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01.
arXiv (CS.CV) 2026-06-17

Universal Image Restoration via Internalized Chain-of-Thought Reasoning

Image restoration seeks to recover high-quality images from degraded inputs but becomes highly ill-posed under complex, mixed degradations. While unified all-in-one models are common, their performance declines as degradation complexity increases. Recent works adopt Chain-of-Thought (CoT) reasoning for multi-round restoration using specialized modules. However, this approach faces two key limitations: (i) increased computational cost due to multi-step processing, and (ii) weak modeling of interactions between degradations during stepwise inference. We introduce CoTIR, a universal image restoration framework that internalizes CoT reasoning within a single model. Concretely, we view image restoration as a specialized subtask of image editing, which implies that a large-scale pre-trained editing model provides a more favorable optimization starting point. Building on this, we fine-tune the model for restoration and further encode structured CoT-style reasoning into the learning objective via a differentiable formulation inspired by Lagrangian optimization, enabling holistic restoration without chaining specialized restorers. To facilitate training and evaluation, we further present CoTIR-Bench, a large-scale benchmark comprising 5.2 million samples with CoT-style reasoning traces. Extensive experiments on CoTIR-Bench and broad real composite degradation scenes show that CoTIR achieves stronger perceptual quality and more competitive fidelity than both all-in-one models and multi-round restoration methods. The source code is available at https://github.com/gy65896/CoTIR.

02.
arXiv (CS.CV) 2026-06-17

MM++: Unsupervised Scale-Invariant Multilayer OOD Detection via Top-K Gated Feature Fusion

We introduce MM++ (Multilayer Mahalanobis++), a fully unsupervised, strictly post-hoc, and scale-invariant framework for Out-of-Distribution (OOD) detection. To address the trade-off between scale invariance and hierarchical expressivity, MM++ constructs a principled joint feature space. It first identifies discriminative intermediate layers by measuring entropy density drops, which mark the boundaries of sharp semantic compression. By fusing these selected layers with the terminal representation, the framework captures latent cross-layer correlations while mitigating early-layer noise. Crucially, a Ledoit-Wolf regularized tied covariance matrix stabilizes this unified space, enabling reliable distance estimation. Requiring no auxiliary OOD data, classifier fine-tuning, or architectural modifications, MM++ delivers robust performance across distinct architectures for both near- and far-OOD detection.

03.
arXiv (CS.CV) 2026-06-12

An Extensible and Lightweight Unified Architecture for Demosaicing Pixel-bin Image Sensors

Pixel-bin image sensors are becoming the default choice for smartphone cameras due to their resolution vs light-gathering trade-off. However, their larger inter-color separation compared to the Bayer color filter array (CFA) makes them challenging to demosaic. Furthermore, existing deep learning-based demosaicing methods are CFA-specific, requiring multiple individual models that take up precious onboard resources and demand larger development and maintenance efforts. In this work, we propose a modular unified architecture for demosaicing various pixel-bin sensors that provides higher image quality while being extensible and lightweight. Additionally, to enable plug-and-play operation, we introduce a learning-free CFA-identification module to detect the CFA type of raw data accurately.

04.
medRxiv (Medicine) 2026-06-11

Large-scale proteomics and timing of hypertensive disorders of pregnancy

Background: Hypertensive disorders of pregnancy (HDP) may first be diagnosed antepartum, during labor, or postpartum. We utilized untargeted large-scale proteomics to identify pathways associated with HDP based on timing of onset. Methods: We performed a nested case-control study comparing differential protein expression, from the SomaScan 7K platform, based on timing of onset of HDP versus controls (referent) using first-trimester samples from the NuMoM2b-Heart Health Study, a multi-site cohort that followed nulliparous individuals from the first trimester. Associations of proteins with timing of onset of HDP, adjusted for co-variates, were assessed using logistic regression q value-based false discovery rates and pathway enrichment and differential expression analysis were conducted. Results: Of 1628 individuals included, 678 had HDP, of which 67% manifested antepartum (AP), 29% intrapartum (IP), and 3% postpartum (PP). After adjusting for co-variates, compared to controls, 698 proteins, 39 proteins, and 144 proteins were differentially expressed in those with HDP according to AP, IP, PP onset, respectively. There was little overlap in individual protein expression based on timing of HDP. Pathway enrichment and graphical summary analyses suggested distinct processes. Specifically, there was downregulation of angiogenic proteins in AP HDP, downregulation of immune-related proteins in IP HDP, and upregulation of complement activation promoting fibrotic changes leading to cardiac dysfunction in PP HDP. Conclusion: There are differences in first-trimester protein expression based on whether HDP first manifests AP, IP or PP. This raises the possibility that there may be distinct mechanistic phenotypes that could uniquely inform diagnostic and therapeutic targets for HDP.

05.
arXiv (CS.AI) 2026-06-19

Multi-Head Attention-Based Feature Extractor Integration with Soft Actor-Critic for Porosity Prediction and Process Parameter Optimization in Additive Manufacturing

arXiv:2606.20087v1 Announce Type: new Abstract: Additive manufacturing process optimization requires precise parameter control to minimize defects such as porosity. Traditional reinforcement learning (RL) approaches using discrete action spaces suffer from slow convergence and susceptibility to local optima, limiting their effectiveness for high-precision manufacturing tasks. This study addresses these limitations by employing a continuous action space combined with a novel architecture that integrates a multi-head attention mechanism with the Soft Actor-Critic (SAC) algorithm. The attention-based feature extractor enhances the agent's ability to capture subtle variations in low-dimensional input features, enabling more effective exploration-exploitation balance for navigating value spaces with local minima. We validate our approach on porosity prediction and process parameter optimization in laser powder bed fusion, demonstrating faster convergence and higher final reward values compared to standard RL methods including DQN, PPO, TD3, and vanilla SAC. The proposed methodology achieves a convergence value of 322.79 within 14 episodes, outperforming existing approaches while maintaining stability throughout training.

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

Where Does Texture Evidence Live in SAM? Features, Proposal Masks, and Texture Segmentation

Texture segmentation stresses foundation segmentation because meaningful regions are defined by material or repeated appearance rather than object identity. Segment Anything Models (SAMs) often fail by default on such texture-defined partitions, but this failure is ambiguous: the texture evidence may be absent, missing from the proposal bank, or present but selected or assembled incorrectly by an object-centric readout. We ask what texture-relevant evidence is already preserved in frozen SAM before adaptation. We study two frozen evidence spaces: multiscale features, probed with a minimal clustering readout, and the automatic proposal bank, treated as evidence for a supervised consolidation readout. SAM is frozen throughout; we do not fine-tune the backbone or retrain the proposal generator. Across RWTD, STLD, an ADE20K-selected refined-crop complement, and a ControlNet-stitched PTD bridge archive, frozen SAM is not a texture segmenter by default, but its failures are not simple texture blindness. Coarse frozen features preserve texture organization, and proposal banks often contain texture-aligned masks or fragments. Natural scenes more often require assembly and commitment over fragments, while cleaner synthetic cases more often reduce to selecting an already coherent proposal. Default mask failure should therefore be decomposed into representation evidence, proposal-bank support, readout mismatch, and commitment failure.

07.
arXiv (CS.AI) 2026-06-12

Toward Instructions-as-Code: Understanding the Impact of Instruction Files on Agentic Pull Requests

arXiv:2606.13449v1 Announce Type: cross Abstract: AI-agents (e.g., GitHub Copilot) collaborate as teammates in different software engineering tasks, including code generation proposed through pull requests (Agentic-PRs). For better agent efficiency, developers create instruction files that guide the AI-agents, including how to navigate the project, locate the right components, run tests, respect best practices, and more. In this paper, we investigate the relationship between the creation of these instructions and the performance of AI-agents in creating better pull requests, which have a higher chance of success (i.e., the merge rate), address more complex tasks (e.g., code churn), and require less effort to be merged (e.g., time to merge). To this end, we analyze 15,549 agentic PRs from 148 projects in the AIDev dataset. Using the three dimensions, we compare each project before and after the creation of the instruction files. We find that specifying instructions for AI-agents does not necessarily lead to better results. With the instruction files, 27.7\% of the projects increased their merge rate by at least 20\%, while 26.35\% decreased it. The same observation is seen with the amount of changes (e.g., code churn, number of modified files) and with the efforts to merge an agentic PR (e.g., merge time and number of comments). From a first exploration, we find that projects that managed to increase their merge rate have substantially longer instruction files, which are also well structured into a higher number of sections and sub-sections. Our results motivate the need for research to assist practitioners in framing the development of instruction files as a software engineering activity (aka, Instructions-as-Code).

08.
medRxiv (Medicine) 2026-06-16

Non-invasive Detection of Fasciculation Using Surface EMG with a Wavelet-Based Analytical Method (DEWCS)

Objective: Needle electromyography (nEMG) is essential for diagnosing neuromuscular disorders but is invasive and often painful. We employed single-channel bipolar surface EMG (sEMG) analyzed with a novel wavelet-based analytical approach, Detecting and Extracting Elemental Wave Components based on a Wavelet Coefficient Set (DEWCS) and investigated whether fasciculation-related activity could be identified. Methods: In this prospective study, 28 patients undergoing nEMG for suspected neuromuscular disorders and 13 healthy controls were included. Resting-state sEMG was recorded from selected muscles using single-channel bipolar active electrodes at a high sampling rate. DEWCS was used to extract indices reflecting fast- and slow-type motor unit (MU)-related activity. These standardized indices were evaluated against nEMG-detected fasciculation potentials using generalized estimating equation logistic regression to account for within-subject clustering. Diagnostic performance was assessed by receiver operating characteristic analysis. Results: A total of 67 muscles from 38 participants were analyzed. Indices of fast- and slow-type MU-related activity were significantly associated with fasciculation potentials (slow: OR 5.10, p = 0.0041; fast: OR 2.38, p = 0.0162). The combined model showed excellent discrimination (area under the curve = 0.97), outperforming either index alone. Muscle region had no significant effect. Conclusions: A single-channel bipolar sEMG setup combined with DEWCS detected fasciculation-related activity with promising accuracy. This method may serve as a non-invasive surrogate marker of lower motor neuron involvement. Further validation in larger cohorts is warranted. Significance: This non-invasive sEMG approach may help detect fasciculation-related activity and complement nEMG in neuromuscular diagnostics.

09.
arXiv (CS.LG) 2026-06-11

Point-Identification of a Robust Predictor Under Latent Shift with Imperfect Proxies

arXiv:2603.15158v2 Announce Type: replace Abstract: Addressing the domain adaptation problem becomes more challenging when distribution shifts across domains stem from latent confounders that affect both covariates and outcomes. Existing proxy-based approaches that address latent shift rely on a strong completeness assumption to uniquely determine (point-identify) a robust predictor. Completeness requires that proxies have sufficient information about variations in latent confounders. For imperfect proxies the mapping from confounders to the space of proxy distributions is non-injective, and multiple latent confounder values can generate the same proxy distribution. This breaks the completeness assumption and observed data are consistent with multiple potential predictors (set-identified). To address this, we introduce latent equivalent classes (LECs). LECs are defined as groups of latent confounders that induce the same conditional proxy distribution. We show that point-identification for the robust predictor remains achievable as long as multiple domains differ sufficiently in how they mix proxy-induced LECs to form the robust predictor. This domain diversity condition is formalized as a cross-domain rank condition on the mixture weights, which is substantially weaker assumption than completeness. We introduce the Proximal Quasi-Bayesian Active learning (PQAL) framework, which actively queries a small, targeted set of diverse domains that satisfy this rank condition. PQAL can recover the point-identified predictor, demonstrates robustness to varying degrees of shift and outperforms previous methods on synthetic data and semi-synthetic dSprites, IHDP, ACS Folktables datasets.

10.
arXiv (CS.CV) 2026-06-19

CUPID: Reconstructing UV Texture Maps for Interpretable Person-of-Interest Deepfake Detection

Deepfakes targeting a high-profile individual, known as Person-of-Interest (POI), are a threat to modern democracies and societies. Current POI deepfake detection methods still struggle to combine robustness to post-processing, efficiency and interpretability, focal aspects of modern deepfake detectors. In this paper we propose CUPID, a POI video deepfake detector that combines UV texture maps, a facial appearance representation derived from 3D face reconstructions, with the representation learning capabilities of the Masked Autoencoder (MAE). Our method does not require any deepfake videos in its training phase. Moreover, it does not even require to include a specific POI in the training set: the combination of UV texture maps extracted from real video frames and the MAE context-guided reconstruction yields a latent space that captures rich and discriminative facial features also for identities unseen during training. In the testing phase, the embeddings extracted from a query video depicting the POI can be matched against pristine reference videos to assess the video authenticity. Furthermore, operating in the UV space naturally provides an additional layer of interpretability. Specifically, we can extract decoded residual maps that highlight which facial regions of a test video deviate most from the identity representation of the corresponding POI. Experiments on four deepfake datasets show that CUPID outperforms current state of the art on most datasets and achieves the best overall robustness against strong downscaling and compression, providing also substantially faster inference. Our experimental code will be released at https://github.com/polimi-ispl/CUPID.

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

From Imitation to Alignment: Human-Preference Flow Policies for Long-Horizon Sidewalk Navigation

arXiv:2606.12603v1 Announce Type: cross Abstract: Autonomous long-horizon sidewalk navigation is essential for micro-mobility applications such as robotic food delivery and assistive electronic wheelchairs. Unlike autonomous driving on the road, long-horizon sidewalk navigation requires precise maneuvering through unpredictable sidewalk terrains and pedestrians, with a lightweight perception stack as minimal as a single monocular RGB camera. While imitation learning (IL) from demonstrations offers a practical solution, the resulting autopilot policy often suffers from compounding errors, a lack of social compliance on sidewalks, and deficiencies in counterfactual reasoning to handle complex situations. To address these challenges, we introduce FlowPilot, a mapless navigation policy that achieves robust and efficient long-horizon navigation performance using only a monocular RGB camera. We first propose to use anchored flow matching as an action representation for policy pre-training on large-scale robot fleet data and to capture the diverse, complex, multimodal distribution of sidewalk navigation behaviors. To bridge the gap between imitation and alignment, we further design a human-in-the-loop preference learning scheme to tune the policy on a small amount of human intervention data. It strengthens the model's counterfactual reasoning and social compliance on sidewalks. We evaluate FlowPilot through extensive simulation and real-world experiments in diverse sidewalk environments. FlowPilot achieves 42% success rate and 66% route completion in simulation, while FlowPilot-HP further improves real-world robustness and social compliance, reducing IR by 40.0% and NIR by 52.1% relative to the base model.

12.
bioRxiv (Bioinfo) 2026-06-13

ADMETron: An AI-driven SaaS platform for comprehensive ADMET prediction and compound prioritisation

ONTOSIGHT(R) ADMETron is an AI-driven platform designed for rapid prediction and visualization of Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties to support modern drug discovery. The platform integrates an interactive web interface with a scalable predictive engine, enabling high-throughput virtual screening and batch analysis of chemical compounds. Its core architecture combines recurrent neural network (RNN)-derived molecular embeddings from SMILES representations with physicochemical descriptors, which are subsequently modeled using gradient boosting machines (GBMs). This framework provides predictions across 34 ADMET endpoints, including physicochemical properties, absorption, CYP450 interactions, hERG liability, and mutagenicity. The predictive performance of ADMETron was evaluated using benchmark datasets from the Therapeutics Data Commons (TDC), demonstrating strong performance and generalizability across both classification and regression tasks. Beyond predictive modeling, the platform introduces an interactive radar graph-based structure-activity relationship (SAR) visualization framework that enables real-time comparison of multiple compounds and reference drugs across selected ADMET parameters. This feature facilitates intuitive interpretation of multidimensional molecular profiles and supports lead optimization and compound prioritization. Comparative assessment against widely used online ADMET tools further demonstrated broad endpoint coverage spanning pharmacokinetic, physicochemical, toxicity, and medicinal chemistry properties within a unified environment. Together, these capabilities establish ADMETron as a comprehensive platform for ADMET assessment and data-driven decision-making in drug discovery. (https://admetron.partex.ai/).

13.
medRxiv (Medicine) 2026-06-12

The Clinical Characteristics and mortality outcomes of Atrial fibrillation complicating Heart failure with reduced ejection fraction: A prospective study from South Africa

Background: A growing burden of cardiovascular risk factors has raised cardiovascular disease-related mortality in Sub-Saharan Africa (SSA), driving higher prevalence of heart failure with reduced ejection fraction (HFrEF) and its complication with atrial fibrillation (AF). No prospective study has examined AF's clinical impact on HFrEF in SSA. Aim: To determine AF prevalence in HFrEF, describe HFrEF-AF clinical characteristics, and determine AF's impact on mortality. Methods: In this prospective observational study at a tertiary hospital in Johannesburg, 136 HFrEF patients were enrolled and categorised as HFrEF- SR (sinus rhythm) or HFrEF-AF. Baseline clinical characteristics and biochemistry were recorded. Comprehensive echocardiography including left atrial strain by 2D speckle-tracking was performed. Median follow-up was 30.6 months. Results: AF was present in 28 patients (21%). The mean age was 58.7 {+/-} 14.9 years (52.9% male) and differed between groups (p < 0.001). Hypertensive heart disease was the leading cause of HFrEF (36%). Compared with SR, HFrEF-AF patients had poorer health status (KCCQ 27 [16-43] vs 45 [32-60], p < 0.001) and lower left atrial strain (26.2 {+/-} 11.3%, p < 0.001). Guideline-directed medical therapy was suboptimal in the AF group: anticoagulation use was higher than SR (60% vs 9.5%, p < 0.001) but overall inadequate; HFrEF-AF patients received lower median doses of carvedilol (15.6 mg vs 25 mg, p = 0.002) and enalapril (10 mg vs 20 mg, p = 0.004), and fewer received spironolactone (50% vs 75.3%, p = 0.013). Survival was significantly lower in HFrEF-AF (0.41 [0.22-0.61]) versus SR (0.73 [0.61-0.82], p < 0.001). Independent predictors of mortality included prior stroke, lower TAPSE and KCCQ, and higher E/e' and heart rate. Conclusion: AF is common among HFrEF patients in this SSA cohort (though lower than in high-income countries) and associates with worse clinical status, suboptimal therapy, and higher mortality.

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

Neuron-based Personality Trait Induction in Large Language Models

Large language models (LLMs) have become increasingly proficient at simulating various personality traits, an important capability for supporting related applications (e.g., role-playing). To further improve this capacity, in this paper, we present a neuron-based approach for personality trait induction in LLMs, with three major technical contributions. First, we construct PersonalityBench, a large-scale dataset for identifying and evaluating personality traits in LLMs. This dataset is grounded in the Big Five personality traits from psychology and is designed to assess the generative capabilities of LLMs towards specific personality traits. Second, by leveraging PersonalityBench, we propose an efficient method for identifying personality-related neurons within LLMs by examining the opposite aspects of a given trait. Third, we develop a simple yet effective induction method that manipulates the values of these identified personality-related neurons. This method enables fine-grained control over the traits exhibited by LLMs without training and modifying model parameters. Extensive experiments validate the efficacy of our neuron identification and trait induction methods. Notably, our approach achieves comparable performance as fine-tuned models, offering a more efficient and flexible solution for personality trait induction in LLMs. We provide access to all the mentioned resources at https://github.com/RUCAIBox/NPTI.

15.
arXiv (quant-ph) 2026-06-15

Efficient Simulation of Szegedy Quantum Walk Formulations and Algorithms

arXiv:2606.14226v1 Announce Type: new Abstract: Quantum walks provide a versatile framework for quantum algorithms across a wide range of applications. We develop efficient classical simulation methods for Szegedy quantum walks that avoid explicit construction of the full unitary evolution operator. Unlike previous approaches restricted to a particular walk formulation, our framework is built from fundamental update and reflection operators, enabling the simulation of a broader class of Szegedy walk formulations. We further extend these methods to phase-estimation-based algorithms coupled to the walk, including implementations suitable for large sparse graphs. The resulting methods achieve optimal $O(N^2)$ complexity for dense graphs with $N$ nodes. For sparse graphs, the computational cost scales linearly with the number of edges, which is $O(N)$ in many cases. We implement the framework in the Python package SQWLib and illustrate its capabilities through simulations of representative algorithms, including quantum simulated annealing and quantum search on graphs. These results provide a practical tool for studying Szegedy-walk-based algorithms numerically beyond purely analytical treatments.

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

OmniVideo-100K: A Dataset for Audio-Visual Reasoning through Structured Scripts and Evidence Chains

Current automated pipelines for audio-visual Question Answering (QA) generally adopt a ``video-caption-QA'' paradigm. However, these methods typically segment videos into short clips and generate separate descriptions for audio and visual modalities. This decoupled processing severs inherent associations between sounds and their visual sources, while independent clip processing often causes inconsistent descriptions of the same entity across segments. Furthermore, coupling long-text comprehension and QA synthesis into a single step often restricts models to localized events, yielding questions lacking long-term temporal connections and deep cross-modal reasoning. To address these issues, we propose an automated data engine featuring two mechanisms: (1) Entity-Anchored Video Scripting transforms videos into structured scripts, comprising summaries, main entity lists, and segment-wise audio-visual descriptions. The entity list serves as a global prior to ensure cross-segment referential consistency and reconstruct audio-visual associations. (2) Clue-Guided QA Generation prompts models to first mine cross-segment, multimodal clues from the script, and subsequently generate QA pairs based on these high-value clues. Leveraging this pipeline, we construct the instruction-tuning dataset OmniVideo-100K and a human-verified test set, OmniVideo-Test. Fine-tuning VITA-1.5, Qwen2.5-Omni-7B and Qwen3-Omni-30B on OmniVideo-100K yields performance gains of up to 20.59% on OmniVideo-Test, demonstrating strong generalization (up to 12.64% improvements) across established benchmarks like Daily-Omni and JointAVBench.

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

Informative Missingness to Generate Irregular Clinical Time Series

arXiv:2606.17106v1 Announce Type: new Abstract: Laboratory tests in electronic health records are collected irregularly, and the absence of a test order can be as informative as the measurement itself. Such missingness reflects clinicians' decisions and patient physiology, making it important to model it directly rather than treat it as a preprocessing artifact. Here we present a diffusion-based approach for generating clinical time series that jointly models laboratory values and their observation patterns using the public Data Analytics Challenge on Missing Data Imputation (DACMI) benchmark derived from MIMIC-III. To preserve realistic sampling, we align chart times into 4-hour intervals and segment admissions into 7-day windows, producing trajectories that pair each lab value with a corresponding observation indicator. Standard transformations and normalization are applied to stabilize training. Our method extends the TimeDiff framework to learn continuous lab values and discrete missingness patterns through complementary diffusion objectives. Experiments show that the generated data closely match real patient trajectories across individual lab distributions and joint value-missingness embeddings, demonstrating that diffusion models can capture clinically meaningful dependencies between patient physiology and clinicians' testing behavior under MNAR-like (missing-not-at-random) missingness. These preliminary results indicate that our model can serve as an initial component toward developing clinical foundation models. By producing synthetic priors that preserve key physiology-missingness relationships, this work motivates the subsequent training of Prior-Data Fitted Networks capable of leveraging informative missingness, which we will investigate in the extended work.

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

VHDLSuite: Unified Pipeline for LLM VHDL Generation with Data Synthesis and Evaluation

arXiv:2606.13735v1 Announce Type: cross Abstract: Large Language Models (LLM) have shown impressive capabilities in Register Transfer Level (RTL) code generation, particularly for Verilog. However, evaluating their performance with other Hardware Description Languages (HDL), especially VHDL, remains limited although its distinct language characteristics, such as stricter semantic rules, introduce evaluation considerations that differ from Verilog. This lack of coverage restricts fully understanding of how well current models generalize across hardware design languages with differing structures and semantics. To address this gap, we introduce VHDLSuite, a benchmark-centered infrastructure for scalable VHDL generation evaluation, integrating automated benchmark synthesis, executable validation, and multi-model diagnostic analysis. First, we propose a data pipeline that automatically converts Verilog designs and their accompanying testbenches into executable VHDL benchmark instances, followed by VUnit/GHDL-based validation to ensure each released task is compilable, runnable, and consistently checkable in the VHDL environment. Second, we introduce VHDLBench, a benchmark with over 200 VHDL problems with complete and validated testbenches across a wide range of complexity levels. Third, we extensively evaluate cutting-edge LLMs and uncover key challenges specific on LLM-aided VHDL generation. Our findings provide important insights and support future work in multi-language hardware design automation.Our data pipeline, benchmark, and evaluation framework will be open-sourced.

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

Graph Grounded Cross Attention Transformer Neural Network for Structurally Constrained Full Event Sequence Generation in Predictive Process Monitoring

arXiv:2606.18726v1 Announce Type: cross Abstract: Structurally constrained event sequence generation remains challenging because generated paths must preserve transition feasibility, temporal order, termination, and attribute consistency. In predictive process monitoring (PPM), this challenge appears as full event sequence generation, whereas existing work mainly addresses component tasks such as next activity, remaining time, outcome, and attribute prediction. This paper proposes the Graph Grounded Cross Attention Transformer Neural Network (GGATN) for this unified PPM task. GGATN uses a global process graph as structured activity memory, contextualizes sequence positions through Transformer self attention, and injects process topology through graph grounded cross attention. Unlike autoregressive decoding, GGATN generates activities, timestamps, length, and event level and sequence level attributes in a single pass, followed by Viterbi style graph constrained decoding for feasible paths and explicit termination. Experiments on six benchmark event logs show more reliable generation quality than local instruction prompted LLM baselines. GGATN achieves strong performance on sequence similarity, Damerau Levenshtein similarity, bigram based control flow similarity, and duration distribution, while maintaining zero hallucinated activities and zero sequence level attribute inconsistency. Ablation analyses confirm the global graph encoder as a stable structural prior. Interpretability analyses show how graph structure, sequence context, feedback refinement, and constrained decoding shape generation.

20.
Nature (Science) 2026-06-10

Structural basis for chaperone-guided assembly of RNA-induced silencing complex

The RNA-induced silencing complex (RISC), comprising an Argonaute (AGO) protein and a small RNA, is the central effector in RNA silencing. Small RNAs are loaded onto AGO as bulky duplexes in an HSP70- and HSP90-dependent process1–3, but the molecular mechanism remains poorly understood. Here we identify the human AGO–HSP90–p23 complex, which captures AGO in an RNA-free state, termed the AGO maturation complex (AMC). The purified AMC enables RNA loading and AGO folding, faithfully recapitulating de novo RISC assembly. Using cryogenic&nbsp;electron microscopy, we determined the structure of AMC bound to a microRNA duplex. In contrast to its conformation&nbsp;in the RISC, AGO adopts a highly open conformation in the AMC: the N domain and the RNA-binding module (PAZ–MID–PIWI) are fully detached and anchored to opposite sides of the HSP90 dimer, connected solely by the unfolded L1 linker. This arrangement exposes a positively charged cleft that accommodates an RNA duplex. AGO folding is facilitated by a small RNA duplex containing a 5′-terminal phosphate—but not by single-stranded RNAs—revealing a role for the RNA duplex as a chaperone-like cofactor that directs AGO domain assembly. These findings elucidate the RISC assembly mechanism and establish the AMC as a molecular tool for probing optimal RNA features and chemical modifications for the&nbsp;rational design of small interfering RNA therapeutics. Our study also sheds light on how chaperones, together with ligands, can guide the folding of client proteins. Structures of the AGO maturation complex reveal how chaperones and an RNA duplex drive assembly of the RNA-induced silencing complex.

21.
arXiv (CS.AI) 2026-06-18

SWE-Future: Forecast-Conditioned Data Synthesis for Future-Oriented Software Engineering Agents

arXiv:2606.18733v1 Announce Type: cross Abstract: Realistic coding-agent benchmarks often replay public GitHub issues and pull requests, making them vulnerable to overlap with model pretraining, fine-tuning, synthetic-data generation, or benchmark-driven model selection. Fully synthetic tasks avoid direct historical replay, but can drift away from real repository needs. We propose SWE-Future, a forecast-conditioned data synthesis method for future-oriented coding tasks. Given a forecast snapshot at time $T_0$, the method uses only pre-$T_0$ repository evidence to forecast future feature implementation/enhancement, bugfix, and refactor task families. We first validate this forecasting step retrospectively: after forecasts are fixed, later pull requests are used only to measure whether the predicted task families match future repository work. In an 80-repository study, the forecaster achieves 58.1\% future-work relevance under the main semantic matching metric. We then use validated forecast families as conditioning signals to synthesize a 200-task coding-agent dataset across 61 repositories from a task-generation snapshot, rather than replaying the later pull requests used for validation. SWE-Future shows that repository-evolution forecasts can guide realistic, future-oriented coding-task synthesis while reducing direct dependence on historical pull-request replay.

22.
arXiv (quant-ph) 2026-06-16

Linear algebra at exponential scale via tensor network dimension reduction

arXiv:2606.15350v1 Announce Type: cross Abstract: Many problems in modern scientific computing are challenging because of a curse of dimension, where their mathematical formulation involves objects whose dimension is exponential in the nominal "size" of the problem. Tensor networks can provide a compact representation for exponentially large vectors and matrices that arise in applications, but these representations do not always lead to reliable algorithms. This paper develops and analyzes techniques for randomized dimension reduction of tensor network data. These techniques support a suite of efficient algorithms for provably solving exponential-scale linear algebra problems, including trace estimation and eigenvalue approximation. The paper includes several stylized illustrations from quantum many-body physics with ambient dimension up to $2^{200}$.

23.
arXiv (CS.LG) 2026-06-15

SemPiper: Interactive Code Synthesis for Semantic Operators in Machine Learning Pipelines

arXiv:2606.14361v1 Announce Type: new Abstract: Machine learning (ML) pipelines require extensive data preparation, feature engineering, and integration across heterogeneous sources, making them tedious and error-prone to develop. While large language models (LLMs) have recently shown promise for assisting programming tasks, chat-based interfaces provide limited control over pipeline behavior and often produce code that is difficult to optimize or integrate into production systems. We demonstrate SemPipes, a novel programming model that extends ML pipelines with declarative, LLM-powered semantic data operators. SemPipes allows developers to specify high-level natural language instructions for data-centric operations, while seamlessly combining these operators with arbitrary Python code from standard data science libraries. For the semantic operators, it synthesizes specialized implementations at pipeline training time, conditioned on dataset characteristics and pipeline context, enabling the flexible yet controlled integration of LLM capabilities. We demonstrate SemPipes through SemPiper, an interactive interface that visualizes computational graphs of the pipelines, synthesized operator implementations, and optimization trajectories produced by an evolutionary search procedure. Attendees can explore three end-to-end scenarios, modify pipelines, inspect generated code, and observe how semantic operators are synthesized and iteratively optimized. The demonstration highlights how declarative semantic operators enable controllable, optimizable, and practical integration of LLMs into ML pipeline development.

24.
bioRxiv (Bioinfo) 2026-06-17

An Integrated Framework for Transcriptomic Characterization and Lorentzian Hyperbolic Visualization of a High-Risk Topological Branch in Alzheimer's Disease

Alzheimer's disease (AD) is a highly heterogeneous brain disorder in which molecular alterations vary across brain regions, disease stages, and patient subgroups. This study introduces an integrated analytical framework for characterizing transcriptomic variation associated with a high-risk topological branch, which was identified based on Lorentz distance in postmortem Brodmann area 36 samples from the Mount Sinai Brain Bank cohort, where over 70% of samples were in Braak stages V-VI. The framework integrates weighted gene co-expression network analysis, repeated stability-based differential expression analysis, network-level gene filtering, Gene Ontology enrichment, and nested stratified cross-validation to evaluate whether topological branch-associated genes capture biologically meaningful signals and carry predictive information for high-Braak group status. The identified gene sets were functionally enriched for neuronal development, neuron projection organization, synaptic signaling, vesicle fusion, and regulated synaptic release, suggesting that the high-risk topological branch reflects biologically relevant transcriptomic programs linked to neurodegenerative progression. Nested cross-validation further showed that the selected genes achieved measurable internal predictive performance for distinguishing high-Braak samples. As a second methodological contribution, we introduced a Lorentzian hyperbolic variant of t-distributed stochastic neighbor embedding (Lorentz t-SNE) to explore latent non-Euclidean structure in transcriptomic data. This method embeds samples in hyperbolic space, providing an alternative to Euclidean embeddings for representing hierarchical or nonlinear structures. Compared with conventional Euclidean embeddings, the proposed Lorentz t-SNE revealed a more localized organization of high-Braak samples. Together, these results demonstrate the utility of the proposed analytical framework and Lorentz t-SNE for investigating heterogeneous, potentially non-Euclidean organization in AD transcriptomes.

25.
arXiv (CS.LG) 2026-06-15

Binary Black Hole Parameter Estimation with Hybrid CNN-Transformer Neural Networks

arXiv:2606.13941v1 Announce Type: cross Abstract: The detection of gravitational waves has revolutionized our ability to explore fundamental aspects of the Universe. Traditionally, modeled gravitational-wave signals have been identified using template-based matched filtering, followed by coincidence analysis across multiple detectors in the signal-to-noise ratio time series. Recent advances in Machine Learning and Deep Learning have sparked growing interest in their application to both signal detection and parameter estimation. In this study, a hybrid Deep Learning strategy is proposed that leverages the effectiveness of Transformer encoders alongside well-established Convolutional Neural Network architectures in an attempt to estimate the intrinsic and extrinsic parameters of non-precessing binary black hole systems. The primary focus of this work is point estimation, producing single best-fit values for each parameter rather than full posterior distributions. This method is evaluated on both simulated signals embedded in Gaussian noise and real gravitational-wave events, and it demonstrates strong predictive performance and robustness across key astrophysical parameters.