Data Science Code Translation (DSCT) is the process of converting code between data science libraries while preserving functional equivalence and enabling interoperability across data science ecosystems. While Large Language Models (LLMs) have demonstrated considerable progress in Data Science Code Generation (DSCG), their performance in DSCT remains insufficiently studied. To address this gap, we introduce ORCA, a comprehensive benchmark with two complementary settings: ORCA-MAIN, which comprises 1,600 carefully curated grounding-level tasks across 3 representative domains: Data Querying, Data Manipulation, and Deep Learning; and ORCA-PROJECT, which contains 200 translation tasks over complete data science projects across 7 data science task types. Each task is accompanied by annotated reference translations and test cases for validating functional equivalence. We further incorporate a multi-stage quality verification process that thoroughly verifies task correctness and test case robustness. Experimental results demonstrate challenges in DSCT, with even frontier LLMs showing limited performance. Specifically, Claude-Opus-4.6 achieves a success rate of 56.92% on ORCA-MAIN and 33.67% on ORCA-PROJECT, indicating considerable room for improvement in DSCT. We also observe a clear directional preference in DSCT, where translation is consistently easier when the source code expresses the task through more explicit, fine-grained operations. Motivated by this, we propose an intent-augmented method, in which the model first infers source-code intent and then uses it as additional context for translation, achieving average absolute success-rate gains of 4.80% and 5.33% on ORCA-MAIN and ORCA-PROJECT, respectively.
https://arxiv.org/abs/2609.30749
A key challenge in medical image analysis is the scarcity of large annotated datasets for specific populations and diseases. As deep learning models rely heavily on labeled data, effective transfer learning strategies are needed to reduce the dependence on manual annotations. Self-supervised learning has emerged as a promising approach for developing foundation models by enabling the learning of transferable feature representations from large-scale unlabeled medical imaging datasets. In this study, we investigate voxel-level brain age prediction as a domain-specific self-supervised pretext task and compare it with image inpainting, a widely used non-domain-specific alternative. We further propose a multitask self-supervised pretraining framework that jointly optimizes both objectives to learn complementary neuroimaging representations. The pretrained models are evaluated on three downstream magnetic resonance image segmentation tasks: multiple sclerosis lesion segmentation, ischemic stroke lesion segmentation, and cortical brain structure segmentation. Overall, the proposed multitask pretraining framework consistently outperformed the single-task pretrained models and training from scratch across most experimental settings, demonstrating the benefit of combining domain-specific and general self-supervised learning pretext tasks for the development of generalizable neuroimaging foundation models.\ Code Availability: The source code used in this study is publicly available at this https URL
https://arxiv.org/abs/2609.30708
CryoEM map interpretation requires features that are spatially localized, consistent across samples, and informative across spatial scales. Most deep learning methods for map annotation extract features from fixed voxel grids. However, implicit neural representations (INRs) are able to model volumetric data as scale-agnostic, coordinate-conditioned functions. INRs are therefore attractive for cryoEM, but fitting a separate INR for each map is too expensive for large-scale feature extraction and produces representations that are not aligned across samples. We introduce Atelier, a self-supervised framework that amortizes INR fitting for reconstructed cryoEM maps. Pretrained on 5,439 Electron Microscopy Data Bank maps, Atelier is a transformer-based hypernetwork that generates high-fidelity reconstructions across a wide range of protein structures, including large multi-subunit assemblies. Beyond reconstruction, the INR generated by the pretrained transformer exposes a continuous, local feature field through its intermediate activations at any spatial query point, a property that voxel grid and patch-tokenizer architectures do not naturally provide. Used as auxiliary channels to a 3D nested U-Net annotation head trained from scratch, these coordinate-conditioned features improve performance on eight voxel-level property prediction tasks over a volume-only baseline. Our results demonstrate that amortized implicit neural representations are an effective primitive for geometry-aware analysis of cryoEM data.
https://arxiv.org/abs/2609.30569
Variable-size inputs are common in deep learning, but dense batching allocates a shared envelope and spends computation on padding. The cost multiplies across varying axes: an explicit pair state allocates $BN_{\max}^2$ positions instead of $\sum_i N_i^2$. Packing removes that waste, but composing packed operations still requires the logical axes and sample boundaries a flat buffer no longer exposes. We present DanLing NestedTensor, a PyTorch tensor abstraction that makes multi-ragged structure a property of the tensor itself. Packed values carry tensor-backed partitions and logical dimension order, so broadcasting creates ragged axes, feature transformations retain them, and reductions consume them. The same representation carries through autograd and both eager and compiled execution. On an A100, the geometric-mean speedup over same-mode padding is 2.74$\times$ eager and 3.39$\times$ compiled across four BERT scales, and 1.97$\times$ eager across four FCN backbones. A four-block Pairformer-style workload runs 2.40-4.32$\times$ faster than a padded reference using native PyTorch kernels across square length regimes in eager execution, with peak allocation falling from 38.08 to 5.41 GiB on its high-variation batch. The tensor interface lets model code built from its supported operators compose efficient variable-size computation without managing offsets at any call site. Code will be released publicly upon publication.
https://arxiv.org/abs/2609.30379
The segmentation of anatomical structures in medical images and particularly in MRI scans, is essential for clinical diagnosis and monitoring disease progression. While Deep Learning (DL) architectures, such as U-Net and its extensions are very effective in medical image segmentation tasks, they often struggle with preserving fine-grained details and global contextual information. This is especially challenging for MRI data segmentation, where anatomical structures are characterized by irregular boundaries and variations in shape, contrast, and scale. To address this challenge, we propose a novel DL architecture for MRI segmentation across different anatomical structures. Specifically, the architecture introduces a module, named Multi-Resolution Feature Fusion (MRFF), that can be easily integrated into any U-Net-like architecture. The MRFF is integrated in all levels of an encode-decoder structure, along with attention mechanisms and skip connections to extract features at multiple resolutions, enabling the model to capture both fine-grained details and global contextual information. We evaluate the MRFFU-Net on two publicly available benchmark MRI datasets of different anatomical targets; one for Cerebrospinal Fluid (CSF) segmentation in spinal MR scans, and one for left atrium cardiac segmentation, from the Medical Segmentation Decathlon (MSD) challenge. Experimental results indicate that MRFFU-Net outperforms state-of-the-art models across multiple evaluation metrics, demonstrating its effectiveness in MRI segmentation.
https://arxiv.org/abs/2610.00279
Deep learning inference and training performance depends critically on GPU kernel efficiency. Modern compilers such as PyTorch Inductor automatically generate GPU kernels from high-level model code, but frequently underperform expert-written implementations by wide margins. Recent LLM-assisted kernel optimizers can close this gap for standalone kernels, yet treat compiled models as black boxes, generally optimizing individual standalone kernels without respecting the compiler's structural decisions or verifying the model end-to-end. We present KernelOPT, a multi-agent system that treats compiled models as structured artifacts. It preserves vendor library calls (cuBLAS, cuDNN) and exclusively targets generated Triton sub-kernels using five profiling-guided LLM agents. A four-gate verification cascade of static validation, multi-seed correctness, model-level float64-fallback verification, and performance gating filters candidates during optimization and verifies the re-stitched model end-to-end. If no candidate passes all four gates, the system preserves the compiler baseline. The system accepts PyTorch this http URL, standalone Triton kernels, and Helion kernels. Evaluated on 250 KernelBench problems, KernelOPT achieves geometric mean speedups over \texttt{this http URL} of 1.40$\times$ (Level 1: 51/100), 1.15$\times$ (Level 2: 31/100), and 1.07$\times$ (Level 3: 12/50) across all problems.
https://arxiv.org/abs/2609.30059
We present NNV3, the latest version of the Neural Network Verification (NNV) tool, a MATLAB framework for formal verification of deep learning models and learning-enabled cyber-physical systems. Building on the set-based reachability foundation of NNV 1.0 (FFNNs, CNNs, NNCS) and NNV 2.0 (RNNs, SSNNs, neural ODEs), NNV3 introduces new members of the Star-set family: ModelStar for verifying networks under weight perturbation, VolumeStar for video and 3D volumetric inputs, and GraphStar for graph neural networks. A conformal-inference-based probabilistic reachability mode complements sound analysis for problems where deterministic verification is intractable, while FairNNV certifies counterfactual and individual fairness properties over continuous input regions. NNV3 introduces new benchmarks for malware detection, graph-based power-system models, medical imaging, variable-length time series data, and action recognition. NNV3 also incorporates tutorials and developer guides through a unified documentation site. This paper details these major updates, demonstrating NNV's maturation into a comprehensive, robust, and accessible verification tool for a diverse range of AI systems.
https://arxiv.org/abs/2609.30050
Deep learning-based speech enhancement is increasingly deployed on-device in hearing aids, headsets, and earbuds. Most of these devices, however, can only accelerate static int8 graphs, so a depth-varying network must be implemented as several graphs, orchestrated by a policy. In this paper, we supervise every intermediate depth of one causal model, then we fine-tune its output heads to guarantee that deeper outputs are never worse than shallower ones. Using this training protocol, we can derive a family of static models that are more Pareto-efficient than their equivalently-sized counterparts trained from scratch on the same budget. Specifically, we achieve up to 0.11 higher PESQ for equivalent compute, and match the best PESQ at 30% less compute. We then quantize the models to int8 and measure the latency-quality frontier on an STM32N6 microcontroller. On VoiceBank-DEMAND, the dynamic enhancer lies on the same frontier as the static models, rather than trading quality for dynamic execution. Running the policy on the companion Cortex-M55 takes only 26 $\mu$s per frame, while splitting the enhancer into separate NPU graphs adds 2.2% latency overhead. The cost of dynamic execution is therefore small.
https://arxiv.org/abs/2609.29867
Background: Artificial intelligence (AI)-based glaucoma detection from colour fundus photographs (CFP) offers scalable screening, but performance may decline on external datasets because of differences in ground-truth definitions, populations, and coexisting conditions such as high myopia (HM). We developed and validated a Vision Transformer-based deep learning (DL) model for glaucoma detection across multi-ethnic cohorts with and without HM. Methods: A ViT-B/16 model with predictive uncertainty estimation was developed using 56,483 CFPs (57.1% with myopia; 14.4% with HM). Glaucoma labels were standardised using clinical, imaging, and perimetry data. The model was validated on 16 independent datasets across three continents, including four datasets with explicit HM labels. Findings: Internal AUROC was 98.7% (95% CI 98.2-99.1%), with sensitivity 94.5% and specificity 97.3%. Across 16 external datasets from eight countries, AUROCs ranged from 86.4% to 99.6%. In HM eyes, internal AUROC was 97.8% (95% CI 96.1-99.2%), with sensitivity 94.8% and specificity 93.7%. External HM AUROCs were 86.5% in the Beijing Eye Study and 93.3%, 91.8%, and 85.5% in hospital-based datasets from Taiwan, Thailand, and South Korea. In an exploratory HM clinical evaluation, the model had higher CFP-only diagnostic accuracy than ophthalmologists and trained graders (92.0% vs 70.0%; p=0.008) and performed comparably to glaucoma specialists using full clinical information. Interpretation: The model showed robust glaucoma detection across myopic and non-myopic multi-ethnic populations and may support AI-assisted screening in settings with high HM prevalence.
https://arxiv.org/abs/2609.29433
This paper presents and evaluates a Deep Learning-based (DL-based) Signal Quality Assessment (SQA) model to distinguish between clean and noisy ambulatory Electrocardiograms (ECG). The model is trained on Copenhagen Center for Health Technology-Contextualized Arrhythmia Database (CACHET-CADB), which, to the best of our knowledge, is the first ambulatory ECG database with both physical and patient-reported contextual data. The model shows stable performance on different databases such as MIT-databases and the latest PyhsioNet/Cinc Challenge 2021 databases. Subsequently, the paper demonstrates how complicated ECG noise can be investigated by the SQA model and the physical contextual data.
https://arxiv.org/abs/2609.29396
Time series analysis is fundamental in domains such as finance, healthcare, and meteorology. Real-world time series often exhibit multiscale characteristics shaped by diverse latent factors, resulting in intricate temporal patterns and rich frequency structures. However, existing approaches typically focus on either frequency-domain decomposition or time-domain pattern extraction in isolation, neglecting their joint structure. This decoupled modeling limits representation expressiveness and undermines performance in tasks requiring simultaneous temporal and spectral reasoning. To address this gap, we propose m-WCN, a novel end-to-end deep learning framework that neuralizes multi-wavelet decomposition for joint extraction of temporal patterns and frequency components. By approximating the classical GHM multi-wavelet transform with trainable convolutional operators and enforcing orthogonality constraints, m-WCN produces interpretable multi-resolution representations. Built on this foundation, we introduce two task-specific architectures: TFBC for time series classification, which boosts discriminative features across frequency scales, and FTB for forecasting, which ensembles frequency-aware predictors. Extensive experiments on 64 UCR datasets and seven public forecasting benchmarks demonstrate the effectiveness of our approach. Built on the neuralized m-WCN, our TFBC and FTB outperform various baseline models across diverse datasets, achieving average improvements of 19.97% in classification and 19.92% in forecasting tasks.
https://arxiv.org/abs/2609.29317
Glaucoma is the leading cause of irreversible blindness, and timely identification of fast progressors is essential to prevent disability. Current practice estimates progression by ordinary least-squares regression of mean deviation (MD) on time, requiring 6--10 visual field (VF) tests over several years to obtain a reliable slope. We present GLAM (Glaucoma Longitudinal Analysis Model), a deep learning framework that ingests longitudinal Humphrey 24-2 total deviation sequences with five clinical features and predicts MD and visual field index progression rates using attention-based fusion and aleatoric uncertainty. On the open-access University of Washington Humphrey Visual Field dataset (4,276 patient-eyes), GLAM achieved an MD-rate mean absolute error of 0.139 dB yr$^{-1}$ ($R^2 = 0.927$; 73.5% reduction over a ridge baseline) and an AUC of 0.990 for fast-progressor detection. VF-only deep learning can match multimodal pipelines for progression prognostication using routinely collected perimetry alone.
https://arxiv.org/abs/2609.29256
Score-informed note separation seeks to extract the performed waveform of all individual notes, often from a polyphonic recording. Existing deep learning systems generally only target instrument-level stems. We present, to our knowledge, the first deep learning approach to score-informed note separation, NoteSep. NoteSep extracts the queried notes by applying an extraction stage model, NoteGrab, once per note. Conditioned on pitch, onset, and offset, NoteGrab separates harmonic and percussive components in two U-Nets linked by bidirectional cross-attention; selective harmonic gating suppresses lower-octave interference while preserving percussive attacks. Finally, a joint separation stage applies Adaptive Set Ownership (ASO) to compare concurrent NoteGrab estimates and reallocate mixture energy. We curate SCNS-Train (25,729 mixtures and 743,920 targets) for training and SCNS-Eval (16 instruments, disjoint scores and libraries) for evaluation. On SCNS-Eval, NoteSep reaches a median SI-SDR of 7.39~dB, compared with 2.49~dB for our strongest baseline. See the demo page at this https URL.
https://arxiv.org/abs/2609.29071
Over the course of a lifetime, robots may encounter novel scenarios unaccounted for in its original training that result in performance degradation. One common approach to mitigating this issue is to further grow the offline training dataset in hopes of producing a policy robust to these changes. In contrast, biological learning occurs moment-to-moment via a stream of experience, unlike the predominantly batch-based and offline nature of deep learning. Although recent works show the feasibility of stream-based deep reinforcement learning, where updates use only the latest experience, none have shown it to be a viable continual learning framework for adapting robotic policies to unseen changes. In this paper, we present the first analysis of streaming deep reinforcement learning for adaptive continual learning in robotics. In particular, we show that, following an initial pretraining phase, streaming deep RL can enable a robot to successfully adapt to unforeseen changes to itself, its environment, or goals. Our primary experiments within quadruped locomotion demonstrate that a deep neural network robotic policy with certain optimizers and plasticity loss mitigation techniques can successfully leverage domain task knowledge from its pretraining to quickly adapt online to diverse changes via stream learning, outperforming batch-based on-policy methods and improving task success rates by up to 90% over the pretrained policy. Furthermore, we perform additional evaluations on robotic manipulation tasks to determine if our previous observations extend to different robotic morphologies and scenarios. Our results show that the successes observed in quadruped locomotion can be partially realized in manipulation with stability and performance limitations. We conclude with a discussion on the limitations of our work and its implications for the future of continual robot learning.
https://arxiv.org/abs/2609.28807
Deploying deep learning models on edge CPUs is bottlenecked by computational and memory constraints. Mixed-precision quantization promises to reduce inference latency while preserving accuracy. However, quantization affects different layer types in inconsistent ways, so identifying where accuracy loss is minimized and latency reduction is maximized is critical, as the effect accumulates over a full deployment into substantial savings or unacceptable task degradation. Such identification relies on sensitivity metrics, proxies that estimate layer-wise degradation without evaluating the task accuracy of every candidate policy. Nevertheless, widely used metrics fail systematically on modern architectures. We present a systematic empirical study of 13 sensitivity metrics for layer-wise INT8 quantization across four distinctly different neural networks, and validate the resulting policies on two ARM64 platforms. Gradient-based sensitivity methods fail on 4 out of 8 model-hardware configurations and weight-based statistics on 2. In contrast, the Jensen-Shannon Divergence achieves zero catastrophic failures, reliably isolating the layers that cannot be safely quantized. A sensitivity metric alone does not define a policy, and the fixed thresholds typically used for that step are fragile over the highly skewed distributions of modern architectures. We address this with K-Means clustering, achieving near-lossless accuracy and a mean speed-up of $1.81\times$ over the full-precision model. Finally, we reveal that excluding from quantization the layers whose speed-up is negligible, regardless of their sensitivity, can be counterproductive, as it induces computational graph fragmentation and disables operator fusion. Our results yield concrete allocation policies for practitioners and researchers deploying quantized vision models on heterogeneous edge CPUs, without GPU access or gradient computation.
https://arxiv.org/abs/2609.28262
Background & Problem: Thyroid Fine-Needle Aspiration Biopsy (FNAB) cytology based on the Bethesda System plays a pivotal role in early thyroid cancer detection; however, deep learning approaches face substantial challenges regarding high false-negative rates and overconfidence under clinical domain shift. Methods: In this study, we propose TAM-Chain, a multi-scale (10x, 20x, 40x) thyroid cytology classification framework leveraging Absorbing Markov Chain theory combined with Shannon Entropy-based Uncertainty Quantification. The framework dynamically models multi-magnification feature extraction as an absorbing stochastic process, enabling optimal stopping criteria and a human-in-the-loop referral mechanism to strictly suppress critical diagnostic errors. Results: Extensive evaluation on an internal test set (N = 235) demonstrates a Macro F1 score of 0.9741 with an absolute False-Negative Rate (FNR) of 0.00%. On an independent external validation set (N = 1015) presenting severe domain shift, TAM-Chain maintains superior stability and classification performance (Macro F1 = 0.7026) by adaptively adjusting the expected stopping step and triggering specialist referrals, significantly outperforming single-magnification baselines. Conclusion: The TAM-Chain framework proves to be a highly effective, safe, and adaptable solution for digital pathology workflows, successfully harmonizing automated diagnostic efficiency with stringent biological safety.
https://arxiv.org/abs/2609.28590
In this paper, we are concerned with matrices formed by block-diagonal factors interleaved with fixed permutations -- a flexible family of structured matrices. This class has recently drawn interest in deep learning architectures for its balanced expressivity-efficiency trade-off, yet efficient computational strategies for working with it remain to be found. We approach this problem through Riemannian geometry and examine under what conditions this class admits a smooth manifold structure. For the practically important case of orthogonal two-factor matrices, we derive the essential Riemannian tools and propose efficient algorithms for their implementation. The algorithms leverage automatic differentiation, support parameter sharing within each factor, and avoid explicit dense matrix construction. We test them within the Riemannian optimization framework on the best matrix approximation problem and for parameter-efficient fine-tuning of large language models. Beyond the two-factor setting, we study the geometric and matrix-theoretic properties of factorizations with a larger number of block-diagonal factors.
https://arxiv.org/abs/2609.27982
We developed an anatomy-aware deep learning framework to synthesize post-contrast breast MRI from pre-contrast images, emphasizing tumor and background parenchymal enhancement (BPE) regions. This retrospective study included 649 patients with 6,251 paired pre-contrast and post-contrast images. The framework integrates breast mask consistency, lesion-region supervision, and BPE-region supervision into an image-to-image translation model. Evaluation included quantitative image quality metrics, a reader study with two breast radiologists, and downstream Ki-67 classification. The proposed method outperformed Pix2Pix, Pix2PixHD, diffusion-based synthesis, and mask-supervised baselines in whole-image and regional evaluations. Ki-67 classification showed no statistically significant performance differences across real- and synthetic-image training and testing settings, although this does not establish equivalence. These findings suggest that anatomy-aware supervision improves synthesis fidelity and support further investigation of synthetic post-contrast MRI for contrast-free imaging workflows.
https://arxiv.org/abs/2609.27015
Cricket is one of the most celebrated sports world-wide, and technological advancement has become deeply embedded in how the modern game is analyzed and coached. Cricket shot classification and automated performance analysis add a further dimension to this trend. Traditional approaches rely on RGB video features or static images, which are sensitive to environmental variations such as camera angle, lighting, and background clutter, and often fail to capture the underlying biomechanics of batting actions. In this paper, we propose a system to improve cricket coaching that takes raw video data, extracts batsmen from video frames using YOLO, and extracts 3D pose data from video frames using MeTRAbs. The system produces sequential skeletal pose data of 30 body points and captures the biomechanical features of a batsman. As part of the system, we also propose a deep learning ensemble for shot classification of four shots: flick, pull, defense, and drive. The ensemble performed well, compared to existing classification works, achieving 97.68% accuracy. In addition, we analyzed the misclassification rates to identify cases where shots were incorrectly classified and examined their possible causes. Our proposed system allows novice players to obtain useful feedback, such as important joint angles relative to expert batsmen, which can also be useful for injury prevention. The shot classifier also helps track class-wise shots over time for further analysis. In addition to novice players, coaches can use the system for player evaluation.
https://arxiv.org/abs/2609.26923
Laryngeal high-speed videoendoscopy (HSV) offers an effective means of observing the motion of different laryngeal structures along with vibratory behaviors of the vocal folds under various voicing conditions. Segmentation of laryngeal tissues enables analysis of different tissue structures and their dynamics, helping characterize the involvement of laryngeal muscles in voice production. Given the large number of HSV frames, automating this task is imperative. While deep learning-based methods have been implemented in previous studies to segment laryngeal structures, they have not been applied to HSV data during connected speech, which poses significant challenges due to excessive tissue movements and image quality limitations associated with fiberoptic image acquisition. The application of deep learning to connected speech data is critical for capturing nonstationary laryngeal behaviors and identifying anomalous patterns associated with voice disorders. The present study aims to address these gaps by training U-Net models to detect the aryepiglottic folds and arytenoid cartilages, vocal folds, epiglottis, and glottal area, using HSV data from both sustained vowel phonation and connected speech obtained from normophonic and disordered voices. Image pre-processing techniques, including noise removal and histogram equalization, were applied to improve the quality of the training HSV images and enhance network performance. Finally, to evaluate the accuracy and reliability of the networks, quantitative performance metrics were used alongside qualitative visual inspection of the test images. The high performance of the developed networks, with overall accuracies exceeding 95%, establishes their potential as reliable tools for automated laryngeal image analysis, quantitative characterization of laryngeal dynamics, and future detection of anomalous laryngeal behaviors in clinical settings.
https://arxiv.org/abs/2609.26636