We present an approach to denoising spatial transcriptomics images that is particularly effective for uncovering cell identities in the regime of ultra-low sequencing depths, and also allows for interpolation of gene expression. The method -- Spatial Transcriptomics via Adaptive Regularization and Kernels (STARK) -- augments kernel ridge regression with an incrementally adaptive graph Laplacian regularizer. In each iteration, we (1) perform kernel ridge regression with a fixed graph to update the image, and (2) update the graph based on the new image. The kernel ridge regression step involves reducing the infinite dimensional problem on a space of images to finite dimensions via a modified representer theorem. Starting with a purely spatial graph, and updating it as we improve our image makes the graph more robust to noise in low sequencing depth regimes. We show that the aforementioned approach optimizes a block-convex objective through an alternating minimization scheme wherein the sub-problems have closed form expressions that are easily computed. This perspective allows us to prove convergence of the iterates to a stationary point of this non-convex objective. Statistically, such stationary points converge to the ground truth with rate $\mathcal{O}(R^{-1/2})$ where $R$ is the number of reads. In numerical experiments on real spatial transcriptomics data, the denoising performance of STARK, evaluated in terms of label transfer accuracy, shows consistent improvement over the competing methods tested.

Binary classification is one of the oldest, most prevalent, and studied problems in machine learning. However, the metrics used to evaluate model performance have received comparatively little attention. The area under the receiver operating characteristic curve (AUROC) has long been a standard choice for model comparison. Despite its advantages, AUROC is not always ideal, particularly for problems that are invariant to local exchange of classes (LxC), a new form of metric invariance introduced in this work. To address this limitation, we propose LxCIM (LxC-invariant metric), which is not only rank-based and invariant under local exchange of classes, but also intuitive, logically consistent, and always computable, while enabling more detailed analysis through the cumulative accuracy-decision rate curve. Moreover, LxCIM exhibits clear theoretical connections to AUROC, accuracy, and the area under the accuracy-decision rate curve (AUDRC). These relationships allow for multiple complementary interpretations: as a symmetric form of AUROC, a rank-based analogue of accuracy, or a more representative and more interpretable variant of AUDRC. Finally, we demonstrate the direct applicability of LxCIM to the bivariate causal discovery problem (which exhibits invariance to local exchange of classes) and show how it addresses the acknowledged limitations of existing metrics used in this field. All code and implementation details are publicly available at github.com/tiagobrogueira/Causal-Discovery-In-Exchangeable-Data.

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

Large Language Models (LLMs) are prone to generating fluent but incorrect content, known as confabulation, which poses increasing risks in multi-turn or agentic applications where outputs may be reused as context. In this work, we investigate how in-context information influences model behavior and whether LLMs can identify their unreliable responses. We propose a reliability estimation that leverages token-level uncertainty to guide the aggregation of internal model representations. Specifically, we compute aleatoric and epistemic uncertainty from output logits to identify salient tokens and aggregate their hidden states into compact representations for response-level reliability prediction. Through controlled experiments on open QA benchmarks, we find that correct in-context information improves both answer accuracy and model confidence, while misleading context often induces confidently incorrect responses, revealing a misalignment between uncertainty and correctness. Our probing-based method captures these shifts in model behavior and improves the detection of unreliable outputs across multiple open-source LLMs. These results underscore the limitations of direct uncertainty signals and highlight the potential of uncertainty-guided probing for reliability-aware generation.

ABSTRACT We develop a Markov decision process (MDP) framework to autonomously make guidance decisions for satellite collision avoidance maneuver (CAM) and a reinforcement learning policy gradient (RL-PG) algorithm to enable direct optimization of guidance policy using historic CAM data. In addition to maintaining acceptable collision risks, this approach seeks to minimize the average propellant consumption of CAMs by making early maneuver decisions. We model CAM as a continuous state, discrete action and finite horizon MDP, where the critical decision is determining when to initiate the maneuver. By deciding to maneuver earlier than conventional methods, the Markov policy effectively favors CAMs that achieve comparable rates of collision risk reduction while consuming less propellant. Using historical data of tracked conjunction events, we verify this framework and conduct an extensive parameter-sensitivity study. When evaluated on synthetic conjunction events, the trained policy consumes significantly less propellant overall and per maneuver in comparison to a conventional cut-off policy that initiates maneuvers 24 hours before the time of closest approach (TCA). On historical conjunction events, the trained policy consumes more propellant overall but consumes less propellant per maneuver. For both historical and synthetic conjunction events, the trained policy is slightly more conservative in identifying conjunctions events that warrant CAMs in comparison to cutoff policies.

Understanding the spatial and temporal dynamics of automated vehicle (AV) crash severity is critical for advancing urban mobility safety and infrastructure planning. In this work, we introduce ST-GraphNet, a spatio-temporal graph neural network framework designed to model and predict AV crash severity by using both fine-grained and region-aggregated spatial graphs. Using a balanced dataset of 2,352 real-world AV-related crash reports from Texas (2024), including geospatial coordinates, crash timestamps, SAE automation levels, and narrative descriptions, we construct two complementary graph representations: (1) a fine-grained graph with individual crash events as nodes, where edges are defined via spatio-temporal proximity; and (2) a coarse-grained graph where crashes are aggregated into Hexagonal Hierarchical Spatial Indexing (H3)-based spatial cells, connected through hexagonal adjacency. Each node in the graph is enriched with multimodal data, including semantic, spatial, and temporal attributes, including textual embeddings from crash narratives using a pretrained Sentence-BERT model. We evaluate various graph neural network (GNN) architectures, such as Graph Convolutional Networks (GCN), Graph Attention Networks (GAT), and Dynamic Spatio-Temporal GCN (DSTGCN), to classify crash severity and predict high-risk regions. Our proposed ST-GraphNet, which utilizes a DSTGCN backbone on the coarse-grained H3 graph, achieves a test accuracy of 97.74\%, substantially outperforming the best fine-grained model (64.7\% test accuracy). These findings highlight the effectiveness of spatial aggregation, dynamic message passing, and multi-modal feature integration in capturing the complex spatio-temporal patterns underlying AV crash severity.

Panoramic imaging enables capturing 360° images with an ultra-wide Field-of-View (FoV) for dense omnidirectional perception, which is critical to applications, such as autonomous driving and augmented reality, etc. However, current panoramic semantic segmentation methods fail to identify outliers, and pinhole Out-of-distribution Segmentation (OoS) models perform unsatisfactorily in the panoramic domain due to pixel distortions and background clutter. To address these issues, we introduce a new task, Panoramic Out-of-distribution Segmentation (PanOoS), with the aim of achieving comprehensive and safe scene understanding. Furthermore, we propose the first solution, POS, which adapts to the characteristics of panoramic images through text-guided prompt distribution learning. Specifically, POS integrates a disentanglement strategy designed to materialize the cross-domain generalization capability of CLIP. The proposed Prompt-based Restoration Attention (PRA) optimizes semantic decoding by prompt guidance and self-adaptive correction, while Bilevel Prompt Distribution Learning (BPDL) refines the manifold of per-pixel mask embeddings via semantic prototype supervision. Besides, to compensate for the scarcity of PanOoS datasets, we establish two benchmarks: DenseOoS, which features diverse outliers in complex environments, and QuadOoS, captured by a quadruped robot with a panoramic annular lens system. Extensive experiments demonstrate superior performance of POS, with AuPRC improving by 34.25% and FPR95 decreasing by 21.42% on DenseOoS, outperforming state-of-the-art pinhole-OoS methods. Moreover, POS achieves leading closed-set segmentation capabilities and advances the development of panoramic understanding. Code and datasets will be available at https://github.com/MengfeiD/PanOoS.

As large AI models become increasingly valuable assets, the risk of model weight exfiltration from inference servers grows accordingly. An attacker controlling an inference server may exfiltrate model weights by hiding them within ordinary model outputs, a strategy known as steganography. This work investigates how to verify model responses to defend against such attacks and, more broadly, to detect anomalous or buggy behavior during inference. We formalize model exfiltration as a security game, propose a verification framework that can provably mitigate steganographic exfiltration, and specify the trust assumptions associated with our scheme. To enable verification, we characterize valid sources of non-determinism in large language model inference and introduce two practical estimators for them. We evaluate our detection framework on several open-weight models ranging from 3B to 30B parameters. On MOE-Qwen-30B, our detector reduces exfiltratable information to <0.5% with false-positive rate of 0.01%, corresponding to a >200x slowdown for adversaries. Overall, this work further establishes a foundation for defending against model weight exfiltration and demonstrates that strong protection can be achieved with minimal additional cost to inference providers.

The Weibull distribution is a commonly adopted choice for modeling the survival of systems subject to maintenance over time. When only proxy indicators and censored observations are available, it becomes necessary to express the distribution's parameters as functions of time-dependent covariates. Deep neural networks provide the flexibility needed to learn complex relationships between these covariates and operational lifetime, thereby extending the capabilities of traditional regression-based models. Motivated by the analysis of a fleet of military vehicles operating in highly variable and demanding environments, as well as by the limitations observed in existing methodologies, this paper introduces WTNN, a new neural network-based modeling framework specifically designed for Weibull survival studies. The proposed architecture is specifically designed to incorporate qualitative prior knowledge regarding the most influential covariates, in a manner consistent with the shape and structure of the Weibull distribution. Through numerical experiments, we show that this approach can be reliably trained on proxy and right-censored data, and is capable of producing robust and interpretable survival predictions that can improve existing approaches.

The interpretation of Chest X-ray is an important diagnostic issue in clinical practice and especially in the resource-limited setting where the shortage of radiologists plays a role in delayed diagnosis and poor patient outcomes. Although the original CheXNet architecture has shown potential in automated analysis of chest radiographs, DenseNet-121 backbone is computationally inefficient and poorly single-label classifier. To eliminate such shortcomings, we suggest a better classification framework of chest disease that relies on EfficientNetV2-M and incorporates superior training approaches such as Automatic Mixed Precision training, AdamW, Cosine Annealing learning rate scheduling, and Exponential Moving Average regularization. We prepared a dataset of 18,080 chest X-ray images of three source materials of high authority and representing five key clinically significant disease categories which included Cardiomegaly, COVID-19, Normal, Pneumonia, and Tuberculosis. To achieve statistical reliability and reproducibility, nine independent experimental runs were run. The suggested architecture showed significant gains with mean test accuracy of 96.45 percent compared to 95.30 percent at baseline (p less than 0.001) and macro-averaged F1-score increased to 91.08 percent (p less than 0.001). Critical infectious diseases showed near-perfect classification performance with COVID-19 detection having 99.95 percent accuracy and Tuberculosis detection having 99.97 percent accuracy. Although 6.8 times more parameters are included, the training time was reduced by 11.4 percent and performance stability was increased by 22.7 percent. This framework presents itself as a decision-support tool that can be used to respond to a pandemic, screen tuberculosis, and assess thoracic disease regularly in various healthcare facilities.