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01.
arXiv (CS.AI) 2026-06-16

Automated ultrasound doppler angle estimation using deep learning

arXiv:2508.04243v2 Announce Type: replace-cross Abstract: Angle estimation is an important step in the Doppler ultrasound clinical workflow to measure blood velocity. It is widely recognized that incorrect angle estimation is a leading cause of error in Doppler-based blood velocity measurements. In this paper, we propose a deep learning-based approach for automated Doppler angle estimation. The approach was developed using 2100 human carotid ultrasound images including image augmentation. Five pre-trained models were used to extract images features, and these features were passed to a custom shallow network for Doppler angle estimation. Independently, measurements were obtained by a human observer reviewing the images for comparison. The mean absolute error (MAE) between the automated and manual angle estimates ranged from 3.9{\deg} to 9.4{\deg} for the models evaluated. Furthermore, the MAE for the best performing model was less than the acceptable clinical Doppler angle error threshold thus avoiding misclassification of normal velocity values as a stenosis. The results demonstrate potential for applying a deep-learning based technique for automated ultrasound Doppler angle estimation. Such a technique could potentially be implemented within the imaging software on commercial ultrasound scanners.

02.
arXiv (math.PR) 2026-06-17

A Tanaka-Type Formula for Compact Sets and Equilibrium Measures of L\'{e}vy Processes

arXiv:2606.17472v1 Announce Type: new Abstract: Tanaka's formula is a classical identity for Brownian motion, and Tsukada (2018) extended it to L\'{e}vy processes not necessarily symmetric. From a potential-theoretic point of view, this formula shows that the invariant function for the process killed upon hitting a singleton can be decomposed into the sum of a martingale part and a local time. In this paper, we generalize this singleton setting and derive a Tanaka-type formula for a compact set $B$. To this end, we introduce the equilibrium measure, defined as the rescaled limit of the $q$-capacity measures, and show that the invariant function for the process killed upon hitting $B$ can be represented as the integral, with respect to the equilibrium measure, of the invariant functions associated with processes killed upon hitting singletons, up to an additive constant called the Robin constant. Moreover, when $B$ is an interval, we obtain explicit representations of the equilibrium measure, the Robin constant, and the martingale part for recurrent stable processes as well as for recurrent spectrally negative L\'{e}vy processes. Finally, we discuss how an analogous Tanaka-type formula can also be established for transient L\'{e}vy processes.

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

DSAEval: Evaluating Data Science Agents on a Wide Range of Real-World Data Science Problems

Recent LLM-based data agents aim to automate data science tasks ranging from data analysis to deep learning. However, the open-ended nature of real-world data science problems, which often span multiple taxonomies and lack standard answers, poses a significant challenge for evaluation. To address this, we introduce DSAEval, a benchmark comprising 641 real-world data science problems grounded in 285 diverse datasets, covering both structured and unstructured data (e.g., image and text). DSAEval incorporates three distinctive features: (1) Multimodal Environment Perception, which enables agents to interpret observations from multiple modalities, including text and vision; (2) Multi-Query Interactions, which mirror the iterative and cumulative nature of real-world data science projects; and (3) Multi-Dimensional Evaluation, which provides a holistic assessment across reasoning, code, and results. We systematically evaluate 13 recent advanced agentic LLMs using DSAEval. Our results show that Claude-Sonnet-4.5 achieves the strongest overall performance, MiMo-V2-Pro and GPT-5.2 lead in duration and step efficiency, respectively, and MiMo-V2-Flash is the most cost-effective. We further demonstrate that multimodal perception consistently improves performance on vision-related tasks, with gains ranging from 2.04\% to 11.30\%. Overall, while current data science agents perform well on structured data and routine data analysis workflows, substantial challenges remain in unstructured domains. Finally, we offer critical insights and outline future research directions.

04.
arXiv (CS.CL) 2026-06-16

A Systematic Evaluation of Large Language Models for PTSD Severity Estimation: The Role of Contextual Knowledge and Modeling Strategies

Large language models (LLMs) are increasingly being used in a zero-shot (generative) fashion to assess mental health conditions, yet we have limited knowledge on what factors affect their accuracy. In this study, we use a clinical dataset of natural language narratives and self-reported PTSD severity scores from 1,437 individuals to comprehensively evaluate the performance of 11 state-of-the-art LLMs. To understand the factors affecting model's assessment accuracy, we systematically varied (i) contextual knowledge prompted to the models like subscale definitions, distribution summary, and interview questions, and (ii) modeling strategies including zero-shot vs few shot, amount of reasoning effort, model sizes, structured subscales vs direct scalar prediction, output rescaling and nine ensemble methods. Our findings indicate that (a) LLMs are most accurate when provided with detailed construct definitions and context of the narrative, even exceeding human raters agreement with self-reported scores; (b) increased reasoning effort leads to better estimation accuracy; (c) performance of open-weight models (Llama, DeepSeek) plateaus beyond 70B parameters while closed-weight (gpt-o3-mini, gpt-5) alternatives improve with newer generations; and (d) best performance is achieved when ensembling a supervised model with the zero-shot LLMs. Beyond agreement with self-reports, LLMs' estimates discriminated PTSD severity from depression, anxiety, and alcohol use, and prospectively predicted future mental healthcare expenditure. Together, these results suggest that contextual knowledge and modeling strategies meaningfully affect accuracy and clinical utility of LLM-based assessments of PTSD severity.

05.
arXiv (CS.CL) 2026-06-17

GameCraft-Bench: Can Agents Build Playable Games End-to-End in a Real Game Engine?

Game generation is an emerging application of coding agents, requiring models to transform natural-language specifications into playable interactive systems. Unlike traditional coding tasks, game generation takes place within a game engine, where scripts, scenes, assets, rendering, and runtime interactions must jointly produce coherent gameplay. We formalize end-to-end game generation as the problem of producing a complete game artifact that realizes a specification through observable player-game interaction in a target environment. We argue that evaluating this setting requires three desiderata: Engine Grounding, Artifact Completeness, and Interactive Verification. We propose an interaction-grounded evaluation framework that assesses executable gameplay through replayed demonstrations and rubric-guided multimodal judging. We instantiate this framework as GameCraft-Bench, a benchmark comprising 140 Godot tasks across 15 game families. Evaluations of frontier coding agents show that end-to-end game generation remains highly challenging: the strongest agent achieves only 41.46%, and most agents score below 40%. Further analysis reveals that while agents often implement recognizable mechanics, they struggle to deliver complete games with sufficient content, functional visual feedback, and coherent presentation. See https://tongxuluo.github.io/gamecraft-bench-website for demos, code, and data.

06.
arXiv (quant-ph) 2026-06-19

Topological Quantum Interferometry

arXiv:2606.19730v1 Announce Type: new Abstract: Structured light provides high-dimensional Hilbert spaces holding tremendous potential for fundamental quantum optics and quantum technologies. However, existing characterization methods, like Hong-Ou-Mandel (HOM) interference, typically assume perfectly tuned conditions, overlooking the geometric physics governing spatial mode evolution. Here, we establish topological quantum interferometry driven by an interaction-based geometric phase, the exchange Berry phase (BPX). Our formalism generalizes $q$-plate state generation and characterization to arbitrary topological charges and (de)tuning conditions, demonstrating that BPX acts as a geometric marker governing spatial interference. We show BPX serves as a deterministic control parameter, decomposing two-photon spatial patterns into geometry-dictated fundamental modes. This mapping reveals topological invariants and phase singularities that function as a non-tomographic witness for state dimensionality estimation, circumventing full-state reconstruction. Being device-independent and highly scalable, this approach enables scalable high-dimensional characterization and topologically protected state selection, with direct applicability to quantum metrology and high-capacity quantum networks.

07.
arXiv (CS.CV) 2026-06-15

Digital Twin Driven Textile Classification and Foreign Object Recognition in Automated Sorting Systems

The increasing demand for sustainable textile recycling requires robust automation solutions capable of handling deformable garments and detecting foreign objects in cluttered environments. This work presents a digital twin driven robotic sorting system that integrates grasp prediction, multi modal perception, and semantic reasoning for real world textile classification. A dual arm robotic cell equipped with RGBD sensing, capacitive tactile feedback, and collision-aware motion planning autonomously separates garments from an unsorted basket, transfers them to an inspection zone, and classifies them using state of the art Visual Language Models (VLMs). We benchmark nine VLM s from five model families on a dataset of 223 inspection scenarios comprising shirts, socks, trousers, underwear, foreign objects (including garments outside of the aforementioned classes), and empty scenes. The evaluation assesses per class accuracy, hallucination behavior, and computational performance under practical hardware constraints. Results show that the Qwen model family achieves the highest overall accuracy (up to 87.9 %), with strong foreign object detection performance, while lighter models such as Gemma3 offer competitive speed accuracy trade offs for edge deployment. A digital twin combined with MoveIt enables collision aware path planning and integrates segmented 3D point clouds of inspected garments into the virtual environment for improved manipulation reliability. The presented system demonstrates the feasibility of combining semantic VLM reasoning with conventional grasp detection and digital twin technology for scalable, autonomous textile sorting in realistic industrial settings.

08.
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.

09.
arXiv (CS.CL) 2026-06-18

Fair Cognitive Impairment Detection Through Unlearning

Mild Cognitive Impairment (MCI) is a medical condition characterized by a noticeable decline in memory, language, or thinking abilities. MCI detection from spontaneous speech is promising for scalable screening. However, learned models often exploit demographic cues correlated with labels, resulting in a large performance gap across subgroups. We present a multimodal framework that combines (i) cross-model fusion between modalities (speech, text, and image), and (ii) unlearning using gradient reversal that discourages the shared embedding from encoding task-irrelevant demographic attributes. Evaluated on the multilingual benchmarks TAUKADIAL and PREPARE, our method outperforms the state-of-the-art multilingual and multimodal baseline in MCI classification while substantially reducing the performance gap across patient subgroups (sex and language). We further analyze transfer across datasets, showing that demographic unlearning helps learn more robust representations for MCI detection.

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

MedRLM: Recursive Multimodal Health Intelligence for Long-Context Clinical Reasoning, Sensor-Guided Screening, Evidence-Grounded Decision Support, and Community-to-Tertiary Referral Optimization

Real-world clinical decision support requires reasoning over heterogeneous and longitudinal patient information rather than answering isolated medical questions. However, current medical large language models and retrieval-augmented generation systems often rely on single-step prompting or retrieval, which can be fragile when clinical evidence is distributed across long electronic health records, medical images, sensor streams, guidelines, and referral constraints. This paper proposes MedRLM, a Recursive Multimodal Health Intelligence framework for long-context clinical reasoning, sensor-guided screening, and community-to-tertiary referral support. Instead of compressing all patient information into one prompt, MedRLM treats the patient case as an external clinical environment that can be recursively inspected, decomposed, retrieved, verified, and synthesized. The framework coordinates specialized agents for clinical text, longitudinal EHR, medical imaging, physiological sensor signals, guideline retrieval, uncertainty auditing, and referral planning. It further introduces a Clinical Evidence Graph Memory to connect patient-specific observations with retrieved evidence, standardized definitions, sensor-derived biomarkers, and referral criteria. A sensor-guided recursive triggering mechanism activates deeper reasoning when abnormal physiological or behavioral patterns are detected, while uncertainty-gated refinement supports clinician review for high-risk or low-confidence cases. We also outline a real-data evaluation design using public and credentialed clinical datasets spanning EHR, radiology, ECG, ICU time series, and referral-proxy outcomes. MedRLM aims to move medical AI from static question answering toward auditable, multimodal, and workflow-aware clinical decision support.

11.
Nature (Science) 2026-06-09

How ice forms is a mystery — now scientists are cracking the case

Theories about how ice crystals grow in cooling liquids are wildly inaccurate when compared with experimental data, but studies are starting to illuminate the earliest moments in freezing. Theories about how ice crystals grow in cooling liquids are wildly inaccurate when compared with experimental data, but studies are starting to illuminate the earliest moments in freezing.

12.
bioRxiv (Bioinfo) 2026-06-16

Expanding gene regulatory networks from transcriptome data through graphical modeling with heterogeneous priors

Gene regulatory network inference is widely used to reconstruct large-scale networks and identify functional genes from transcriptome data. Meanwhile, in many biological fields, core regulatory genes have been extensively studied, leading to the establishment of small-scale gene regulatory networks, and novel genes connected to these networks remain to be identified. However, methods for expanding existing gene networks by identifying novel regulatory interactions, rather than reconstructing the entire network, are not well established. Here, we propose a method for gene network expansion that incorporates known regulatory relationships and evaluates each candidate gene individually to infer its regulatory connections to the existing network. Using simulated datasets from the DREAM4 benchmark and the PRECISE-1K experimental dataset, our method outperformed conventional methods by incorporating prior knowledge. In particular, it improved the ability to distinguish true regulatory interactions from indirect associations arising from strong correlations among genes in the existing network. The method also showed strong performance for interactions involving genes with high outdegree or centrality. Furthermore, it maintained stable performance as the size of the existing network increased and was robust to noise in prior information. These results demonstrate that our method provides an effective framework for expanding existing gene regulatory networks by leveraging prior knowledge.

13.
arXiv (CS.AI) 2026-06-11

Sample-Efficient Hypergradient Estimation for Decentralized Bi-Level Reinforcement Learning

arXiv:2603.14867v4 Announce Type: replace-cross Abstract: Many strategic decision-making problems, such as environment design for warehouse robots, can be naturally formulated as bi-level reinforcement learning (RL), where a leader agent optimizes its objective while a follower solves a Markov decision process (MDP) conditioned on the leader's decisions. In many situations, a fundamental challenge arises when the leader cannot intervene in the follower's optimization process; it can only observe the optimization outcome. We address this decentralized setting by deriving the hypergradient of the leader's objective, i.e., the gradient of the leader's strategy that accounts for changes in the follower's optimal policy. Unlike prior hypergradient-based methods that require extensive data for repeated state visits or rely on gradient estimators whose complexity can increase substantially with the high-dimensional leader's decision space, we leverage the Boltzmann covariance trick to derive an alternative hypergradient formulation. This enables efficient hypergradient estimation solely from interaction samples, even when the leader's decision space is high-dimensional. Additionally, to our knowledge, this is the first method that enables hypergradient-based optimization for 2-player Markov games in decentralized settings. Experiments highlight the impact of hypergradient updates and demonstrate our method's effectiveness in both discrete and continuous state tasks.

14.
arXiv (CS.AI) 2026-06-12

Decentralized Autoregressive Generation

arXiv:2601.03184v3 Announce Type: replace-cross Abstract: The decentralization of autoregressive generation has attracted considerable attention in recent years as a solution to scaling bottlenecks. However, despite promising empirical results, this paradigm currently lacks rigorous theoretical justification. In this work, we formally establish the theoretical equivalence between decentralized and centralized training. To achieve this, we adapt the Discrete Flow Matching framework for autoregressive generation, leveraging its inherent properties to demonstrate that global models naturally decompose into independent experts. Finally, we conduct extensive experiments across diverse multimodal benchmarks, empirically validating that decentralized training maintains competitive parity with standard centralized architectures.

15.
bioRxiv (Bioinfo) 2026-06-11

Sequence-Based Therapeutic Peptide Classification with Augmented Negative Sampling

Therapeutic peptides offer high target specificity, low toxicity, and the ability to modulate protein-protein interactions, yet experimental functional characterization remains costly and slow. Computational prediction of therapeutic function directly from sequence could accelerate peptide screening and enable generative design pipelines, but requires reliable discrimination between therapeutic and non-therapeutic peptides. Existing multi-label predictors cover few functions, rely on limited datasets, and exhibit high glspl{fpr}, limiting their practical utility. We present a lightweight CNN classifier trained on the most comprehensive therapeutic peptide database to date (54,655 peptides, 48 functional categories). A key contribution is a statistically motivated negative sampling strategy using Markov models to generate diverse synthetic decoys at multiple difficulty levels. When evaluated on this controlled decoy benchmark, the FRP is reduced from over 60% for previous models to 2.1% for our approach. Our fine-tuned five-model ensemble achieves 78.9% Micro F1 and 54.6% Macro F1 while requiring only amino acid sequences as inputs. Analysis using a sparse L1-constrained variant of our model shows that convolutional filters capture conserved functional motifs and statistically improbable non-therapeutic patterns, with downstream layers combining these signals, providing mechanistic evidence that the network learns biologically meaningful structure. In a generalization task on the TPpred-LE benchmark, our model achieves 55.3% Micro F1 and 38.6% Macro F1, comparable to TPpred-LE trained on its native dataset (57.9%/38.1%) while predicting four times more therapeutic functions with four times fewer parameters. Code and models will be made available at https://github.com/terra-quantum-public/tq-therapep-ai.

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

Exponentially many initializations to avoid barren plateaus

arXiv:2606.18515v1 Announce Type: cross Abstract: Barren plateaus are stated as an average-case phenomenon: pick an ansatz, initialize it naively, and concentration follows. This has led to the common view that a potential cure for barren plateaus is simply to initialize the parameters more carefully. Here we show that the situation is subtler. We introduce a first-moment framework that gives a simple operator-level diagnostic for when an initialization may escape the fully concentrated barren-plateau fixed point, and for comparing the biases induced by different initialization strategies. Our framework recovers several known initialization schemes such as identity and Gaussian initialization, but also shows that barren-plateau avoidance is highly non-unique. Indeed, many shifted, biased, and non-symmetric parameter distributions can avoid concentration, and these choices need not be equivalent. In fact, our results show that one can generate exponentially many families of inequivalent initialization strategies. Then, our numerics indicate that different first-moment-distinct initializations can lead to different attained minima, suggesting that avoiding barren plateaus via smart initializations can trade the exponential concentration problem for the challenge of selecting the right trainable pocket amongst many options.

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

Exploring the potential of AlphaEarth and TESSERA embeddings for Fine-scale Local Climate Zone Mapping: A case study across five cities in Switzerland

arXiv:2606.20034v1 Announce Type: new Abstract: Understanding urban spatial morphology is critical for climate modeling, risk assessment, and sustainable urban design, and Local Climate Zone (LCZ) mapping provides the basic framework for this. However, many cities still use coarse ~100-m resolution LCZ records, which are unsuitable for fine-scale urban research. In this study, precomputed embeddings from TESSERA (Feng et al., 2025) and AlphaEarth (Brown et al., 2025) are compared to traditional Sentinel-1/2 (S1S2) composites in five Swiss cities to see if they can upscale coarse LCZ maps to 10-m resolution using an attention-based U-Net. Three experiments assess multi-city transferability, the impact of higher-resolution reference data, and temporal robustness to year-to-year phenology changes. We find that all datasets achieve strong performance with test data Intersection-over-Union (IoU) ranging from 0.59-0.69 and 0.77-0.82 in the first two experiments. TESSERA consistently outperforms both S1S2 and AlphaEarth across both settings As expected, we find that the transfer of embedding-based models from one year to another remains an open challenge. Overall, however, our results demonstrate the promising potential of embeddings derived from EO foundation models to reduce time consuming preprocessing, respectively, manual feature engineering tasks and to guide a universal deep learning-based LCZ mapping workflow. When combined with a simple location-aware attention U-Net architecture, the embeddings enhance regional transferability and scalability, supporting the development of comprehensive and reproducible fine-scale LCZ maps for global urban climate applications Improving reference data quality remains the strongest lever for further accuracy gains.

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

UrbanWell: Benchmarking Multimodal Large Language Models for Spatio-Temporal Urban Wellbeing Analytics

arXiv:2606.15890v1 Announce Type: new Abstract: Understanding urban wellbeing from multimodal data requires integrating heterogeneous spatial and temporal signals, posing significant challenges for current multimodal large language models (MLLMs). We introduce UrbanWell, a large-scale benchmark designed to systematically evaluate the spatio-temporal reasoning capabilities of MLLMs for urban wellbeing analytics through joint modeling of satellite and street view imagery. UrbanWell spans 38 cities across multiple years and includes diverse indicators covering (1) environmental conditions (CO$_2$, NO$_2$, PM${2.5}$, and Normalized Difference Vegetation Index), (2) spatial accessibility (minimum distance to supermarkets and restaurants), (3) urban form (road length, road density, and land use), (4) urban vitality (population, economic activity diversity, and land use diversity), and (5) subjective perception attributes (e.g., safety, beauty, liveliness, wealth, and quietness). All indicators are aligned at grid level to enable standardized evaluation. Beyond static prediction, UrbanWell defines temporal reasoning tasks, including future value forecasting from historical observations and temporal trend classification. We benchmark 15 state-of-the-art representative MLLMs in a zero-shot setting, providing a comprehensive comparative evaluation across spatial and temporal dimensions. Experimental results indicate that while MLLMs capture salient spatial and perceptual cues, their performance varies substantially across heterogeneous urban indicators spanning environment and subjective perception. UrbanWell serves as a unified benchmark for evaluating multimodal spatial and temporal reasoning in urban wellbeing analytics, offering a standardized testbed for systematic assessment and future research on multimodal urban intelligence. Our codes and datasets are accessible via https://github.com/axin1301/UrbanWell-Benchmark.

19.
arXiv (CS.CV) 2026-06-16

Unlocking Diffusion Hierarchies: Adaptive Timestep Selection for Zero-Shot Segmentation

Zero-shot segmentation has recently shown notable improvement by leveraging the rich visual priors in large-scale text-to-image diffusion models, such as Stable Diffusion. However, current diffusion-based methods often face limitations due to the trade-off between spatial resolution and contextual information, as well as their reliance on a single static timestep for feature extraction. To overcome these challenges, our work introduces two key advancements. First, our Contextual Similarity Maps fuse high-resolution attention maps with rich U-Net encoder features, providing both fine-grained and robust per-pixel representations. Second, we identify an emergent hierarchical semantic progression within the denoising process of various diffusion models: representations transition from part-level abstractions at earlier timesteps to object-level abstractions at later stages. Leveraging this insight, we introduce a mechanism to adaptively select the optimal timestep for each pixel. Extensive experiments demonstrate that our method consistently outperforms existing zero-shot segmentation baselines, validating the efficacy of combining contextual features with dynamic, hierarchical timestep selection.

20.
arXiv (CS.LG) 2026-06-12

From Parameters to Feature Space: Task Arithmetic for Backdoor Mitigation in Model Merging

arXiv:2606.12498v1 Announce Type: cross Abstract: Model merging (MM) has gained significant attention as a cost-effective approach to integrate multiple task-specific models into a unified model. However, recent work reveals that MM is highly susceptible to backdoor attacks. Existing defenses based on task arithmetic often fail to eliminate backdoors without substantially degrading clean-task performance, owing to their reliance on direct parameter-space editing. To address this gap, we propose Linear Feature Path Minimization (LFPM), a backdoor mitigation framework for model merging, which introduces an anti-backdoor task vector into the backdoored merged model. Unlike prior approaches, LFPM formulates the backdoor robustness of the merged model from a unified feature-space perspective under the Cross-Task Linearity (CTL) framework, which leverages the approximate linearity of features across tasks. This perspective guides the optimization of the anti-backdoor task to suppress backdoors while preserving clean-task performance. Furthermore, we introduce an effective optimization mechanism based on gradient accumulation and loss path-integral, ensuring robust backdoor suppression along the interpolation path. Extensive experiments demonstrate that LFPM consistently exhibits strong robustness against backdoor attacks in both full fine-tuning and Parameter-Efficient Fine-Tuning (PEFT) settings.

21.
medRxiv (Medicine) 2026-06-18

Automated Airways Characterization and Assessment of Cystic Fibrosis from CT Imaging

Background Advancements in medical imaging have enabled non-invasive diagnosis and staging of cystic fibrosis (CF) using CT scans, revealing dilated airways, an increased number of visible airways, and airway generation splits in these patients. However, manual characterization of airways remains time-consuming and challenging due to the numerous structural changes, thereby limiting clinical feasibility. This study aims to develop an automated algorithm to characterize airways from segmented lung CT scans and apply this to a retrospective population. This approach reduces the time required to analyze images and obtain disease-staging results. Methods This framework consists of two stages. The first stage extracts and skeletonizes the airway tree from lung CTs, while the second stage measures lung features, including airway volumes, branch counts, generation splits, diameters, and cross-sectional areas. This permits comprehensive characterization for use in clinical assessment. Results The airways analysis was performed on 169 CT volumes ranging in age from 6 to 18 years of age, revealing substantial differences in detected airway branches, generation splits, and normalized airway volume between the control and CF groups. The framework also measures airway diameters and cross-sectional areas, revealing an increase in the number of small airways in cystic fibrosis patients, due to early bronchiectasis. These findings align with previous research and demonstrate the framework's ability to accurately quantify airway changes in patients with CF. Discussion The framework extracts entire airway trees, facilitating measurements of volume, branch count, diameters, and cross-sectional areas, which change with CF severity and/or treatment. However, partial lung atelectasis can limit the accuracy of airway detection in moderate-to-severe cases. Funding NIA U54 AG054345 and NIA R21 AG07857501

22.
arXiv (CS.AI) 2026-06-17

Prototype-Based Semantic Consistency Alignment for Domain Adaptive Retrieval

arXiv:2512.04524v4 Announce Type: replace-cross Abstract: Domain adaptive retrieval aims to transfer knowledge from a labeled source domain to an unlabeled target domain, enabling effective retrieval while mitigating domain discrepancies. However, existing methods encounter several fundamental limitations: 1) neglecting class-level semantic alignment and excessively pursuing pair-wise sample alignment; 2) lacking either pseudo-label reliability consideration or geometric guidance for assessing label correctness; 3) directly quantizing original features affected by domain shift, undermining the quality of learned hash codes. In view of these limitations, we propose Prototype-Based Semantic Consistency Alignment (PSCA), a two-stage framework for effective domain adaptive retrieval. In the first stage, a set of orthogonal prototypes directly establishes class-level semantic connections, maximizing inter-class separability while gathering intra-class samples. During the prototype learning, geometric proximity provides a reliability indicator for semantic consistency alignment through adaptive weighting of pseudo-label confidences. The resulting membership matrix and prototypes facilitate feature reconstruction, ensuring quantization on reconstructed rather than original features, thereby improving subsequent hash coding quality and seamlessly connecting both stages. In the second stage, domain-specific quantization functions process the reconstructed features under mutual approximation constraints, generating unified binary hash codes across domains. Extensive experiments validate PSCA's superior performance across multiple datasets.

23.
bioRxiv (Bioinfo) 2026-06-20

Systematic Evaluation of Feature Representations for Cancer-Associated sORF Prediction in Non-coding RNA

Short open reading frames (sORFs) within non-coding RNAs (ncRNAs) have arisen as a hidden layer of gene regulation, encoding small peptides that represent a new class of cancer regulators with diagnostic and therapeutic potential. However, inferring associations between sORFs to specific cancer types remains challenging and requires computational approaches for accurate prediction. Recently, the CoraL framework introduced the first computational approach for predicting cancer-associated peptides, focusing primarily on model architecture while overlooking how feature extraction strategies influence predictive accuracy. We present a systematic evaluation of machine learning models and feature extraction approaches to predict cancer-associated sORFs across 15 cancer types. We benchmarked seven traditional machine learning algorithms combined with three feature extraction methods: k-mer frequency, Word2Vec embeddings, and genomic language model (gLM)-based embeddings. To our knowledge, this is the first study applying gLM-derived embeddings to the prediction of cancer-associated sORFs in ncRNA. Our results show that traditional machine learning models with appropriate feature extraction outperform the CoraL baseline across all cancer types, achieving up to 10% higher accuracy in some of the 15 evaluated datasets. Interestingly, k-mer features consistently outperformed gLM embeddings without fine-tuning, suggesting that local sequence composition may provide more discriminative information for this task and that pre-trained genomic representations may require task-specific adaptation to fully capture these patterns. Additionally, we observed that the way sequences are tokenized, such as the k-mer length, can affect performance: longer fragments (e.g., k=7) sometimes reduced accuracy for Random Forest but had a smaller effect on MLP. Our findings suggest that appropriate feature engineering can provide greater improvements than increasing model complexity.

24.
arXiv (CS.CV) 2026-06-18

APT: Atomic Physical Transitions for Causal Video-Language Understanding

Physical events are not understood by their names alone, but by the causal state changes that compose them. A clip-level label such as "bounce" can be correct while hiding the process that makes the event physically valid, from support loss and contact onset to rebound and settling. To make this hidden process explicit, we introduce Atomic Physical Transitions (APTs): minimal, temporally localized state changes that bind a visible cue to an active physical mechanism and before/after dynamical regimes. An APT chain represents a video as an ordered causal transition sequence rather than a single aggregate event label: event labels tell what happened; APT chains explain why it happened. To make APTs learnable by VLMs, we construct mixed-source APT data from human annotations and simulator ground truth, covering 14 transition types across contact, gravity, friction, and rotation/stability, with 27,303 timed instances over 1,246 trials. Using this data, we find that current VLMs miss transition-level physics, with zero-shot recall at most 14% and errors dominated by missed transitions. Direct fine-tuning on APT chains improves transition detection but causes event-level forgetting, indicating that the model learns a specialized answer format rather than a reusable physical representation. We therefore propose APT-Tune, a parameter-efficient recipe that teaches VLMs to use causal transitions without forgetting how to answer video questions. It combines image-pad-aware supervision, format-conditional co-training, and mechanism-conditioned domain-to-type decoding to make APT learning format-robust and physically grounded. With only 11 M LoRA parameters on Qwen3-VL-2B, APT-Tune substantially improves APT recall while also improving event-level video transfer. These results show that APTs are not a new answer format, but a human-aligned causal supervision signal for physical video understanding.

25.
arXiv (CS.LG) 2026-06-16

Whole-Brain Connectomic Graph Model Enables Whole-Body Locomotion Control in Fruit Fly

arXiv:2602.17997v3 Announce Type: replace Abstract: Animals perform coordinated whole-body movements under the control of neural systems shaped by brain-wide connectivity. The mapping of the whole-brain neural connections, or the connectomes, provides a natural graph for modeling sensorimotor information flow, yet its potential as a neural controller for embodied agents remains largely unexplored. Here, we introduce the Fly-connectomic Graph Model, which directly instantiates the whole-brain connectome of an adult Drosophila as a graph-structured neural controller for movements of a simulated biomechanical fruit fly via deep reinforcement learning. We achieve stable performance across diverse locomotion tasks, as well as better sample efficiency compared to both graph and non-graph baselines. Our results demonstrate a biologically informed way towards effective control policy design by translating whole-brain wiring principles into actionable architectural priors, while also improving the interpretability through dynamic information flow. This work also highlights the potential to bridge neuromechanics with embodied intelligence by providing a computational platform for investigating the sensorimotor transformation underlying animal behavior and a paradigm to advance the development of more nature-aligned intelligent systems.