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01.
medRxiv (Medicine) 2026-06-17

Real-World Effectiveness and Safety of Avacopan in ANCA-Associated Vasculitis: A Systematic Literature Review and Meta-analysis

Background: The efficacy and safety of avacopan in ANCA-associated vasculitis (AAV) has been established in randomized trials of of avacopan as a glucocorticoid (GC) sparing therapy. However, real world evidence (RWE) has an important role in confirming effectiveness and evaluating safety in more generalizable settings. This study aimed to synthesize RWE on the effectiveness and safety of avacopan in adults with AAV. Methods: A systematic literature review and meta analysis of non interventional real world studies was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) guidelines. Eligible studies included adults with AAV treated with avacopan in routine clinical practice. Pooled estimates of effectiveness and safety outcomes were calculated using random effects meta-analyses. Primary outcomes included remission at 6 and 12 months and sustained remission at 12 months. Secondary outcomes included relapse, GC use and dosing, hepatotoxicity, infections, and treatment discontinuation. Exploratory outcomes included changes in estimated glomerular filtration rate (eGFR) and dialysis related endpoints. Results: A total of 71 studies were included and contributed to quantitative analyses. Pooled remission for patients on avacopan was 87% (95% CI: 75%-94%) at 6 months and 93% (95% CI: 86%-97%) at 12 months, and sustained remission was 86% (95% CI: 74%-93%) at 12 months. Relapse at 12 months was low (7%; 95% CI: 4%-11%). GC use was 36% at both 6 and 12 months. Improvements in eGFR were observed at 6 months (18 mL/min/1.73 m2) and 12 months (18 mL/min/1.73 m2), and dialysis liberation was 66% in a limited subset. Among avacopan patients, 11% experienced any hepatotoxicity, including 7% with serious (defined as directly reported or requiring hospitalization) hepatotoxicity, while 7% experienced serious (defined as directly reported or requiring hospitalization) infection. Conclusions: In real world clinical practice, avacopan is associated with high remission rates, low relapse rates, and a consistent GC sparing effect, with effectiveness comparable to standard of care regimens. Findings support its clinical use with appropriate safety monitoring; however, the observed heterogeneity in hepatotoxicity and the limited comparative effectiveness evidence highlight areas requiring further investigation.

02.
Nature Biotechnology 2026-06-23

Efficient generation of epitope-targeted antibodies with Germinal

Obtaining antibodies to specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success rates that require resource-intensive screening. Here we introduce Germinal, a broadly enabling generative pipeline that designs antibodies against specific epitopes with nanomolar binding affinities while requiring only low-n experimental testing. Our method co-optimizes antibody structure and sequence by integrating a structure predictor with an antibody-specific protein language model to perform de novo design of functional complementarity-determining regions onto a user-specified structural framework. When tested against four diverse protein targets, Germinal designed functional antibodies across all targets and binder formats, testing only 43–101 designs for each antigen. Validated designs also exhibited robust expression in mammalian cells and high sequence and structural novelty. We provide open-source code and full computational and experimental protocols to facilitate wide adoption. Germinal achieves epitope-targeted, de novo complementarity-determining region design with high experimental success rates.

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

Scratched Lenses, Shifted Depth: Passive Camera-Side Optical Attacks

Physical adversarial attacks on vision systems are typically studied through scene manipulation, such as adversarial patches or projections, where the adversary controls what the camera observes. Camera-side attacks using stickers or auxiliary optics have also been explored, but they treat attacks as image-space perturbations from designed patterns. This misses how physical imperfections interact with scene-dependent lighting and optics. We identify a threat: passive lens-side damage that is persistent yet trigger-conditioned, producing optical artifacts that bias geometric inference under particular visual conditions. We instantiate this threat through Scratch-induced Lens Adversarial Streak Hijacking SLASH, a physical-world attack caused by small scratches on a camera lens or protective cover. Scratches interact with bright light sources and specular reflections to create structured streak artifacts that distort depth cues. Since the perturbation is fixed in the optical path but triggered by the scene, it is both persistent and selective. We formulate the attack in optical space, model the scratch pattern as a trigger-conditioned optical channel, and optimize one fixed configuration across diverse viewing conditions. We evaluate SLASH on monocular depth estimation and monocular 3D object detection in digital and real-world settings. Under the fixed-scratch constraint, directional depth shifts reach up to 32% relative error for monocular depth estimation, with consistent effects on monocular 3D object detection. Physical experiments confirm transfer to real camera recordings, inducing depth shifts above the model's natural prediction baseline. These findings reveal an attack surface where benign-looking hardware imperfections act as latent, scene-triggered adversarial mechanisms, challenging assumptions about physical robustness and motivating defenses for secure vision systems.

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

Getting Better at Working With You: Compiling User Corrections into Runtime Enforcement for Coding Agents

Interactive LLM agents are becoming part of daily work, but they do not reliably become easier to work with over time: a correction remembered in one session may still be violated in the next. We study this gap between preference access and preference compliance. In tasks derived from anonymized real-user friction cases, Mem0 memory still leaves 57.5% of applicable preference checks violated. We introduce Test-time Rule Acquisition and Compiled Enforcement (TRACE), a drop-in skill-layer pipeline for coding-agent runtimes that mines user corrections, rewrites them as atomic rules, and compiles them into runtime checks that must pass before an agent completes future tasks. Unlike runtime checks written ahead of time by developers, TRACE skills come from the user's own chat corrections. We evaluate TRACE with simulated user-in-the-loop experiments on ClawArena coding-agent tasks and MemoryArena-derived memory-intensive tasks. On ClawArena, TRACE reduces held-out preference violation from 100.0% to 37.6% on in-distribution tasks and from 100.0% to 2.0% on out-of-distribution tasks. On MemoryArena-derived tasks, TRACE reduces in-distribution violation from 100.0% to 60.5% while matching or exceeding the strongest memory baseline on task pass. These results suggest that compiling corrections into runtime enforcement can address a repeated-friction failure mode that memory alone does not reliably solve, reducing the need for users to restate the same correction across future sessions. Experiment code is available at https://github.com/YujunZhou/TRACE_exp, and the deployable skill is available at https://github.com/YujunZhou/tellonce.

05.
arXiv (CS.LG) 2026-06-11

Finding Multiple Interpretations in Datasets

arXiv:2606.12277v1 Announce Type: new Abstract: In this paper, we propose an approach to finding sets of similar-performing models (in terms of loss/accuracy measurements) with highly different context-aware characteristics. Through experiments on the METABRIC dataset, we show that the proposed method finds multiple models with highly different gene expressions than those found by the control methodology without performance penalties. We argue that the proposed methodology is important whenever one aims to analyze any global characteristic of a model to extract insight into the underlying phenomenon being studied.

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

Towards Physically Realizable Adversarial Attenuation Patch against SAR Object Detection

Deep neural networks have demonstrated excellent performance in SAR target detection tasks but remain susceptible to adversarial attacks. Existing SAR-specific attack methods can effectively deceive detectors; however, they often introduce noticeable perturbations and are largely confined to digital domain, neglecting physical implementation constrains for attacking SAR systems. In this paper, a novel Adversarial Attenuation Patch (AAP) method is proposed that employs energy-constrained optimization strategy coupled with an attenuation-based deployment framework to achieve a seamless balance between attack effectiveness and stealthiness. More importantly, AAP exhibits strong potential for physical realization by aligning with signal-level electronic jamming mechanisms. Experimental results show that AAP effectively degrades detection performance while preserving high imperceptibility, and shows favorable transferability across different models. This study provides a physical grounded perspective for adversarial attacks on SAR target detection systems and facilitates the design of more covert and practically deployable attack strategies. The source code is made available at https://github.com/boremycin/SAAP.

07.
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.

08.
medRxiv (Medicine) 2026-06-16

Usability testing with a prototype user interface of an Artificial Intelligence driven air-Safety Tool (AISaT)

Involving end-users in the development of an AI tool is an important facilitator to its implementation. Usability testing was therefore conducted with a prototype user interface of an Artificial Intelligence driven air-Safety Tool (AISaT) to capture the perspectives and user experiences of AISaT from 10 staff members across two hospitals working within estates, infection prevention and control, and clinical areas, to inform the development of next iterations of AISaT. The perspectives shared could be grouped under improvements to the understand-ability; content; navigation; visibility; usability; workflow; ownership; and frequency of use of the tool. There were key areas that can and will be easily improved within AISaT, however there were areas that required a deeper level of critical reflection, such as incorporating data on more existing variables in a room (i.e., existing ventilation) and whether all patients should be assumed as infectious and breathing heavily. The research team must consider if the target audience of end users and recommended frequency of AISaT use will be pre-defined by the tool developers, or whether this level of detail should be left to each individual hospital to decide.

09.
arXiv (CS.AI) 2026-06-16

Mojo: A Promising Tool for Scalable Financial AI Efficiency

Authors:

arXiv:2606.16059v1 Announce Type: cross Abstract: For thirty years, quantitative finance has paid a costly two-language tax: models researched in Python are rewritten in C++ for production, often introducing numerical discrepancies. GPU-accelerated deep learning exacerbates this problem, as nondeterministic floating-point reductions can produce drift in long backtests, challenging regulatory reproducibility and auditability expectations. This article surveys Mojo, Modular's 2026 Python-like systems language, as a structural response for capital markets engineering. While closing the Python-to-C++ performance gap, Mojo uniquely combines native interoperability with the low-level systems control required to construct bit-exact deterministic kernels. Its MLIR compilation infrastructure further allows a single codebase to target scalar, SIMD, multicore, and GPU execution, reducing the translation bottleneck between research and production. We benchmark four core financial AI workloads: Monte Carlo option pricing, LLM sentiment inference, multi-asset backtesting, and portfolio Value at Risk. On Apple Silicon, Mojo demonstrates 20x to 180x speedups over pure Python on directly measured kernels; larger-scale GPU workload results are projections calibrated from published benchmarks. Alongside transparent performance data, we introduce mojo-deterministic, an open-source library of reproducible reduction kernels, and provide a candid assessment of the problems Mojo does and does not yet solve.

10.
bioRxiv (Bioinfo) 2026-06-22

EventHorizon: A Foundation Model for Clinical Flow Cytometry

Flow cytometry is an essential tool for diagnosis of hematologic malignancies, but existing clinical workflows are highly dependent on expert manual interpretation. Existing machine learning approaches typically require extensive labeled data and are sensitive to variability in panel design, instrumentation, and laboratory workflows, limiting their generalizability. We present EventHorizon, a self-supervised foundation model for clinical flow cytometry that produces unified specimen-level representations from heterogeneous multi-panel data. EventHorizon employs a two-stage hierarchical transformer architecture with marker-aware tokenization, enabling seamless integration of cells measured across different antibody panels into a single shared latent space. We pre-train the model using a DINO-inspired self-distillation strategy with a variety of flow cytometry-specific augmentations on a dataset of more than 100,000 clinical specimens across 17 distinct panels. We evaluate the resulting embeddings on three clinically relevant classification tasks spanning common and rare panels, demonstrating that simple k-nearest neighbor probing of frozen EventHorizon embeddings achieves performance comparable to a fully supervised baseline model and a prior panel-specific self-supervised model. To ensure EventHorizon is not simply shortcut learning on features such as the markers/panels run for a given specimen, we perform a graph-theoretic analysis of EventHorizon's latent space which argues that specimen embeddings are organized primarily by biological diagnosis. Taken together, these results demonstrate that EventHorizon produces biologically meaningful, panel-agnostic specimen representations from clinical flow cytometry data which, with further development and validation, could provide a potential basis for scalable, reproducible diagnostic support across diverse clinical laboratory settings.

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

Does Mixture-of-Experts Actually Help Inference on Consumer and Edge Hardware? An Empirical Study

arXiv:2606.21428v2 Announce Type: replace-cross Abstract: Mixture-of-Experts (MoE) language models are often described as ideal for resource-constrained inference. Each token activates only a small subset of experts, so the per-token compute cost, in floating-point operations (FLOPs), resembles that of a much smaller dense model. Whether that FLOP advantage survives in practice is far less clear. We ask whether MoE models actually run faster and cheaper than comparable dense models on consumer-grade and edge hardware. We benchmark OLMoE-1B-7B (1.3 B active of 6.9 B total) against three dense baselines on an Apple M2 Pro and an NVIDIA Jetson Orin Nano 8 GB through \texttt{llama.cpp}, measuring throughput, memory, and on-device energy. The answer is device-dependent: OLMoE's active-parameter advantage is only partly realised on the laptop (~10% behind the same-active Llama-3.2-1B) and erodes on the edge device (~31% behind, at 2.1$\times$ the energy per token, with peak memory at the 8 GB ceiling). Patching \texttt{llama.cpp} to time the decode graph node-by-node shows routing accounts for under 9% of MoE-block compute on the cleaner edge backend, so the gap reflects total-parameter memory footprint, expert dispatch, and KV-cache pressure rather than routing. The implication is that on bandwidth-bound edge hardware, inference cost tracks total parameters, not active ones, and sparse activation does not buy back what the device is constrained on. These findings are bounded to one MoE model at this parameter scale and two devices, and we release the full measurement harness and per-run data.

12.
arXiv (CS.LG) 2026-06-11

Family-Aware Residual Architecture for Predicting Quantum Circuit Simulation Performance

arXiv:2606.11620v1 Announce Type: cross Abstract: Approximate tensor-network simulators enable classical simulation of quantum circuits beyond the reach of exact methods, but selecting optimal approximation parameters – such as bond dimension thresholds – remains a costly trial-and-error process. We present a family-aware neural architecture that predicts both the minimum approximation threshold required to achieve target fidelity and the expected wall-clock runtime for quantum circuit simulation, given only the circuit's OpenQASM description and execution context. Our key insight is that quantum circuits from different algorithmic families (e.g., QFT, Grover, VQE) exhibit fundamentally distinct simulation cost profiles due to their differing entanglement structures. We employ family-conditioned residual corrections – additive, family-specific adjustments atop a shared backbone, drawing on established conditional computation techniques – enabling the model to capture both universal circuit properties and algorithmic nuances. The architecture incorporates a pretrained family classifier (97.5% accuracy) and domain-informed algorithm fingerprint features derived from gate-composition heuristics. Evaluated on circuits spanning 7–130 qubits across 10 algorithm families, our system achieves 79.5% exact threshold accuracy (91.2% within one rung) and $R^2 = 0.82$ runtime correlation, with inference completing in approximately 50 ms – replacing trial-and-error simulation runs that may take minutes to hours. Ablation studies confirm that family-aware modeling provides the single largest performance improvement (+3.2 percentage points), validating the hypothesis that algorithm family is a first-class feature for simulation cost prediction.

13.
arXiv (CS.LG) 2026-06-15

A Longitudinal Attribute-Conditioned Neural Network for Modeling Health-State Transition Probabilities in Temporally Irregular Data: The LANTERN Framework

arXiv:2606.13880v1 Announce Type: new Abstract: Accurate estimation of long-term care transition probabilities is central to disability insurance pricing, reserving, and solvency assessment. Classical actuarial multi-state models commonly rely on Markov, semi-Markov, or proportional-hazard specifications, which provide a direct connection to cohort projection but may be restrictive for irregular longitudinal health data with nonlinear aging patterns and heterogeneous covariate histories. This paper develops a well-calibrated estimator of multi-state transition probabilities for irregular longitudinal health data. The model learns from individual health history, incorporates the time elapsed between observations, and conditions transition probabilities on demographic and socioeconomic attributes. It produces a valid probability distribution over the next observed health state, with four possible states: healthy, mild disability, severe disability, and death. Individual probabilities are aggregated by age group and origin state to form transition matrices compatible with actuarial cohort projection. Using longitudinal data from the Health and Retirement Study, we compare the proposed estimator with logistic regression, gradient-boosted trees, a recurrent neural network, and a last-state persistence benchmark. The evaluation considers probabilistic accuracy, endpoint discrimination and calibration for severe disability and death, risk concentration, and transition matrix error after aggregation. The proposed estimator improves severe disability discrimination relative to logistic regression and gradient-boosted tree benchmarks, maintains strong calibration, and yields the lowest transition matrix error among the evaluated models in the held-out test analysis. Results show that a structured machine learning estimator can support long-term care transition modeling when judged by calibration and projection fidelity, beyond discrimination.

14.
arXiv (CS.CL) 2026-06-11

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

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.

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

PaAno+: Multiscale Encoding and Cross-Variable Attention for Time Series Anomaly Detection

arXiv:2606.20055v1 Announce Type: new Abstract: Time-series anomaly detection has significant practical value for industrial and medical monitoring, as well as other critical domains. Current Transformer- and large-model-based detection approaches incur excessive computational overhead, while existing lightweight alternatives are constrained by insufficient feature extraction and inadequate modeling of dependencies across multivariate variables. To mitigate the above drawbacks, this study develops a lightweight, efficient anomaly detection model, dubbed PaAno, within the patch-oriented representation learning paradigm. In the encoder module, a multiscale feature-extraction backbone is constructed using convolutional kernels with differentiated receptive fields to capture hierarchical temporal characteristics; subsequent cross-scale adaptive attention aggregation, combined with residual connection optimization, further stabilizes feature representation learning. A cross-variable fusion attention module is embedded to explicitly characterize inter-variable correlations, empowering the model to identify anomalous patterns amid intricate operational conditions. Moreover, a novel pretext task based on temporal patch-window sorting is customized to uncover intrinsic structural properties of time series, and triplet loss is leveraged to optimize the patch embedding space for enhanced feature discrimination. Extensive experiments on the TSB-AD benchmark demonstrate that the proposed PaAno achieves state-of-the-art detection accuracy on both univariate and multivariate tasks, yielding significant performance gains across evaluation metrics, including VUS-PR, relative to the original PaAno. Leveraging a compact network design, the presented model achieves favorable computational efficiency, enabling deployment on resource-limited terminals for real-time anomaly inference.

16.
arXiv (CS.CV) 2026-06-17

Pareto LoRA: Mitigating Modality Imbalance in Unified Multimodal Models via Pareto-Optimal Gradient Integration

Unified multimodal models (UMMs) have recently emerged as a promising paradigm for integrating multimodal understanding and generation within a single autoregressive transformer. However, during multimodal instruction tuning, these models often exhibit pronounced modality imbalance: language gradients dominate optimization, thus leading to lower image generation quality, especially under parameter-efficient fine-tuning such as LoRA. In this work, we systematically analyze modality imbalance in LoRA-based fine-tuning of UMMs for interleaved text-image generation. We show that vision modality performance degrades substantially more than text modality performance when compared to unimodal counterparts, and that modality-specific gradients can differ by orders of magnitude across various tasks and layers. Motivated by this observation, we reformulate the multimodal instruction tuning as a bi-objective optimization problem and propose Pareto LoRA, a Pareto-optimal gradient integration strategy that balances the text and image objectives by modulating the gradient direction and strength. Experiments on the CoMM benchmark with Emu2 demonstrate that Pareto LoRA consistently improves multimodal generation balance, achieving up to 44.9% gains in perceptual image quality over vanilla LoRA while maintaining comparable text performance.

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

Token-Operations-Oriented Inference Optimization Techniques for Large Models

Large model inference optimization serves as a key foundation for supporting the scalable, low-cost, and highly stable operation of large model services. Centered on token-oriented inference optimization technology, this paper proposes for the first time a four-layer technical architecture consisting of Multi-model Fusion, Model Optimization, Compute-Model Fusion, and Compute-Network-Model Fusion. It systematically reviews the key technologies and current industry status across these four levels and analyzes the application value of related technologies in real-world business scenarios. This paper provides a practical technical path for reducing token production costs, improving token service efficiency, ensuring the stability of token supply, and driving the transition of large model services from being merely callable to being operable.

18.
arXiv (CS.AI) 2026-06-16

Imperfect Visual Verification for Code Edition : A Case Study on TikZ

arXiv:2606.15693v1 Announce Type: cross Abstract: LLMs have significantly advanced code generation, enabling the synthesis of functional programs. While recent systems achieve strong performance on many coding benchmarks, tasks involving programs such as TikZ that generate visual artifacts remain challenging, in particular on visual code customization. Unlike generation from scratch, customization requires localized, semantics-preserving edits: the model must locate relevant code, modify it according to the instruction, and preserve the remaining structure and rendering. Approaches based on post-hoc iterative refinement/correction where a verifier provides feedback to guide corrections, have shown promise. However, in the case of programs with a visual outcome such as in TikZ, where correctness is harder or likely impossible to formalize and evaluate automatically, deterministic verifiers do not exist. Hence, developers can only rely on imperfect verifiers. In this paper, we conduct an empirical study to answer:to what extent can iterative refinement remain effective when the verifier itself is unreliable?} We use TikZ as a focused case study that isolates the core difficulties of the problem (weak code structure, fine-grained visual semantics, and difficult feature localization) in a controlled and challenging setting. We define visual code customization as an iterative editing problem with an imperfect oracle, and introduce a framework for analyzing such iterative refinements. We conduct a large-scale study and evaluate multiple LLM-based and tool-augmented visual verifiers within iterative refinement pipelines, and perform extensive manual annotation of refinement trajectories to assess verifier behavior and feedback quality. Our findings show that even imperfect verifiers can determine with moderate accuracy whether visual instructions are applied to code, achieving F1-scores up to 0.815. Feedback improves iterative refinement, especially for weaker models, adding 11–20 perfect customizations for Qwen3-vl-30b-a3b-Instruct, while stronger models like Gemini-3 gain fewer improvements (+5) but benefit more from accurate verification that prevents premature acceptance. Feedback is effective only when it precisely identifies image issues, provides actionable guidance, addresses all relevant problems, and remains grounded in the original instruction.

19.
bioRxiv (Bioinfo) 2026-06-11

SPARK: A Systems-level Computational Framework for Reconstructing Transcriptomic State Organisation in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits substantial molecular heterogeneity, which complicates tumour stratification and limits the ability of mutation-centric models to capture tumour behaviour and predict patient outcomes. This study investigates whether coordinated transcriptomic programs can provide a systems-level representation of tumour states. Bulk RNA-sequencing data from the TCGA-LUAD cohort were analysed to reconstruct pathway-level transcriptomic organisation using a stability-optimised network framework (SPARK). This analysis identified eight transcriptomic modules representing coordinated biological processes active across tumours. Module activity scores were subsequently used to derive a composite Transcriptomic Risk Score through elastic-net Cox proportional hazards modelling. The resulting risk score showed a significant association with overall survival in the discovery cohort and improved prognostic discrimination beyond clinical variables. An independent evaluation in the CPTAC-LUAD cohort confirmed the prognostic signal and preserved risk stratification across patient groups. Unsupervised clustering of module activity further revealed three transcriptomic patient groups characterised by distinct biological programs, genomic alteration patterns, and survival outcomes. Single-cell analysis also demonstrated that the identified transcriptomic modules reflect coordinated organisation of the tumour-immune-stromal ecosystem across cellular compartments. Together, these findings suggest that LUAD heterogeneity can be organised into coordinated transcriptomic programs with measurable clinical relevance, providing a systems-level framework for representing tumour molecular states.

20.
medRxiv (Medicine) 2026-06-19

Performance of family history-based colorectal cancer screening criteria by race and age at diagnosis in the Disparities and Cancer Epidemiology (DANCE) study

Importance: Family history (FH) and age are the primary criteria employed for early colorectal cancer (CRC) risk stratification. We evaluated how well these criteria identify individuals diagnosed with CRC across age and racial groups. Objective: To evaluate the performance of FH and age based screening criteria for identifying individuals with CRC, with attention to differences by race and age at diagnosis. Design, Setting, and Participants: This case control and case only analysis used data from the Disparities and Cancer Epidemiology (DANCE) cohort, a population based study of invasive CRC cases diagnosed from 2013 to 2022, recruited through the Metropolitan Detroit Cancer Surveillance System and the Louisiana Tumor Registry. Analyses included 1,158 non-Hispanic Black (NHB) and non-Hispanic White (NHW) CRC cases and 1,434 cancer-free controls from the Inflammation Health and Lung Epidemiology (INHALE) study, enrolled from the same Detroit catchment area. Data were analyzed in 2025. Exposures: Self reported cancer FH among first-degree (FD) relatives and grandparents, summarized into three FH-based screening criteria: at least one FD relative with CRC (colon early-screening criterion), any FH of Lynch syndrome related cancers, and meeting NCCN criteria for Lynch syndrome genetic testing. Main Outcomes and Measures: Proportion of cases meeting each FH based screening criterion stratified by race and age at diagnosis (

21.
arXiv (CS.CL) 2026-06-24

Layer-wise Probing of wav2vec 2.0 and Whisper for Consonant Cluster Reduction in African American English

Self-supervised and supervised speech models are increasingly used to investigate which linguistic information their internal representations encode, and at what level of abstraction they encode it. One underexplored phenomenon is consonant cluster reduction (CCR) in African American English (AAE), a widespread phonological process and a source of automatic speech recognition (ASR) disparity. To examine how CCR is represented, we conduct speaker-independent layer-wise probing of wav2vec2-base and Whisper-small using two tasks: segmental reduction detection and segmental restoration of underlying cluster identity. Both models distinguish reduced and canonical forms with high accuracy. Crucially, reduced segments retain cues to their underlying stops, indicating that CCR is encoded as structured gradient phonological variation rather than simple segmental deletion. These results demonstrate structured phonological encoding of AAE CCR patterns in modern speech models.

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

Retrieve, Don't Retrain: Extending Vision Language Action Models to New Tasks at Test Time

arXiv:2606.15631v1 Announce Type: cross Abstract: Extending a vision-language-action (VLA) policy to a new task typically requires task-specific teleoperated demonstrations and per-task fine-tuning, making adaptation costly in both data collection and compute. In this paper, we show that this target-side per-task adaptation cost can be replaced by retrieval. Our retrieval-augmented policy is trained once on paired demonstrations from the target embodiment (query) and a cheaper embodiment (pool, e.g., human-hand video), then frozen. New tasks are added at deployment by appending pool-side demonstrations to a retrieval pool. The frozen policy conditions on retrieved trajectories at every control step, so new tasks are absorbed by indexing data rather than updating parameters. Fine-tuning is needed only to take on a new, unseen embodiment, not for each new task. We show that retrieval improves policies beyond a specific backbone, including standard VLA policies, but its effect is especially pronounced in Cosmos Policy, a video-generation-based world-action model (WAM). In this setting, retrieval supplies coarse task progression, while the WAM's future-image objective provides an additional visual consistency signal that strengthens the retrieval-conditioned actions. On PushT, we study how retrieval provides a reusable high-level motion prior for cross-embodiment generalization to unseen goal angles, while on RoboTwin 2.0 our method outperforms cross-embodiment baselines on unseen tasks, and we additionally demonstrate the method on a real robot.

24.
arXiv (CS.LG) 2026-06-16

Graphical conditional generative modeling for digital twin modeling

arXiv:2606.16219v1 Announce Type: cross Abstract: Digital twin modeling, including control and data assimilation under model uncertainty, often faces an open-ended fidelity problem: adding variables, data streams, and time scales can indefinitely increase model complexity, ultimately producing systems that are difficult to maintain, validate, interpret, and use for stress or safety testing. As an alternative, one can seek parsimonious stochastic surrogate models built only on the variables needed to describe the relevant quantities of interest. We introduce a framework for discovering such variables from observational data by identifying which candidate inputs influence the full conditional law of a target quantity, rather than only its conditional mean. This distinction is essential in stochastic, coarse-grained, or partially observed systems, where dependencies may appear through changes in variability, tail behavior, multimodality, or uncertainty rather than through deterministic functional relationships. The framework couples conditional generative modeling, which learns the conditional distribution of the target given candidate inputs, with Gaussian-process-based analysis of variance (through kernel mode decomposition), which enables iterative pruning of non-influential inputs and interpretable structure discovery. In control settings, the resulting surrogate can be interpreted as a learned Markov decision process: the method identifies not only a transition model, but also the state, action, and memory variables needed to make the learned dynamics effectively Markovian. Across examples involving stochastic dynamical systems, missing variables, PDE control, reinforcement learning, and economic data, the discovered structures yield interpretable stochastic surrogates whose downstream performance is comparable to models trained on the full variable set.

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

CFCamo: A Counterfactual Detect-or-Abstain Framework for Camouflaged Object Detection

Vision-language reinforcement learning has recently shown strong target-present localization for camouflaged object detection (COD). Yet localization is only one side of the decision: when the agent faces an ordinary image with no camouflaged target, will it still claim that a camouflaged object exists? Standard COD training and evaluation data are positive-only, so agents optimized under this setting can acquire an over-detect bias, a task-specific form of object hallucination that standard COD evaluation leaves unmeasured. To quantify this target-absent behavior, we construct Counterfactual COD (CF-COD), a paired benchmark that removes the camouflaged target from each held-out COD evaluation image while preserving a plausible background. CF-COD evaluates whether a model detects the target on the original image and abstains on the target-absent counterfactual, summarized by Pair Accuracy (PA). We further introduce CFCamo, a paired counterfactual framework for COD with abstention. For training, CFCamo optimizes a Qwen3-VL-4B-Instruct agent with Counterfactual Sequence Policy Optimization (CSPO), which samples paired original-counterfactual rollouts and uses a Counterfactual Paired Reward (CPR) to couple original-image detection with counterfactual abstention. On CAMO-test, CFCamo improves S_alpha by +3.7 pp over the prior RL-based COD baseline; across CF-COD, it reaches 80.0-90.8% PA. Ablations show that removing counterfactual coupling reduces PA to 1.4-5.2% despite strong target-present COD scores, showing that target-present evaluation alone does not characterize detect-or-abstain behavior. Overall, these results indicate that CFCamo improves COD agents by coupling target-present detection with target-absent abstention, rather than merely strengthening target-present localization. Code and data are available at https://github.com/suhang2000/CFCamo.