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01.
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.

02.
medRxiv (Medicine) 2026-06-17

Womens intentions and motivations towards health behaviour change before pregnancy: a cross-sectional survey of pregnant women in Australia

Introduction: The preconception period (i.e. the weeks and months before pregnancy) is a critical window during which parental health behaviours can influence pregnancy outcomes and the childs long-term health. Modifiable factors such as nutrition, physical activity, substance use, and environmental exposures play a key role, yet womens ability to adopt and sustain healthy behaviours is shaped by complex psychological, social and environmental influences. This study applies the Theory of Planned Behaviour to identify the beliefs underpinning womens preconception behaviours, with the aim of informing support for effective and sustained health behaviour change. Methods: An Australian national retrospective cross-sectional survey of pregnant women (18-49 years), recruited through social media platforms. The 92-item survey captured respondent socio-demographics, pregnancy status and health conditions, health behaviours, and beliefs regarding preconception health behaviours. Respondents level of pregnancy planning was categorised using the London Measure of Unplanned Pregnancy (LMUP). Items regarding preconception beliefs were structured in accordance with the Theory of Planned Behaviour, with a focus on regular exercise, healthy diet, and alcohol avoidance. These beliefs variables were analysed using structured equation modelling to identify paths between latent variables and the items used to estimate each concept. Results: The study was completed by 430 pregnant women of whom 72.7% had a planned pregnancy. Most had a partner, were university educated and in good health. Structural equation modelling showed intention strongly predicted exercise ({beta}=0.65), healthy diet ({beta}=0.54) and alcohol avoidance ({beta}=0.64). Perceived control and partner norms influenced intentions, whereas health professional norms had limited effect. Positive beliefs were associated with folate supplement use and smoking cessation. Conclusion: These findings highlight intention as a key driver of preconception health behaviours, with perceived control and partner influences playing a more significant role than individual beliefs or health professional input. Effective interventions should therefore address structural barriers and actively involve partners, while respecting womens autonomy. Overall, couples-focused, multi-level strategies are likely essential to support meaningful and sustained preconception health behaviour change.

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

Arbitrary control over multimode wave propagation for machine learning

arXiv:2402.17750v2 Announce Type: replace-cross Abstract: Controlled multimode wave propagation can enable more space-efficient photonic processors than architectures based on discrete components connected by single-mode waveguides. Instead of defining discrete elements, one can sculpt the continuous substrate of a photonic processor to perform computations through multimode interference in two dimensions. Here we designed and demonstrated a device with a refractive index that can be rapidly reprogrammed across space, allowing arbitrary control of wave propagation. The device, a two-dimensional programmable waveguide, uses parallel electro-optic modulation of the refractive index of a slab waveguide with about $10^4$ programmable spatial degrees of freedom. We implemented neural network inference on benchmark tasks with up to $49$-dimensional vectors in a single pass, without digital pre-processing or post-processing. Theoretical and numerical analyses further indicated that two-dimensional programmable waveguides may offer not only a constant-factor reduction in device area but also a scaling benefit, with the area required growing as $N^{1.5}$ rather than $N^2$.

04.
arXiv (CS.LG) 2026-06-18

Investigating Faithfulness in Large Audio Language Models

arXiv:2509.22363v4 Announce Type: replace Abstract: Large Audio Language Models (LALMs) integrate audio encoders with pretrained Large Language Models to perform complex multimodal reasoning tasks. While these models can generate Chain-of-Thought (CoT) explanations, the faithfulness of these reasoning chains remains unclear. In this work, we propose a systematic framework to evaluate CoT faithfulness in LALMs with respect to both the input audio and the final model prediction. We define three criteria for audio faithfulness: hallucination-free, holistic, and attentive listening. We also introduce a benchmark based on both audio and CoT interventions to assess faithfulness\footnote{The benchmarking interface and evaluation results are available at https://poonehmousavi.github.io/faithfulness/. Experiments on Audio Flamingo 3 and Qwen2.5-Omni suggest a potential multimodal disconnect: reasoning often aligns with the final prediction but is not always strongly grounded in the audio and can be vulnerable to hallucinations or adversarial perturbations.

05.
arXiv (CS.LG) 2026-06-15

Adaptive Nucleus Truncation for Long-Form Reasoning

arXiv:2606.13982v1 Announce Type: cross Abstract: Sampling plays an important role in long-form language-model reasoning. Over thousands of decoding steps, small changes in the candidate token set can compound into different reasoning trajectories, stability profiles, and final answers. Existing truncation methods such as top-$p$, min-$p$, and fixed top-$n\sigma$ sampling improve over unrestricted sampling, but they rely on fixed thresholds that cannot adapt to changes in entropy, task difficulty, training stage, or generation budget. We introduce Adaptive Nucleus Truncation Sampling (ANTS), which extends top-\(n\sigma\) sampling from a fixed decoding rule into an adaptive rollout-control mechanism for long-form generation. ANTS selects standardized neighborhoods around the maximum logit before temperature scaling, adapts the truncation width using an entropy-conditioned controller, and retains a no-truncation fallback arm to stabilize training when truncation becomes unsafe. On a 33B-total / 4B-active sparse Mixture-of-Experts reasoning model, ANTS improves average performance over percentage-based benchmarks by +1.9, +3.8, and +5.2 points at 8K, 16K, and 32K generation budgets, respectively. The strongest gains appear on instruction following and mathematical reasoning, with IFBench improving by more than 10 points at 32K and AIME 2025 improving by 7 points. Code generation reveals an important budget interaction. On Codeforces, ANTS trails the baseline at 8K, but reverses this gap and substantially improves ELO at 16K and 32K. These results suggest that sampler design should be treated not just as a decoding hyperparameter, but as part of how we stabilize and scale long-budget reasoning.

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

Giving AI a Headache: Acoustic Adversarial Attacks to Computer Vision Applications

Artificial Intelligence (AI) is increasingly used to automate a variety of real-world computer vision (CV) applications, such as autonomous vehicle control, facial recognition, and security cameras. Recent research has shown that acoustic vibration can induce real physical motion in cameras, interfering with their internal stabilization mechanisms. Because the motion falls outside the conditions the stabilization system was designed to handle, the system introduces artifacts into the frame, causing AI-based CV models to misclassify, miss targets, or hallucinate objects. Previous work used ultrasonic frequencies (>20 kHz) to perform short-range attacks, which limits them to short distances due to the attenuation exhibited by high frequencies. In this work, we investigate acoustic attacks using lower frequencies in the audible range (

07.
arXiv (CS.CL) 2026-06-18

UniECG: Understanding and Generating ECG in One Unified Model

Electrocardiogram (ECG) interpretation is a fundamental skill in medical education, yet students often need more than static examples to connect waveform evidence with diagnostic reasoning. This paper presents UniECG as a step toward interactive ECG education. UniECG supports two complementary learning interactions: given an ECG signal or image, it generates an evidence-based explanation; given a textual learning objective, it generates a corresponding ECG signal example for case-based learning. The model follows a two-stage design. First, it learns grounded ECG explanation from ECG signal–image–text data. Second, it introduces special ECG generation tokens and aligns their hidden representations with a pretrained text-conditioned ECG diffusion model, enabling controllable signal-level ECG generation. We evaluate UniECG through grounded ECG explanation and generation-oriented qualitative analysis, examining its potential to support explanation and case-based learning. UniECG is intended as an educational aid and a research step toward interactive AI-assisted ECG learning, rather than a clinically validated diagnostic system.

08.
arXiv (CS.CV) 2026-06-18

Quantification of Uncertainty with Adversarial Models in Medical Image Segmentation

Reliable pixel-level uncertainty quantification holds the potential to transform clinical workflows by enabling high-fidelity longitudinal monitoring and distinguishing true pathological changes from artifacts. Ideally, these models provide the stability required for critical treatment planning and surgical intervention. However, standard deep learning models often suffer from miscalibration, yielding overconfident predictions that mask underlying vulnerabilities at subtle pathological boundaries. To address this, we propose QUAM-SM, a post-hoc framework using targeted adversarial search to identify "adversarially fragile" pixels. By actively seeking perturbations that expose predictive instability, our method highlights regions where decisions are most vulnerable to being flipped. Importantly, the framework disentangles epistemic uncertainty from aleatoric uncertainty. Experiments on two public datasets with multiple expert annotations demonstrate that QUAM-SM outperforms both standard and recent uncertainty estimation approaches in terms of reliability and boundary sensitivity. Code is available at https://github.com/HanaJebril/quam_sm

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

scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

arXiv:2606.13007v1 Announce Type: cross Abstract: Clustering is fundamental to scRNA-seq analysis, serving as a cornerstone for identifying cell populations and resolving tissue heterogeneity. However, existing methods focus on mining numerical statistical patterns, suffering from semantic agnosticism by neglecting the intrinsic biological functions encoded by genes. While Large Language Models (LLMs) offer promising semantic capabilities, their direct adaptation to cell clustering is hindered by the structural mismatch between generative pre-training objectives and discriminative downstream tasks. To bridge this gap, we propose scLLM-DSC, a novel LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering framework. Diverging from data-driven paradigms, scLLM-DSC establishes a semantically-grounded representation by synergizing two views: a Knowledge-Driven Semantic View derived from NCBI gene priors and contextualized Cell2Sentence embeddings, and a Structure-Aware Topological View extracted via a graph-guided encoder. Crucially, we introduce a cross-modal contrastive alignment mechanism to enforce consistency between biological semantics and transcriptomic features within a unified latent space. Extensive benchmarks demonstrate that scLLM-DSC significantly outperforms eleven state-of-the-art baselines in clustering accuracy.

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

Million-scale multimodal pollen microscopy with expert-guided foundation models

Automated pollen identification from microscopy remains a bottleneck in aerobiology, palaeoecology and biodiversity monitoring, because scalable systems must generalise across specimen preparation, scanner settings and geographic origins while retaining palynological interpretability. To address this gap, we present a million-scale multimodal pollen microscopy resource, Pollen AI Atlas, assembled from pure-species whole-slide bright-field images spanning four geographic origins, four scanner settings and 46 taxon labels across 31 botanical families. Seeded by one manually selected exemplar per source slide, token-level mining and filtering produced 1,511,390 released grain detections with 99.6\% proposal precision in expert-curated test regions. Each detection was paired with machine-generated grain-level morphological captions from five open-weight vision-language models, guided by expert-verified palynological anchors, yielding structured descriptions of aperture systems, wall ornamentation, shape and size. Among the evaluated models, Gemma4 provided the most controlled primary caption set, combining tight length control, no leakage and the strongest text-retrieval performance. Baseline benchmarks with frozen visual features reached 88.16\% top-1 accuracy, while cross-regional retrieval showed that caption-derived text embeddings remained robust when image similarity degraded (mAP@20 0.811 versus 0.262). Released data, annotations, captions, splits, code, and weights provide a benchmark for pollen recognition, cross-regional domain adaptation and domain-specific multimodal microscopy learning.

11.
arXiv (CS.LG) 2026-06-15

Curvature-Guided Geometric Representation for Protein-Ligand Binding Affinity Prediction

arXiv:2606.14159v1 Announce Type: new Abstract: Protein-ligand binding affinity (PLA) prediction is critical in drug discovery. Despite the notable advancements in machine learning-based approaches, existing methods struggle to jointly characterize local geometric organization and globally coordinated cross-molecular interactions, limiting their ability to model complex binding mechanisms. Here, we propose RicciBind, a geometric representation framework that integrates curvature-guided hierarchical structure learning with optimal transport (OT)-based cross-domain alignment to model molecular interactions. Specifically, RicciBind leverages Ricci curvature to capture local interaction tightness within molecular structures, enhancing structural awareness and organizing atomic interactions into curvature-aware hierarchical representations. An OT-based cluster matching mechanism then aligns protein and ligand clusters across heterogeneous domains under geometric constraints, enabling globally consistent correspondences and revealing higher-order interaction patterns beyond local neighborhoods. By coupling curvature-guided structure encoding with OT-driven cross-domain alignment, RicciBind effectively models complex interaction semantics and substantially improves both the accuracy and interpretability of binding affinity prediction. Extensive experiments demonstrate that RicciBind achieved superior predictive performance and generalization across PLA benchmarks and virtual screening tasks. Ablation studies further confirmed the essential role of Ricci curvature in enhancing molecular interaction representations.

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

Rigel: Reverse-Engineering the Metal 4.1 Tensor Compute Path on the Apple M4 Max GPU

Apple's Metal 4.1 exposes a tensor compute path: the Metal Performance Primitives (MPP) matmul2d operation over cooperative_tensor fragments, whose interface is documented but whose hardware behavior is deliberately hidden. The specification states which data-type rows are supported, never whether they are hardware-accelerated, where the operation physically executes, what its accumulator width is, or how it partitions matrix fragments across threads. We present Rigel, an empirical characterization of this path on a single Apple M4 Max (a pre-neural-accelerator generation). Using a checksum-gated, provenance-tracked microbenchmark harness, Rigel recovers eleven facts the v4.1 specification hides or contradicts. The headline finding: the Metal 4.1 fp8 (E4M3) matmul2d is emulated, not accelerated: it sustains 0.94x the throughput of fp16 despite reading half the operand bytes, so on M4 it is a memory-footprint feature, not a performance feature. We further show, via a three-signal triangulation (throughput ceiling, comparison against simdgroup_matrix, and per-rail power attribution), that matmul2d executes entirely on the GPU shader cores with no dedicated matrix datapath and no evidence of Apple Neural Engine routing; that it accumulates in >=fp32; and we reconstruct the opaque 8x8 cooperative_tensor fragment layout Apple documents nowhere. Acting on the characterization, a hand-fused GEMM + bias + GELU kernel beats the decomposed path by +6.5-12.9% in the cache-resident regime. All findings are reproducible from committed MIT-licensed code and per-cell CSVs.

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

Mask Proposal Voting Based on Geodesic Framework for Robust Image Segmentation

Despite great advances, finding accurate segmentation remains a challenging task, especially in scenarios with cluttered backgrounds, complex intensity variations and topology appearance. Minimal path models have exhibited their strong ability in addressing image segmentation tasks. However, the performance of minimal paths-based segmentation approaches is heavily influenced by model initialization, hence limiting their application scope in practice. In this work, we propose a novel mask proposal voting framework that overcomes the major drawback of classical approaches, allowing robust segmentation even in complicated scenarios. Firstly, we introduce an efficient method for constructing adaptive domain cuts as a constraint for initializing the region-based min-cut evolution, by which diverse and reliable mask proposal candidates can be generated, substantially increasing the possibility of accurately covering the objective region by these proposals. Secondly, we propose a new mask voting scheme to build a voting score map encoding the final segmentation information. In contrast to classical path voting methods, our model allows incorporating priors to assign different importance to each individual mask. As a consequence, the proposed segmentation model is capable of accurately delineating object boundaries under complex scenarios, and is insensitive to initialization. Experiments demonstrate that our method consistently outperforms state-of-the-art minimal path-based approaches in both accuracy and robustness.

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

Bernstein-Schur Kernels: Random Features by Sketched Modulation and Radial Randomization

arXiv:2606.11255v1 Announce Type: new Abstract: Bernstein–Schur kernels are products of a finite-feature kernel (one with an explicit finite-dimensional feature map) and a completely monotone shift-invariant kernel: nonstationary kernels that fall between the shift-invariant and dot-product templates random features usually exploit, so in general neither Bochner sampling nor polynomial sketching applies to the full kernel directly. We give one random-feature construction for the whole class that randomizes both factors: it sketches the finite modulation and randomizes the completely monotone radial factor, sampling the latter's one-dimensional Bernstein–Widder scale and then applying Gaussian random Fourier features (whose frequency is still $d$-dimensional). The feature dimension is then $Dm$, set by the sketch size $m$ and the radial-draw count $D$, free of the $O(d^2)$ size of the exact modulation feature. Keeping the modulation \emph{exact is the analyzable limit ($m\to\infty$): there we prove unbiasedness, an exact variance for the recommended flat estimator, an expected matrix-Bernstein operator-norm bound (with a matching high-probability tail) controlled by the top eigenvalues of the kernel and modulation Gram matrices together with an intrinsic dimension rather than the crude $N\max_{ij}$ entrywise route, and a deterministic relative-spectral kernel-ridge stability result. By conditioning on the sketch, the doubly-randomized estimator inherits the same intrinsic-dimension operator-norm guarantee plus a single additive sketch term, tunable by $m$ independently of $D$. The motivating instance is the biased $yat$-kernel $k_{yat,b}(w,x)=(w^\top x+b)^2/(\|w-x\|^2+\varepsilon)$, $b\ge0$, whose family span contains the inverse-multiquadric kernel by finite differences in $b$; for it the radial mixture is the IMQ spectral sampler, and one frequency per scale is variance-optimal at a fixed radial-feature budget.

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

OTCHA: Optimal Transport-driven Confidence-aware Latent Hub Alignment for Multi-View Medical Image Classification

Multi-view imaging, such as mammography and chest radiography, is a standard component of clinical practice. However, medical images are often unregistered and contain view-specific artifacts or irrelevant background cues that can obscure diagnostically relevant findings. Many existing methods directly fuse per-view representations, allowing such irrelevant content to contaminate the fused embedding and reducing robustness under varying view configurations. We propose OTCHA, a confidence-aware latent hub token alignment module based on optimal transport (OT) that refines patch tokens before fusion for multi-view classification. OTCHA introduces a set of learnable latent hub tokens shared across views. For each view, we compute an OT plan between patch tokens and hub tokens that jointly considers feature similarity and geometry, and augment the OT formulation with token-conditional dustbins to enable partial matching and discard irrelevant tokens. The resulting transport plan provides token-wise matching confidence, which gates hub-mediated message passing and weights a novel optimal-transport-based representation alignment loss to stabilize refinement. Experiments on three multi-view medical image datasets demonstrate consistent improvements over competing baselines across diverse anatomies and view configurations. Our code is available at https://github.com/labhai/OTCHA.

16.
medRxiv (Medicine) 2026-06-18

Urinary Creatine Riboside Complements PSA to Improve Disease Detection in the Diagnostic Gray Zone of Prostate Cancer

Circulating prostate-specific antigen (PSA) discriminates poorly in the diagnostic gray zone (3.0-9.99 ng/mL), where ~75% of biopsies yield no clinically significant prostate cancer (PCa). We evaluated whether urinary creatine riboside (CR), a tumor-derived metabolite excreted through the prostatic urethra, complements PSA for gray-zone detection and independently predicts prostate-cancer-specific mortality (PCSM). In the NCI-Maryland PCa Case-Control Study (951 cases, 962 controls; 47.6% African American men; median follow-up 11.5 years), urinary CR was quantified by UPLC-MS/MS. Within the PSA gray zone (n = 668), urinary CR was complementary to PSA, with markedly higher single-marker discrimination than PSA (AUC 0.93, 95% CI 0.88-0.98 vs 0.77, 0.66-0.89) and additive when combined ({Delta}AUC +0.17, p < 0.001; 91.4% sensitivity at 80% specificity). After adjustment for 11 clinical and sociodemographic covariates, urinary CR independently predicted PCSM complementary to PSA (Fine-Gray SHR 1.72, 1.35-2.19 for CR; 1.35, 1.08-1.68 for PSA; Harrell's C 0.85 for CR + PSA vs 0.77 for PSA alone), with strongest signal in African American men (SHR 2.43, 1.57-3.75 for CR). We conclude that urinary CR is a candidate non-invasive biomarker complementary to PSA - improving gray-zone triage and predicting PCSM; prospective validation in biopsy-referred cohorts is warranted.

17.
arXiv (quant-ph) 2026-06-16

Optimizing Wigner Negativity in Scattering Processes Using Energetic Cost Functions

arXiv:2606.15101v1 Announce Type: new Abstract: Wigner negativities (WNs) are key signatures of non-Gaussian bosonic states and essential resources for quantum technologies. We study their generation in the scattering of coherent pulses by a two-level atom coupled to a one-dimensional reservoir, a unitary and energy-preserving platform. Optimization in this multimode setting is hindered by the complexity of evaluating Wigner functions. We overcome this challenge by introducing energetic cost functions that identify output modes most likely to host large negativities. First using incoherent energy and then isolating a genuinely non-Gaussian contribution, we demonstrate a strong correlation between these quantities and WNs. This correlation extends beyond short, intense pulses to encompass pulses of finite energy, where photons are scattered while the two-level atom is driven. Focusing on the energy-efficiency of the process, we show that maximally efficient generation takes place for one input photon, on average, spectrally mode-matched with the atom.

18.
arXiv (quant-ph) 2026-06-19

Single-Step Phase-Engineered Pulse for Active Readout Cavity Reset in Superconducting Circuits

arXiv:2512.08393v2 Announce Type: replace Abstract: In a circuit QED architecture, we experimentally demonstrate a hardware-efficient and qubit-state-dependent Single-Step Phase-Engineered (SSPE) pulse scheme for actively depopulating a readout cavity. The protocol appends a reset segment with tailored amplitude and phase to a standard square readout pulse. Within the linear-response regime, the optimal reset amplitude scales proportionally with the readout amplitude, while the optimal reset phase remains invariant, significantly simplifying the experimental calibration procedure. Time-resolved measurements of the cavity photon number dynamics demonstrate that the SSPE scheme significantly outperforms the CLEAR protocol in terms of reset speed. Crucially, this approach enables arbitrarily fast, overshoot-free depletion of the cavity photon population, with the ultimate reset rate constrained by the finite analog bandwidth of the measurement chain. Furthermore, a comprehensive evaluation of the QND nature demonstrates that the SSPE scheme introduces no additional non-QND measurement errors. It exhibits non-QNDness comparable to both the free-decay and CLEAR protocols, with residual errors predominantly governed by state switching induced by qubit relaxation during the readout process. Thses results establish the SSPE scheme as a practical and scalable approach for achieving rapid and smooth cavity reset in superconducting quantum circuits.

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

The algebra of Krom logic programs

arXiv:2606.15719v1 Announce Type: cross Abstract: This paper investigates the algebraic structure of Krom logic programs, consisting only of facts and rules with at most one body atom. We show that sequential composition endows the class of Krom programs with a natural monoid structure and that this structure admits rich algebraic extensions to Krom seminearrings, Krom quemirings, Krom-Conway seminearrings, and Krom-Conway omegaseminearrings. Furthermore, we establish explicit generating sets and canonical decompositions, study the associated ${}^\omega$-operator, characterize the Kleene star in graph-theoretic terms, and relate finite Krom monoids to transformation monoids and finite-state automata. These results provide new connections between logic programming, algebraic automata theory, and algebraic graph theory.

20.
bioRxiv (Bioinfo) 2026-06-12

PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust proteome identification across complex biological samples. However, analytical depth achieved with fast chromatographic gradients remains lower than that obtained using long-gradients, reflecting a throughput-depth trade-off. Here, we present PeptiDIA, a machine learning framework that enhances peptide identification in fast-gradient DIA data by leveraging paired fast and long-gradient acquisitions from identical samples. PeptiDIA processes DIA-NN outputs generated at relaxed false discovery rate thresholds to obtain expanded candidate peptide pools and trains gradient-boosted decision tree models using long-gradient identifications as reference labels. The model integrates DIA-NN features with engineered peptide descriptors and applies isotonic regression to calibrate probabilities, enabling controlled peptide recovery relative to the long-gradient reference. Applied to human and murine datasets spanning six tissues acquired on an Orbitrap Exploris 480, PeptiDIA increased peptide identifications by 25-34% at 1% target reference-discordance rate (RDR) and increased the number of protein groups containing at least one rescued peptide by 15-17%. Overall, PeptiDIA improves the identification depth of fast-gradient DIA-NN workflows without altering acquisition strategies. The framework is available as a web application and command-line tool at https://github.com/Jordano700/PeptiDIA.

21.
arXiv (CS.AI) 2026-06-17

Blueprint First, Model Second: A Framework for Deterministic LLM Workflow

arXiv:2508.02721v2 Announce Type: replace-cross Abstract: While powerful, the inherent non-determinism of large language model (LLM) agents limits their application in structured operational environments where procedural fidelity and predictable execution are strict requirements. This limitation stems from current architectures that conflate probabilistic, high-level planning with low-level action execution within a single generative process. To address this, we introduce the \textsc{Source Code Agent} framework, a new paradigm built on the ``Blueprint First, Model Second'' philosophy that decouples workflow logic from the generative model. An expert-defined operational procedure is first codified into a source code-based Execution Blueprint, which is then executed by a deterministic engine. The LLM is strategically invoked as a specialized tool to handle bounded, complex sub-tasks within the workflow, but never to decide the workflow's path. We evaluate on the TravelPlanner benchmark for constraint-aware travel planning. The \textsc{Source Code Agent} achieves a 35.56\% final pass rate, a 97.6\% improvement over the state-of-the-art ATLAS baseline (18.00\%) on the same Claude-Sonnet-4 backbone. Critically, it reduces constraint violations by 96.0\% (11 vs 275) while improving execution efficiency by 27.1\% (10.2$\pm$0.7 steps vs 14.0). Two production incident-diagnosis deployments and additional results on ScienceWorld and ALFWorld confirm that the architecture transfers beyond travel planning to procedurally well-defined, constraint-intensive workflows. Our work enables the verifiable and reliable deployment of autonomous agents in applications governed by strict procedural logic.

22.
bioRxiv (Bioinfo) 2026-06-18

Elucidating the Design Space of Generative Models for Single-Cell Perturbation Prediction

Next-token prediction has produced predictable scaling in language, but the recipe presumes a sequence of tokens with a meaningful order. Single-cell RNA-seq counts have no natural gene ordering, so applying the recipe directly to raw expression fails under an ill-suited left-to-right bias. We instead ask whether a learned latent can supply the structure the recipe needs. We introduce texttt{ExpressionVAE} (eVAE), a discrete-latent perturbation model that compresses each cell into a short sequence of discrete codes through a finite-scalar-quantization (FSQ) bottleneck and trains a perturbation-conditioned discrete prior over those codes. On Replogle and Parse~1M, eVAE sets a new state of the art on every distributional metric and leads on most cell-eval perturbation metrics, with Fr'echet distance and $mathrm{MMD}^2$ roughly $3$ to $20times$ lower than the strongest continuous-latent baseline. Swapping the prior between autoregressive and masked discrete diffusion leaves performance near-identical, isolating the gain to the discrete latent itself rather than the prior family. A decoder-head ablation then exposes a single design axis, the richness of the predictive distribution at inference, that splits the standard metrics into two groups, variance-sensitive and mean-sensitive, which move in opposite directions along the axis. Finally, on a held-out CRISPRi reversion benchmark of $1{,}732$ perturbations under inflammatory cytokine stress, the frozen eVAE encoder outperforms UMAP and differential expression and matches scGPT on perturbation ranking at a fraction of the data.

23.
arXiv (CS.LG) 2026-06-16

CREST: Deployment-Realistic Hardware-in-the-Loop NAS for Embedded Sensing Systems

arXiv:2606.15004v1 Announce Type: cross Abstract: Deploying neural networks on low-power microcontrollers (MCUs) requires selecting model architectures under tight memory, latency, and energy constraints. Existing workflows often simplify this process along one or more axes: static proxy costs such as FLOPs or parameters, treating one MCU as representative, and continuous-inference tests instead of deployed sensing schedules. These assumptions can mis-rank Pareto-front candidates, miss infeasible deployments, and obscure schedule-dependent energy. We present CREST (Cross-platform Runtime Evaluation and Search Tool), a deployment-realistic hardware-in-the-loop (HIL) neural architecture search (NAS) framework for MCU sensing systems. CREST keeps the optimizer, HIL measurement boundary, logging, and replay workflow fixed while exposing workload, model family, target backend, schedule, quantization, and scoring policy as configurable axes. This makes deployment effects experimentally separable within one reusable workflow. We evaluate CREST on inertial odometry and audio classification across three Arm Cortex-M targets. For inertial odometry, measured-energy HIL search reduces median per-inference energy by 41.7% versus FLOPs-based selection and 40.8% versus memory-traffic-based selection at similar error. FLOPs-based selection also chooses infeasible deployments on memory-constrained targets. On the STM32 N657 target, continuous-inference and duty-cycled searches produce different Pareto frontiers. For audio classification, the same application-level policy selects different DS-CNN architectures on different boards, and cross-board replay changes deployment cost substantially. Overall, CREST shows that deployment-realistic MCU NAS must jointly optimize model architecture, target platform, runtime schedule, and deployment policy rather than relying only on static proxy costs or continuous-inference measurements.

24.
arXiv (math.PR) 2026-06-11

A Hybrid LSMC-PDE Method for Bermudan Option Pricing under the Gatheral Double Mean-Reverting Model

arXiv:2606.11237v1 Announce Type: cross Abstract: We study Bermudan option pricing under the Gatheral Double Mean-Reverting (GDMR) stochastic volatility model. The model features a variance process together with a stochastic long-run mean variance process and allows Constant Elasticity of Variance (CEV)-type exponents in the diffusion coefficients. This model is attractive since it provides a flexible specification for volatility dynamics. However, the pricing of early-exercise derivatives under the GDMR model remains largely unexplored in the literature. To address this challenge, we adapt a Hybrid Least-Squares Monte Carlo-Partial Differential Equation (LSMC-PDE) framework to the GDMR model and provide a detailed model-specific implementation. Conditioning on simulated variance paths, the pricing problem reduces to a one-dimensional problem in the asset price, which is solved by a Fourier-based approach, while the remaining dependence on the variance variables is approximated by least-squares regression. Our numerical experiments demonstrate that the Hybrid LSMC-PDE approach yields accurate pricing estimates and often lower pricing errors than plain LSMC, particularly for low and moderate numbers of simulation paths, showing the benefit of using the model structure in early-exercise option pricing.

25.
arXiv (CS.CL) 2026-06-12

When Iterative RAG Beats Ideal Evidence: A Diagnostic Study in Scientific Multi-hop Question Answering

Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains with multi-hop reasoning, sparse domain knowledge, and heterogeneous evidence. We provide the first controlled, mechanism-level diagnostic study of whether synchronized iterative retrieval and reasoning can surpass an idealized static upper bound (Gold Context) RAG. We benchmark eleven state-of-the-art LLMs under three regimes: (i) No Context, measuring reliance on parametric memory; (ii) Gold Context, where all oracle evidence is supplied at once; and (iii) Iterative RAG, a training-free controller that alternates retrieval, hypothesis refinement, and evidence-aware stopping. Using the chemistry-focused ChemKGMultiHopQA dataset, we isolate questions requiring genuine retrieval and analyze behavior with diagnostics spanning retrieval coverage gaps, anchor-carry drop, query quality, composition fidelity, and control calibration. Across models, Iterative RAG consistently outperforms Gold Context, with gains up to 25.6 percentage points, especially for non-reasoning fine-tuned models. Staged retrieval reduces late-hop failures, mitigates context overload, and enables dynamic correction of early hypothesis drift, but remaining failure modes include incomplete hop coverage, distractor latch trajectories, early stopping miscalibration, and high composition failure rates even with perfect retrieval. Overall, staged retrieval is often more influential than the mere presence of ideal evidence; we provide practical guidance for deploying and diagnosing RAG systems in specialized scientific settings and a foundation for more reliable, controllable iterative retrieval-reasoning frameworks.