across the adenoma-carcinoma and serrated-carcinoma progression pathways. Pathway enrichment analyses implicated pathways involved in DNA double-strand break repair, TP53 regulation, TGF-{beta} signaling, and innate immune responses. Among prioritized genes, 14 were identified as putative druggable targets linked to 90 FDA-approved or clinical-stage drugs. Experimental validation supports an oncogenic role for SF3A3. These findings demonstrate that deconvolution-informed integrative analyses enable cell-type-resolved identification of epigenetic and transcriptional mechanisms underlying CRC susceptibility and provide insights into disease biology, prevention, and therapeutic target discovery.

22.
arXiv (CS.CL) 2026-06-16

PaperJury: Due-Process Review for Bounded LaTeX Revision

Pre-submission hardening of human-authored LaTeX computer science papers differs from drafting assistance because it requires adversarial whole-paper review, explicit no-fix outcomes, and bounded artifact-safe revision. Existing writing assistants, critique generators, and judge-centered loops lack durable issue identity across rounds, deterministic routing from critique to adjudication, and manuscript control that can reject invalid concerns or defer author-dependent ones. We present PaperJury, a closed-loop review-verdict-revise-verify system built on a deterministic-versus-semantic split: deterministic orchestration manages decomposition, a frozen claim spine, a durable ledger, routing, stopping, and exact-once patch application, while semantic agents are limited to bounded review, judgment, and repair. PaperJury combines bounded holistic review, contestability-based routing, a due-process trial, and risk-proportional guard chains for anchor-bounded edits, yielding terminal outcomes of invalid-drop, valid-fixable, and author-required. In a two-arm expert-review evaluation on held-out Vision, natural language processing, and machine learning papers against four baselines, we assess issue quality, verdict and routing quality, edit safety, convergence behavior, and cost, supporting the thesis that load-bearing safety and completion logic should reside in deterministic orchestration rather than model discretion. PaperJury is available at https://github.com/u7079256/paperjury.

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

TacCoRL: Integrating Tactile Feedback into VLA via Simulation

arXiv:2606.11743v1 Announce Type: cross Abstract: Vision-language-action (VLA) models provide strong visual, language, and action priors for robot manipulation, but visual observations alone often miss the local contact state required for contact-rich tasks. We present TacCoRL, a scalable framework that injects Tactile feedback into VLA policies and improves them through sim-real Co-training and simulation-based reinforcement learning (RL), without requiring large-scale tactile pretraining or extensive real-world contact exploration. The key idea is not only adding touch as an input, but learning how contact readings should modulate action responses in near-failure states that are rare in demonstrations and risky to collect on hardware. We use a real-aligned simulator as a closed-loop training environment for contact interaction. Mixed simulated and real trajectories first warm-start tactile-conditioned actions in the pretrained policy. Reinforcement learning with verifiable task rewards then optimizes the policy using simulated contact rollouts. It reinforces tactile-conditioned actions that lead to task completion, while a supervised objective on real trajectories keeps the refined policy anchored to deployment visual, tactile, and action distributions. The resulting policy transfers directly to the real robot without privileged simulation state or online real-world RL. Across four bimanual contact-rich tasks, the final visuo-tactile policy achieves an average success rate of 72.5%, compared to baseline of 50.0%. Result videos and more details are available at https://tac-corl.github.io/

24.
medRxiv (Medicine) 2026-06-10

General-purpose large language models can achieve physician-level accuracy in complex medical data extraction

Background: Unstructured data represent about 80% of total electronic health records (EHR) data. Structuring this free text is essential for advancing clinical research, including cohort selection for trials, retrospective studies, and the development of disease registries. While manual chart review (MCR) remains the gold standard for extracting this clinical data, the process is inherently slow, resource-intensive, and susceptible to errors from human fatigue. We evaluated the extraction accuracy, safety, and efficiency of the HeLIX (Hepatology Logic-Integrated Extraction) framework, a Large Language Model (LLM) protocol using Google Gemini 3 Pro, compared to a gold-standard Manual Chart Review (MCR). Methods: A prospective validation study was conducted using 50 high-complexity, simulated hepatology discharge summaries designed to replicate the real-world heterogeneity of EHRs. The HeLIX framework employed a Zero-Shot, Structured Chain-of-Thought (CoT) prompting strategy enforced by a three-layer architecture: Clinical Reasoning Trace, Schema Enforcement, and Evidence Verification. The model extracted 45 distinct clinical variables. Performance was benchmarked against a consensus MCR. Results: Across 2,250 evaluated data points, the model achieved an overall Extraction Accuracy of 99.24% (95% CI: 98.8%-99.5%), with perfect concordance in 35/45 (77.8%) variables. For binary diagnostic variables, the model demonstrated an overall F1-score of 0.98, Recall of 0.99 and substantial inter-rater reliability (Cohens {kappa} = 0.97). Hallucinations were exceptionally rare (2/2250; 0.08%). Critical errors affecting clinical management occurred in only 2 instances (

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

Graph Neural Networks for Semi-Supervised Image Classification with Multi-Feature Aggregation

Feature extraction involves the identification and extraction of salient characteristics or patterns, including edges, textures, shapes, and color attributes. Contemporary feature extractors predominantly leverage deep learning architectures, such as Convolutional Neural Networks (CNNs) and Vision Transformers (VITs). The availability of diverse feature extractors in the literature provides a wide range of feature representations. Features extracted from an image depend on the specific application, the chosen extractor, and its configuration. Therefore, integrating complementary information by combining distinct extractors offers a promising way to enhance performance. Graph Neural Networks (GNNs), particularly Graph Convolutional Networks (GCNs), have emerged as powerful and widely adopted approaches for semi-supervised image classification, as they effectively leverage both labeled and unlabeled data while exploiting the underlying graph structures that capture relationships among samples. This study proposes a novel approach for GNNs in scenarios where labeled data is scarce, by integrating diverse sets of feature and graph representations derived from various extractors in classification scenarios. Experimental investigations were conducted, encompassing combinations of distinct feature and graph extractors, as well as rank aggregation strategies. The primary contributions of this work are underscored by the experimental findings, which demonstrate that the strategic combination of feature and graph representations, coupled with the application of manifold learning for graph processing, leads to significant improvements in classification accuracy across the majority of experimental conditions. Furthermore, the utilization of rank aggregation techniques to integrate features from different extractors was shown to enhance classification accuracy.