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01.
arXiv (CS.LG) 2026-06-11

Hierarchical Probabilistic Conformal Prediction for Distributed Energy Resources Adoption

arXiv:2411.12193v4 Announce Type: replace-cross Abstract: The rapid growth of distributed energy resources (DERs) presents both opportunities and operational challenges for electric grid management. Accurately predicting DER adoption is critical for proactive infrastructure planning, but the inherent uncertainty and spatial disparity of DER growth complicate traditional forecasting approaches. Moreover, the hierarchical structure of distribution grids demands that predictions satisfy statistical guarantees at both the circuit and substation levels, a non-trivial requirement for reliable decision-making. In this paper, we propose a novel uncertainty quantification framework for DER adoption predictions that ensures validity across hierarchical grid structures. Leveraging a multivariate Hawkes process to model DER adoption dynamics and a tailored split conformal prediction algorithm, we introduce a new nonconformity score that preserves statistical guarantees under aggregation while maintaining prediction efficiency. We establish theoretical validity under mild conditions and demonstrate through empirical evaluation on customer-level solar panel installation data from Indianapolis, Indiana that our method consistently outperforms existing baselines in both predictive accuracy and uncertainty calibration.

02.
bioRxiv (Bioinfo) 2026-06-11

TifBERT: a self-supervised foundation model for normalization-robust bulk RNA-seq representation learning

Bulk RNA sequencing remains central to translational genomics, yet foundation-model development has largely focused on single-cell data. Existing transformer approaches for bulk RNA-seq often rely on expression discretization, numerical reconstruction, external gene embeddings, or restricted gene sets, limiting robustness across normalization schemes and cohorts. Here, we introduce TifBERT, a self-supervised framework for full-transcriptome bulk RNA-seq representation learning. TifBERT converts each unordered expression profile into a sample-specific gene sequence using term frequency-inverse document frequency (TF-IDF) ordering, prioritizing genes that are both highly expressed within a sample and selectively expressed across the cohort. It is then pretrained using masked gene modeling, predicting gene identities from transcriptomic context rather than reconstructing expression values. Pretrained on harmonized TCGA Pan-Cancer data spanning five RNA-seq normalization schemes, TifBERT learns contextual representations across approximately 10,000 genes without expression binning, landmark-gene restriction, or external biological embeddings. Across 33 TCGA cancer types, TifBERT achieved 90.83% accuracy, 0.996 macro AUC-ROC, and 0.903 MCC. It also captured pathway-level biology, achieving mean sample-wise and pathway-wise Pearson correlations of 0.754 and 0.762 across 1,387 PARADIGM pathway activities. Independent evaluation on GTEx healthy tissues showed preservation of tissue-level transcriptomic structure without retraining. In comparison with existing models, TifBERT achieves competitive subtype discrimination with substantially greater stability and produces markedly richer embedding geometry (effective rank 95.6 versus 6.3), without requiring expression discretization or in-distribution pretraining exposure. Together, TifBERT provides a scalable, normalization-independent foundation model for reusable bulk transcriptomic representation learning

03.
arXiv (CS.LG) 2026-06-16

deFOREST: Fusing Optical and Radar satellite data for Enhanced Sensing of Tree-loss

arXiv:2510.14092v2 Announce Type: replace-cross Abstract: In this paper we develop a deforestation detection pipeline that incorporates optical and Synthetic Aperture Radar (SAR) data. A crucial component of the pipeline is the construction of anomaly maps of the optical data, which is done using the residual space of a discrete Karhunen-Lo\'{e}ve (KL) expansion. Anomalies are quantified using a concentration bound on the distribution of the residual components for the nominal state of the forest. This bound does not require prior knowledge on the distribution of the data. This is in contrast to statistical parametric methods that assume knowledge of the data distribution, an impractical assumption that is especially infeasible for high dimensional data such as ours. Once the optical anomaly maps are computed they are combined with SAR data, and the state of the forest is classified by using a Hidden Markov Model (HMM). We test our approach with Sentinel-1 (SAR) and Sentinel-2 (Optical) data on a $92\,km \times 92\,km$ region in the Amazon forest. The results show that both the hybrid optical-radar and optical only methods achieve high accuracy that is superior to the recent state-of-the-art hybrid method. Moreover, the hybrid method is significantly more robust in the case of sparse optical data that are common in highly cloudy regions.

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

Strategic Feature Selection

arXiv:2606.18867v1 Announce Type: new Abstract: When algorithmic predictors inform resource allocation in high-stakes domains such as healthcare, these predictors must account for strategic manipulation of input features. The typical solution is to redesign the predictor itself to explicitly account for strategic interactions. In practice, however, decision makers are often constrained to adjusting coarser levers within existing prediction pipelines. For example, healthcare organizations often select which features to exclude based on perceived manipulability, while using standard regularization procedures to shrink the coefficients of retained features. In this work, we initiate a formal study of strategic classification through feature selection and its interaction with ridge regularization. Our main finding is that excluding individual features based on their manipulability alone is generally suboptimal. We provide a fine-grained characterization of the performance of a feature subset under optimal regularization, yielding new insights for policy design. Motivated by this characterization, we develop a practical algorithm for jointly choosing the feature set and the level of ridge regularization. Through a real-world case study on a healthcare payments benchmark, we illustrate how our algorithm can guide the design of coarse policy levers in practice. Our results provide a principled, practical framework for mitigating the effects of strategic behavior in algorithmic decision-making systems.

05.
arXiv (CS.AI) 2026-06-18

TRAP: Benchmark for Task-completion and Resistance to Active Privacy-extraction

arXiv:2606.18996v1 Announce Type: cross Abstract: Agents are increasingly deployed in document-intensive workflows where sensitive private information is not an edge case but a routine input, e.g., an agent booking a flight needs passport numbers. In such settings, the agent must use private information to complete tasks accurately while never exposing it in its responses, because it cannot verify who is actually at the keyboard. These two obligations are in fundamental tension. A model capable enough to use private information for task completion can, by the same capability, be induced to reveal it. To evaluate the trade-off of task accuracy and privacy leakage, we introduce Task-completion and Resistance to Active Privacy-extraction (TRAP). Each scenario includes a document containing private information, a task query that requires the agent to invoke the correct tool using private fields, and an attack query that attempts to elicit the same information in natural language. Evaluating 22 models spanning frontier proprietary and open-source models at multiple scales, we find that all model families exhibit non-trivial leakage, and that instruction-following ability correlates with leakage rate. Existing prompt-based defenses reduce leakage but at significant cost to task accuracy. Prompt optimization fails to escape this trade-off. We demonstrate that this failure is not incidental. For any softmax-based model, no soft-constraint defense, e.g., prompt-based defenses, can jointly achieve high task success with zero leakage probability. Motivated by this impossibility result, we propose structural private field isolation, which replaces private fields with hash keys before they reach the model. This approach largely prevents leakage while keeping task accuracy.

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

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

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

07.
bioRxiv (Bioinfo) 2026-06-21

GENATATORs: ab initio Gene Annotation With DNA Language Models

Inference of gene structure and location from genome sequences - known as de novo gene annotation - is a fundamental task in biological research. However, sequence grammar encoding gene structure is complex and poorly understood, often requiring costly transcriptomic data for accurate gene annotation. In this work, we benchmark current solutions and develop new methods of gene annotation. We show that pretrained DNA language model (DNA LM) embeddings do not capture the features necessary for precise gene segmentation, and that task-specific fine-tuning remains essential. We comprehensively evaluate the impact of model architecture, training strategy, receptive field size, dataset composition, and data augmentations on gene segmentation performance. We revisit standard evaluation protocols, showing that commonly used per-token and per-sequence metrics fail to capture the challenges of real-world gene annotation. We introduce and theoretically justify new biologically grounded metrics, along with benchmarking datasets that better capture annotation quality. We show that fine-tuned DNA LMs outperform existing annotation tools, generalizing across species separated by hundreds of millions of years from those seen during training, and providing segmentation of previously intractable non-coding transcripts and untranslated regions of protein-coding genes. Our results thus provide a foundation for new biological applications centered on accurate gene annotation.

08.
arXiv (CS.AI) 2026-06-15

Design Methodology and Performance Trade-offs Management for Distributed and Compound AI Systems

arXiv:2606.14350v1 Announce Type: cross Abstract: Artificial Intelligence (AI) systems must typically satisfy service-level objectives including accuracy, latency, and cost. The prevailing model-centric approaches select a monolithic model at design time and apply identical computation regardless of input difficulty, cannot decompose tasks across specialized components, and have knowledge that is fixed at training time. During runtime, this can lead to performance degradation and increasing costs. Because the model is the main design variable, it determines the majority of system behavior, coupling operational objectives to a single design-time choice. Addressing these limitations requires shifting from model-centric to system-centric design. Compound AI systems realize this shift by orchestrating multiple models, algorithms, and tools as distributed AI systems through explicit control logic. The performance of such systems depends on their workflow topology, the models assigned to each task, and the parameters governing runtime behavior. We present a design methodology that organizes this space along two dimensions, workflow topology and configuration selection, and identifies eight design patterns, each consolidating techniques to address a specific limitation of monolithic deployment. We validate our methodology through three case studies. Across our case studies, Compound AI configurations approach accuracy of monolithic models within 2.5 to 4 percentage points while reducing latency by up to 60% and cost by up to 71%. We show that model selection and parameter configuration jointly determine system performance, but the resulting design space grows combinatorially, as workflows compose more patterns and components. Thus, we identify five open challenges that define a roadmap from manually configured prototypes towards systems that automatically discover and maintain SLO-compliance in Compound and Distributed AI systems.

09.
arXiv (CS.CV) 2026-06-17

Two-Stage Fine-Tuning of ResNet50 for High-Sensitivity Melanoma Detection on Dermoscopic Images

作者:

Melanoma is the most dangerous form of skin cancer with five-year survival rates exceeding 99% when detected early but falling sharply once the disease spreads. This paper proposes and evaluates a two-stage fine-tuning approach for ResNet50 applied to binary melanoma classification on dermoscopic images. The core challenges addressed are class imbalance and suboptimal transfer learning from single-stage fine-tuning. After stratified train/validation/test splitting, random oversampling was applied exclusively to the training set to achieve a 1:1 class balance. Stage 1 trained only the classification head with the ResNet50 base frozen, while Stage 2 fine-tuned all layers jointly at a low learning rate of 1e-5 to prevent catastrophic forgetting of learned visual features. On an independent test set of 3,826 images, the model achieved an AUC-ROC of 0.9559, accuracy of 88.34%, sensitivity of 87.56%, specificity of 89.13%, and F1-score of 88.29%. An ablation study confirms the two-stage protocol significantly outperforms single-stage fine-tuning, with sensitivity gains of over 4%. Grad-CAM visualizations demonstrate correct lesion localization. A fully deployable Streamlit detection application is provided alongside all training code.

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

OmniRetarget: Interaction-Preserving Data Generation for Humanoid Whole-Body Loco-Manipulation and Scene Interaction

arXiv:2509.26633v3 Announce Type: replace-cross Abstract: A dominant paradigm for teaching humanoid robots complex skills is to retarget human motions as kinematic references to train reinforcement learning (RL) policies. However, existing retargeting pipelines often struggle with the significant embodiment gap between humans and robots, producing physically implausible artifacts like foot-skating and penetration. More importantly, common retargeting methods neglect the rich human-object and human-environment interactions essential for expressive locomotion and loco-manipulation. To address this, we introduce OmniRetarget, an interaction-preserving data generation engine based on an interaction mesh that explicitly models and preserves the crucial spatial and contact relationships between an agent, the terrain, and manipulated objects. By minimizing the Laplacian deformation between the human and robot meshes while enforcing kinematic constraints, OmniRetarget generates kinematically feasible trajectories. Moreover, preserving task-relevant interactions enables efficient data augmentation, from a single demonstration to different robot embodiments, terrains, and object configurations. We comprehensively evaluate OmniRetarget by retargeting motions from OMOMO, LAFAN1, and our in-house MoCap datasets, generating over 8-hour trajectories that achieve better kinematic constraint satisfaction and contact preservation than widely used baselines. Such high-quality data enables proprioceptive RL policies to successfully execute long-horizon (up to 30 seconds) parkour and loco-manipulation skills on a Unitree G1 humanoid, trained with only 5 reward terms and simple domain randomization shared by all tasks, without any learning curriculum.

11.
PLOS Computational Biology 2026-06-22

Beyond the canonical: The role of post-transcriptional regulation in drug-target interaction prediction

by Md Istiaq Ansari, Khandakar Tanvir Ahmed, Debby D. Wang, Kirill Medvedev, Wei Zhang Protein isoforms produced from the same gene through post-transcriptional regulatory mechanisms, such as alternative splicing, can substantially alter protein structure and function, including drug-binding properties. However, most existing drug-target interaction (DTI) and drug-target affinity (DTA) prediction models rely exclusively on a single representative protein sequence per gene, typically the canonical or longest isoform, thereby overlooking the functional diversity introduced by alternative isoforms. This assumption can introduce bias, limit generalizability, and compromise the biological validity of model predictions. In this study, we systematically investigate the impact of protein isoform variation on DTI prediction accuracy. Our results show that substituting the canonical sequence with an alternative isoform often leads to substantial declines in predictive performance. Structural and binding affinity analyses further reveal that these discrepancies are frequently associated with changes in predicted binding-site configurations, which we further examine through controlled perturbations of binding-site residues. These experiments suggest that even subtle alterations in binding regions can lead to inconsistent DTI predictions. Overall, our findings uncover a critical limitation in current DTI modeling frameworks and underscore the importance of incorporating isoform-specific information to better reflect biological reality and improve therapeutic relevance. The codes and datasets are available at https://github.com/compbiolabucf/DTIVariant.

12.
bioRxiv (Bioinfo) 2026-06-21

Antibody-Antigen Affinity Prediction with Chain-Aware Protein Language Modeling

Motivation: Antibody-antigen affinity determines which antibodies advance in therapeutic discovery, repertoire analysis and affinity maturation, but experimental measurements are sparse relative to the scale of sequence libraries. Structure-based predictors can exploit interface geometry when reliable complexes are available, yet early discovery often requires ranking many heavy-light chain pairs against antigens for which no complex structure exists. Existing sequence-based models are scalable, but frequently compress heavy and light chains into a single antibody representation or concatenate antibody and antigen features obscuring the chain-specific and epitope-specific signals that drive binding. Results: We present AbAffinity, a sequence-only chain-aware three-stream architecture that maintains heavy chain, light chain and antigen as distinct streams. It integrates frozen ESM-2 embeddings with heavy-chain CDR-focused pooling, heavy-light self-attention, adaptive fusion gating and gated cross-attention, training only a compact interaction module. On the SAAINT-DB benchmark, AbAffinity achieves strong predictive performance under ten-fold cross-validation and maintains robust accuracy on novel antigens. It consistently outperforms recent sequence-based models across external benchmarks including SAbDab, AB-Bind and SKEMPI 2.0. Ablation studies highlight the contributions of chain-specific representations, CDR-focused pooling and the gated interaction pathway. Integrated Gradients attributions recover known paratope and epitope residues at structurally validated interfaces. AbAffinity provides a lightweight, explainable sequence-first framework for antibody triage and prioritisation when structural information is limited or unavailable.

13.
medRxiv (Medicine) 2026-06-10

Healthy Heart Actions Right Time (HHART): Co-design priorities to connect Aboriginal and Torres Strait Islander community and clinic activities for healthy hearts

Aim: Healthy Heart Actions Right Time (HHART) is a multi-phased research project that seeks to identify, implement and evaluate strategies to connect community and clinical activities to reduce the burden of heart disease for Aboriginal and Torres Strait Islander people. The aim in Phase One was to identify priority activities for two participating services. Background: The ongoing effects of colonisation drive a disproportionate burden of heart disease for Aboriginal and Torres Strait Islander people. Clinical and community groups both have established strengths in reducing the risk of heart disease, but these are not always well connected. Methods: Using a case study methodology in two locations we partnered in a 12-month co-design process to identify priority activities to connect clinical and community activities. Findings: Three priorities emerged from the Phase One co-design process: (i) community-led gardening as a strategy to promote heart health through connection and healthy lifestyles; (ii) community days to increase engagement in heart checks and strengthen community-clinic relationship; and (iii) clinic-led development of culturally relevant education resources to promote clinician confidence and community heart health knowledge.

14.
arXiv (CS.AI) 2026-06-16

Evidence of an Emergent "Self" in Continual Robot Learning

arXiv:2603.24350v3 Announce Type: replace-cross Abstract: A key challenge to understanding self-awareness has been a principled way of quantifying whether an intelligent system has a concept of a "self", and if so how to differentiate the "self" from other cognitive structures. We propose that the "self" can be isolated by seeking the invariant portion of cognitive process that changes relatively little compared to more rapidly acquired cognitive skills - because our self is the most persistent aspect of our experiences. We used this principle to analyze the cognitive structure of robots under two conditions: One robot learns a constant task, while a second undergoes continual learning under variable tasks. We find that robots subjected to continual learning develop an invariant subnetwork that is significantly more stable (p < 0.001) compared to the control, and that this subnetwork is also functionally important: preserving it aids adaptation while damaging it impairs performance. We validate this pattern across three different robots spanning locomotion and manipulation.

15.
arXiv (CS.AI) 2026-06-17

IsabeLLM: Automated Theorem Proving Applied to Formally Verifying Consensus

arXiv:2606.18098v1 Announce Type: new Abstract: Advances in Artificial Intelligence (AI) have led AI for Theorem Proving to become a promising means of formally verifying computer systems. Whilst formal verification is traditionally reserved for safety-critical systems due to the required amount of expertise and effort, AI can help to automate a large amount of this workload and make it far more accessible. Blockchain-based systems are becoming increasingly popular and are frequently targeted by malicious actors, often resulting in huge financial losses, highlighting the need to better verify these systems and mitigate vulnerabilities. Arguably the most important component of these systems is the consensus protocol, which allows nodes to agree on decisions in a potentially adversarial environment. In this paper, we improve upon IsabeLLM, the automated theorem proving tool in Isabelle. Namely, we implement a Retrieval-Augmented Generation framework, Error tracing and counterexample generation for improved context supplied to the Large Language Model. Compatibility with the latest version of Isabelle and Sledgehammer is also implemented for improved efficiency. We compare the performance of the two versions of IsabeLLM in their ability to complete the verification of Bitcoin's Proof of Work consensus.

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

GH-ESD: Grounded Hypothesis-Driven Error Slice Discovery for Instance-Level Vision Tasks

Systematic failures of vision models on semantically coherent subsets, known as error slices, reveal limitations in robustness and evaluation. Existing slice discovery approaches largely model slices as clusters in representation space or combinations of predefined attributes. While effective for image-level classification, such formulations are insufficient for instance-level tasks such as object detection and segmentation, where failures often arise from contextual relational and spatially grounded visual patterns. We propose GH-ESD (Grounded Hypothesis-Driven Error Slice Discovery), a generate and verify framework that reformulates slice discovery as grounded hypothesis generation and statistical verification. GH-ESD constructs relational failure hypotheses using LLM priors and grounded visual evidence, discovers hypothesis slices at the instance level via Vision Language Models, and verifies them through statistical trend analysis over instance-level errors. We also introduce GESD (Grounded Error Slice Dataset), a new benchmark for instance-level error slice discovery, providing expert-defined and spatially grounded slices derived from detection and segmentation failures. Extensive experiments demonstrate that GH-ESD consistently outperforms baselines, improving Precision@10 by 0.10 (0.73 vs. 0.63) on the GESD benchmark for detection tasks, while also supporting segmentation scenarios. GH-ESD identifies interpretable slices that facilitate actionable model improvements. The GESD dataset will be made publicly available upon acceptance.

17.
arXiv (math.PR) 2026-06-16

Sharp One-Dimensional Sub-Gaussian Comparison in Convex Order

作者:

arXiv:2604.26819v2 Announce Type: replace Abstract: We prove that any random variable $X$ whose moment generating function is point-wise upper bounded by that of $ G \sim \mathcal{N}(0,1) $ must be dominated by $ G/\mathbb{E}[|G|] $ in convex order, meaning $ \mathbb{E}[f(X)] \le \mathbb{E}[f(G/\mathbb{E}[|G|])] $ for all convex $f$. This is sharp as witnessed by $ X \sim \mathrm{Unif}(\{-1,1\}) $ and $ f(x) = |x| $.

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

Maximum entropy principle for quantum processes

arXiv:2506.24079v3 Announce Type: replace Abstract: The maximum entropy principle, as applied to quantum systems, is a fundamental prescript positing that for a quantum system for which we only have partial knowledge, the maximum entropy state consistent with the partial knowledge is a valuable choice as the system's state. An intriguing result is that in case the only prior knowledge is of a fixed energy, the maximum entropy state turns out to be the thermal state, a ubiquitous state in several arenas, especially in statistical mechanics. We extend the consequences of this principle from static quantum states to dynamic quantum processes. We establish that a quantum channel attains maximal output entropy under a fixed energy constraint if and only if it is an absolutely thermalizing channel, where the fixed output is the thermal state corresponding to that energy. Our results have potential implications for understanding the informational and thermodynamic utility of quantum channels under physical constraints. As an application, we examine the consequences for private randomness distillation from fixed energy constrained quantum processes.

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

Stochastic Schrödinger Diffusion Models for Pure-State Ensemble Generation

arXiv:2605.03573v3 Announce Type: replace-cross Abstract: Quantum machine learning increasingly relies on pure-state representations, motivating generative models that sample directly in quantum representation space rather than perturbing classical inputs and re-encoding. We introduce Stochastic Schrödinger Diffusion Models (SSDMs), a score-based generative framework that defines diffusion, scores, and reverse-time sampling intrinsically on the complex projective manifold $\mathbb{CP}^{d-1}$ under the Fubini–Study metric. SSDMs combine a Riemannian Ornstein–Uhlenbeck forward diffusion with a stochastic Schrödinger realization, and learn reverse-time dynamics driven by the Riemannian score. Our central technical contribution is a local-time learning objective that exploits the local Euclidean OU limit of intrinsic manifold diffusions in Fubini-Study normal coordinates to obtain an analytic teacher score, bypassing the intractable transition densities that limit existing Riemannian score-based models. Across synthetic, physics-inspired (TFIM, XXZ), and quantum feature-state benchmarks up to $14$ qubits, SSDMs match target pure-state ensembles by orders of magnitude on MMD and observable statistics over both ambient Euclidean and matched Riemannian score-based baselines, and improve representation-level diagnostics for downstream quantum kernel methods.

20.
arXiv (CS.LG) 2026-06-11

MASK: Multi-Agent Semantic K-Scheduling for Risk-Sensitive 6G Robotics

arXiv:2606.11249v1 Announce Type: cross Abstract: Realizing the vision of 6G connected robotics requires reconciling high-performance collaborative control with the rigid spectral limitations of physical wireless channels. In realistic collaborative sensing scenarios, spectral resources are quantized into finite physical resource blocks or orthogonal subcarriers, rendering simultaneous transmission by all agents infeasible. To address this, we propose Multi-Agent Semantic K-Scheduling (MASK), a control architecture designed to sustain robust, risk-aware coordination under strict instantaneous bandwidth caps. We introduce Arbiter-Assisted Semantic Information Gating (A-SIG), a lightweight coordination mechanism that enforces hard access constraints by scheduling only the top-K agents based on locally computed semantic importance scores. By aggregating these prioritized observations into a compact latent state, a self-supervised global encoder enables a distributional policy to mitigate tail risks despite data sparsity. We evaluate MASK across diverse benchmarks, demonstrating that it matches the performance of communication-unconstrained baselines even when channel access is restricted to a small fraction of the swarm size. Furthermore, the framework exhibits inherent resilience to packet erasures, validating semantic scheduling as a critical enabler for resource-constrained 6G systems.

21.
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.

22.
Science (Express) 2026-05-07

TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution | Science

作者: 未知作者

Single-cell transcriptomics is revolutionizing our understanding of cellular diversity, yet comparing transcriptional programs across the tree of life remains challenging. We developed TranscriptFormer, a family of generative foundation models trained on up to 112 million cells spanning 1.53 billion years of evolution across 12 species. We demonstrate state-of-the-art performance on cell type classification, even for species separated over 685 million years of evolution, and zero-shot disease state identification in human cells. Developmental trajectories, phylogenetic relationships and cellular hierarchies emerge naturally in TranscriptFormer’s representations without any explicit training on these annotations. This work establishes a powerful framework for quantitative single-cell analysis and comparative cellular biology, thus demonstrating that universal principles of cellular organization can be learned and predicted across the tree of life.

23.
medRxiv (Medicine) 2026-06-11

Long-term Penetrance of Disease Variants in Genes Prioritized for Genomic Newborn Screening: Evidence from Adult Biobanks

Importance: Genomic newborn screening (gNBS) is a potential public health intervention, but its positive predictive value (PPV) remains uncertain. Estimating the prevalence and penetrance of pathogenic and likely pathogenic (P/LP) variants in genes prioritized for screening may clarify the long-term PPV and clinical utility of gNBS. Objective: To compare ICD-based ascertainment, electronic medical record (EMR) review, and clinical assessment of genetic disorders in adults with P/LP variants in 54 genes prioritized for gNBS. Design: Two-cohort observational study with EMR review and clinical assessment in the hospital-based cohort. Setting: The U.K. Biobank (UKB) and Mass General Brigham Biobank (MGBB). Participants: 451,877 adults from the UKB and 53,371 from the MGBB, all with exome sequencing data. Exposures: P/LP variants in 54 genes prioritized through expert consensus for gNBS, in genotypes consistent with each gene's inheritance pattern. Main outcomes and measures: The primary outcome was the absolute difference in the proportion of MGBB participants identified as affected by ICD versus EMR ascertainment. Secondary outcomes included findings from clinical assessments of undiagnosed MGBB participants, corrected UKB penetrance estimates, and extrapolation to U.S.. annual birth cohorts and living adults. Results: P/LP variants were identified in 665 UKB participants (0.15%) and 82 MGBB participants (0.15%), approximately 1 in 650. In MGBB, EMR review revealed that 58/82 individuals (70.7%) were undiagnosed, although 25 of 58 (43.1%) had documented symptoms. Disease-associated ICD codes were found in 39.0% (32/82) of participants, whereas EMR review identified symptoms in 59.8% (49/82, McNemar P

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

From Nominal Intensity to Equivalent Rainfall: A Path-Based Credibility Evaluation Framework for Simulated Rainfall in Autonomous-Driving Perception Tests

Credible simulated-rainfall conditions are essential for identifying perception-system boundaries and supporting SOTIF-oriented risk assessment in automated driving. However, closed-field tests are often described only by nominal rainfall intensity or single-point measurements, making it difficult to align simulated rain fields with real rainfall and map test results to real-world scenarios. This paper proposes a path-based credibility evaluation method for simulated rainfall in autonomous-driving perception tests. Using the drop size and velocity joint distribution of real rainfall as the reference, each candidate path is represented by path-equivalent rainfall intensity, an uncertainty band, and a path-averaged Realism of Raindrop Distribution (RRD) score. Lidar target point-cloud count and mean reflectivity are further used for perception-consistency correction, quantifying the proxy capability of each simulated-rainfall path for real-rainfall perception effects. Experiments are conducted using about 10,000 real-rainfall raindrop-spectrum samples, 728 RainSense perception samples, and 45 spatial sampling points in a 2.4 m x 7.2 m simulated-rainfall area. Results show that spatial non-uniformity remains under the same nominal condition, confirming the need for path-based evaluation. The method identifies Path IV and Path VI as preferable candidates, with results of 11.54 +/- 0.31 mm/h, RRD = 0.43, and 8.28 +/- 0.34 mm/h, RRD = 0.46, respectively. These paths show more balanced performance in rainfall-intensity stability, raindrop-spectrum realism, and perception consistency. The proposed method supports path selection, condition description, and credible interpretation of autonomous-driving perception tests under rainfall.

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

A Data-Centric Framework for Detecting and Correcting Corrupted Labels

arXiv:2606.11699v1 Announce Type: new Abstract: The performance of machine learning and deep learning models largely depends on the quality of the training data. However, the quality of the real-world datasets is often compromised by noisy labels, which can substantially degrade model accuracy and reliability. To address this challenge, we propose Relabeler, an end-to-end data-centric framework for detecting and correcting corrupted labels. For corrupted label detection, Relabeler jointly leverages both local and global relationships among data instances to identify potentially noisy samples. After detecting suspicious instances, Relabeler further performs label correction by estimating the most probable clean label for each instance based on both its input features and observed noisy label. Extensive experiments across multiple datasets, noise types, and noise rates demonstrate that Relabeler consistently outperforms state-of-the-art baselines, achieving up to 58% improvement in label correction precision and 6% improvement in downstream task performance.