Papers

Bulk gene expression profiling, which aggregates pooled RNA across cells within a biological sample, remains important in the single-cell era because it is typically less noisy, more sensitive, and more cost-effective than single-cell assays. Accordingly, a growing body of computational methods seeks to recover causal relations among genes from bulk expression data. However, aggregation is a lossy, non-invertible coarsening of the underlying cellular system, and it remains unclear whether and under what conditions causal relations are recoverable from aggregated bulk gene expression data. To answer this, we formalize recoverability under aggregation through two notions of consistency: functional-form consistency and conditional-independence consistency. We then derive necessary and sufficient conditions for recoverability, showing that these properties are preserved only under linear aggregations (e.g., sum/mean) coupled with affine structural equations. To assess the practical plausibility of these conditions, analyses of four bulk and four single-cell gene expression datasets further reveal that the estimated pairwise regulatory functions among genes deviate from linearity in both data types, providing limited empirical support for the linearity assumptions required for recoverability. Together, these results caution against recovering causal relations from aggregated bulk expression data without strong additional assumptions.

As language models take on agentic roles that call APIs, read tool outputs, and act on third-party content, their attack surface expands beyond what users type. Whether they treat a malicious instruction the same way regardless of where it arrives has not been studied systematically. We introduce the Safety Asymmetry Score (SAS), measuring how a model's susceptibility to adversarial content shifts depending on whether it arrives in the user message, tool metadata, or tool output, using matched payload pairs that hold the malicious text identical and vary only the channel. Across 10 production LLMs and three attack families, general-purpose models sharply discount instructions arriving as tool metadata relative to identical instructions in the user message, while agent-native models discount them far less. This differential survives an affordance-matched control equalizing tool availability and scoring, and a size-controlled mixed-effects analysis. Within the tool surface the pattern reverses: the same content is far more instruction-like in a tool's description than in its output, with affordances identical. Models treat tool metadata as instructions and tool results as data. In Llama 3.3-70B and GPT-OSS-120B this signal is causally present at mid-to-late depths but non-linearly encoded, so linear probes miss what activation patching recovers.

Selection bias is a common and often unavoidable aspect of real-world data that challenges the generalizability of machine learning models. When models trained on biased data are deployed in the broader target population, poor model generalization may lead to real harm, particularly in high-risk settings such as healthcare. This risk highlights the need for practitioners to reliably assess model generalizability prior to deployment. However, existing methods for predicting model performance rely on unrealistic access to the target distribution or knowledge of the selection mechanism causing bias. To address these limitations, we propose a novel upper bound on the worst-case model performance on the target population under the realistic setting where the selection mechanism and the target population data are only partially observed. We demonstrate the validity and practical utility of our method through experiments on fully synthetic data, semi-synthetic data derived from the All of Us Research Program, and real-world selection bias in MIMIC-IV. Our work offers a principled and practical tool to estimate the impact of selection bias in an otherwise intractable setting, thereby enabling practitioners to build safer and more generalizable models in healthcare and beyond.

The emerging paradigm of "thinking with images" embeds visual states into intermediate reasoning steps, defining a new frontier for Vision-Language Models. Existing approaches diverge along two lines. Tool-assisted methods apply explicit visual operations but suffer from high latency and restricted manipulation types. Latent reasoning methods autoregressively produce implicit visual states, but underperform tool-assisted methods, and their latent tokens fail to capture effective visual information. In this work, we propose DeepLatent, a parallel framework for latent visual reasoning. First, we introduce LatentFormer. It uses learnable 2D tokens to generate context-conditioned latent states in parallel, anchoring every visual update directly in the original image features. Second, we design a continuous-space reinforcement learning algorithm. It optimizes latent modulation parameters directly in the embedding space, significantly improving latent representation quality. The framework is trained via knowledge distillation followed by this continuous-space RL algorithm. Furthermore, we contribute DeepLatent-180K, a large-scale dataset tailored for latent visual reasoning. Extensive evaluations across multiple benchmarks demonstrate that DeepLatent achieves state-of-the-art performance.

Deep reinforcement learning (RL) offers a promising route to real-time power grid operation, yet large neural policies are costly to evaluate, hard to deploy on constrained hardware, and opaque to operators. We ask whether a Proximal Policy Optimization (PPO) agent for grid topology control can be compressed into compact tree-based surrogates without losing operational performance. A PPO teacher is trained on Grid2Op's standard 14-bus environment with a stability-oriented reward, using stress-focused data collection on critical, high-loading states. The policy is then distilled into a decision tree and a random forest. Across held-out validation episodes, both surrogates exceed the teacher in mean reward and survival length at a fraction of the inference cost. The decision tree shows high exact-action agreement with the PPO argmax and near-complete agreement within its top-ranked actions, while remaining small enough to be inspected directly. Feature-importance analysis reveals a representational shift: the PPO policy relies mainly on line-loading signals, while the distilled tree is driven primarily by bus-topology variables. These results suggest that stress-focused distillation can convert a black-box neural controller into a lightweight, auditable rule-like surrogate suited for real-time deployment, while also surfacing risks tied to deterministic actions and topology-specific generalization.

Neural algorithmic reasoning has emerged as a popular research direction. It aims to train neural networks to mimic the step-by-step behavior of classical rule-based algorithms. More specifically, the execution of such algorithms can be abstracted as a sequence of states, where each state represents the intermediate outcome after an execution step. The training objective is to generate state sequences that replicate the underlying algorithmic process. A common framework for this task adopts an encoder-processor-decoder architecture, where the encoder learns representations of states, the processor simulates algorithmic steps, and the decoder reconstructs output states. While prior work has focused on improving the processor, the role of the encoder in representation learning has received little attention. Most methods rely on simple MLP encoders, raising the question of whether such representations are sufficiently informative for supporting algorithmic reasoning. This paper investigates how to improve encoder representations for neural algorithmic reasoning. We propose a reconstruction module that aims to recover the input state from its encoded representation. This auxiliary reconstruction task encourages the encoder to retain critical information about the input. We demonstrate that incorporating this task during training improves the performance of existing neural architectures on standard benchmarks. Furthermore, we observe that current encoders often underutilize the correlations among features within a state. To address this, we draw inspiration from self-supervised learning and design an enhanced variant of the auxiliary task that encourages the encoder to capture intra-state feature dependencies. Experimental results show that our method enables the encoder to learn richer representations, thereby enhancing the performance of existing processors on algorithmic reasoning tasks.

Transfer learning aims to facilitate the learning of a target domain by transferring knowledge from a source domain. The source domain typically contains semantically meaningful samples (*e.g.*, images) to facilitate effective knowledge transfer. However, a recent study observes that the noise domain constructed from simple distributions (*e.g.*, Gaussian distributions) can serve as a surrogate source domain in the semi-supervised setting, where only a small proportion of target samples are labeled while most remain unlabeled. Based on this surprising observation, we formulate a novel problem termed *Semi-Supervised Noise Adaptation* (SSNA), which aims to leverage a synthetic noise domain to improve the generalization of the target domain. To address this problem, we first establish a generalization bound characterizing the effect of the noise domain on generalization, based on which we propose a Noise Adaptation Framework (NAF). Extensive experiments demonstrate that NAF effectively leverages the noise domain to tighten the generalization bound of the target domain, leading to improved performance. The codes are available at https://github.com/AIResearch-Group/SSNA.

To understand how a neural network (NN) functions and makes predictions, it has become increasingly clear that analyzing only the input domain is insufficient – one must also examine its internal inference mechanisms to capture the complete picture. To explain the internal inference mechanisms of such models, it is essential to analyze the importance of latent representations for a given task. In this paper, we propose the normalized relevance measure (NRM) framework – a novel general explanation procedure that attributes relevance to arbitrary sets of neurons across layers of arbitrary architectures. In the NRM framework, relevance of selected neurons is explicitly defined as a normalized signed measure, constructed using simple operations – marginalization and conditioning based on additive and multiplicative laws – in analogy to the probability measures. The normalization property further guarantees comparability across layers. The NRM framework subsumes existing propagation-based explanation algorithms by explicitly identifying the underlying quantity being computed. We demonstrate the utility of the framework in computer vision applications, where joint relevance analysis across multiple layers reveals key information flows in VGG16 networks. Overall, the NRM framework provides a general, mathematically grounded approach to understanding how modern NNs propagate information, offering a versatile and broadly applicable foundation for explainable artificial intelligence.

Concentrated Animal Feeding Operations (CAFOs) play an important role in agricultural production but are also associated with environmental, public health, and disease surveillance concerns. Large-scale mapping of CAFOs from remote sensing imagery remains challenging due to heterogeneous infrastructure layouts, noisy location records, inconsistent annotations, and incomplete inventories. We introduce CAFOSat, a strongly annotated, infrastructure-aware dataset for CAFO mapping across the United States. CAFOSat integrates high-resolution National Agriculture Imagery Program (NAIP) imagery with multi-source CAFO inventories collected across multiple states and transforms weak geolocation records into refined annotations through a human-in-the-loop pipeline combining AI-assisted annotation, GradCAM-based localization, and geometric clustering. To improve dataset quality, we curate challenging negative samples using land-cover-guided sampling with spatial exclusion constraints and provide infrastructure-level annotations, including barns, manure ponds, and grazing-related features, through manual verification. The resulting dataset contains more than 45,000 image patches spanning 20 states and four major CAFO categories. We benchmark a diverse set of convolutional, transformer-based, and vision-language models, demonstrating the value of refined annotations and curated negative samples for CAFO classification and generalization. In addition, we introduce a synthetic augmentation pipeline that generates infrastructure-aware variations to increase training diversity and improve robustness under distribution shifts. CAFOSat provides a large-scale benchmark for advancing infrastructure-aware agricultural monitoring and CAFO mapping from high-resolution remote sensing imagery.

Post-trained language models can recognize their own outputs from a sentence or two out of context. In a companion paper \citep{jack2026twomodes} we showed they can also recognize when they are currently acting on-policy, through the sharp entropy drop of assistant-mode generation. Both signals are tied to the Assistant persona that post-training mainly shapes. This paper widens the frame to cross-persona authorship judgement on Llama-3.1-70B-Instruct. We measure a matrix of authorship claim rates over a panel of evaluator and generator personas spanning librarian to dragon to Shakespeare, and make two claims. First, on the Assistant's own row of the matrix, the Assistant's claim rate, the persona-vector distance from the Assistant in activation space, and the entropy gap between the Assistant's surprise on a persona's text and the persona's surprise on its own text are all tightly coupled. This extends the entropy signature of acting from the companion paper to a retrospective signature of having acted. Second, this coupling fails off the Assistant's row: the natural symmetric extension of the entropy gap does not predict authorship for distinctive evaluators (pirate, dragon, Shakespeare); what does is asymmetric – the evaluator's surprise compared to the Assistant's surprise on the same text, not to the generator's. We rule out the alternative that any persona could play this reference role by trying many candidate substitutes; none does. We interpret the asymmetry as the model performing an implicit Bayesian likelihood-ratio test against the Assistant as the canonical alternative hypothesis, with the persona-vector geometry of \citet{chen2025persona} (every persona a delta off the Assistant) ensuring that the Assistant is the only persona universally accessible to that test.

Modern language-model fine-tuning typically pairs each prompt with a single response, even though many prompts admit multiple valid completions. This effectively reduces a multi-modal conditional distribution to a one-sample view, a phenomenon we call the "mode lottery," where training emphasizes a subset of plausible modes while leaving others underrepresented. We study multi-response training (MRT), which retains multiple responses per prompt, and develop a principled account of when and why it helps. Our key insight is that prompts and responses are distinct statistical resources: additional prompts reduce uncertainty about the input distribution, while additional responses reduce uncertainty about the conditional output distribution. This yields a variance-budget tradeoff that predicts when retaining multiple responses is worthwhile, shows diminishing returns as prompt-level uncertainty dominates, and explains why large redundant corpora can exhibit an implicit multi-response effect. We further analyze response selection, and show that Random-K-of-N is the unbiased default for distributional fine-tuning, reward-based selection can induce mode collapse, and a submodular quality-diversity objective provides an efficient alternative with theoretical guarantees. Controlled simulations validate the predicted variance and selection effects, including a striking failure mode where reward-only selection produces gradients misaligned with the true objective. Across structured and real-world datasets, including a new multi-prompt, multi-response benchmark, MRT consistently improves distributional generalization, with the largest gains in high response-diversity, low prompt-redundancy regimes. MRT reframes response multiplicity as a data-allocation problem with clear guidance: when responses are cheap and diverse, keeping more than one is not a heuristic, but a statistically grounded choice.

Shampoo-style optimizers approximate gradient covariance matrices using Kronecker-factored structures. Recent work~\cite{lin2026understanding} showed that such approximations can be viewed as projections under Bregman matrix divergences, leading to different Kronecker-factored preconditioners. However, it remains unclear what role the choice of divergence plays when the covariance is not exactly Kronecker-factored. We study this question through the spectrum of the covariance matrix. We show that Frobenius, von Neumann, and LogDet divergences distribute the unavoidable Kronecker approximation error differently across the covariance spectrum. We further show that their Kronecker factors are governed by divergence-weighted residuals rather than the raw approximation error, explaining how these spectral preferences are realized in the resulting preconditioners. Empirically, we observe that the top covariance eigenspace is substantially better aligned with the Hessian matrix, while the tail spectrum is much noisier and unreliable. Motivated by these findings, we propose a subspace-aware Kronecker optimizer that applies eigenvalue-based preconditioning in the top subspace and uses an adaptive isotropic acceleration constant in the bottom subspace.

Training stability is a key bottleneck in low-precision language model training: efficient low-cost paths can still produce short-lived numerical risks at a small set of operators. We formulate this as runtime stability control and present Gradient Norm-to-Mean Ratio (GNMR), a lightweight controller that compares each recoverable unit's current gradient norm with its historical mean. Together with $\Delta$-GNMR for abrupt short-window increases, GNMR maps local risk signals to bounded recovery actions under a hard $\mathrm{maxO}$ budget and a short lock interval, without changing the numerical format, kernel, or backend recipe. Across activation-quantization stress, DeepSeek-style recipe-level training, and LLaMA-2 13B fine-tuning, GNMR preserves high-fidelity quality with sparse, budgeted recovery. These results support GNMR as a backend-agnostic controller to improve low-precision training stability while preserving low-cost execution.

Speculative decoding (SD) has proven to be an effective technique for accelerating autoregressive generation in large language models (LLMs) however, its application to vision-language models (VLMs) remains relatively unexplored. We propose~DREAM-S, a novel SD framework designed specifically for fast and efficient decoding in VLMs. DREAM-S leverages a neural architecture search (NAS) framework with target-aware supernet training to automatically identify both the optimal interaction strategy between the draft and target models, and the most suitable draft model architecture for the underlying hardware implementation platform. DREAM-S additionally incorporates adaptive intermediate feature distillation, guided by attention entropy, to enable efficient draft training. Experiments on a range of well-established VLMs show that DREAM-S achieves up to a $3.85\times$ speedup compared to standard decoding approaches and significantly outperforms existing SD baselines. The code is publicly available at: https://github.com/SAI-Lab-NYU/DREAM-S .

Many stochastic gradient methods are believed not to converge when the noise in stochastic gradients has only a finite $p$-th moment for $p\in\left(1,2\right)$, a setting known as the heavy-tailed noise assumption. However, some recent studies have found that Stochastic Gradient Descent ($\textsf{SGD}$), without any modification to its update rule, can surprisingly converge in expectation for convex problems with bounded domains, highlighting the potential of classical stochastic gradient methods. Inspired by this recent progress, we provide a comprehensive study of stochastic optimization under heavy-tailed noise and establish new in-expectation convergence results for Stochastic Mirror Descent ($\textsf{SMD}$) and Accelerated Stochastic Mirror Descent ($\textsf{ASMD}$) in convex optimization, and for $\textsf{SGD}$ and Stochastic Gradient Descent with Momentum ($\textsf{SGDM}$) in nonconvex optimization. Notably, our results not only hold without algorithmic changes but also avoid restrictive assumptions, such as bounded domains, imposed in prior work. More importantly, our analysis provides a new, elegant, and powerful framework for studying heavy-tailed stochastic optimization, opening a new route to understanding first-order stochastic gradient methods.

Generative modeling and self-supervised representation learning (SSL) optimize structurally different objectives: generative training rewards distributional fidelity, while SSL rewards semantic coherence. Yet recent work repeatedly finds that SSL features improve generative training, though the mechanism of this synergy remains unclear. Here, we study the benefits of SSL in generative modeling in the framework of one-step generation where the role of representation is explicit: frozen SSL features are used to match generated samples to real data. We use the Sinkhorn divergence in that feature space, providing a tractable surrogate for the Wasserstein distance, the population-level discrepancy approximated by Fréchet-style evaluation metrics (such as FID). We find that this objective becomes highly effective when computed in a semantically structured SSL feature space (a 39$\times$ reduction in ImageNet FID). We trace this behavior primarily to matching estimation: semantic SSL features that suppress nuisance reconstruction details induce a more compact geometry, making distribution matching more tractable. As a consequence, the best training SSL features need not match the features used by the evaluation metric. In particular, we show that using Inception as the feature extractor can improve FID while degrading matching stability and sample quality, revealing a form of metric hacking. Using extensive experiments on ImageNet, we identify which SSL feature families lead to best generation performance and show that matching stability is a quantitative criterion for selecting them. Code is available at https://github.com/Genentech/semantic-transport-generation.

In many modern machine learning pipelines, abundant pretrained representations serve as noisy proxy covariates, while task-specific labels remain scarce. We study semi-supervised regression in this setting, and propose a simple two stage estimator that learns kernel eigenfeatures from all proxy covariates and fits a ridge predictor on labeled data. We derive finite sample bounds showing that fast labeled sample rates are recovered when proxy perturbation is controlled and unlabeled proxy covariates are sufficiently abundant. We also show that distribution regression is a direct special case, with analogous guarantees when the finite bag size is large enough. Experiments show consistent gains over supervised and semi-supervised baselines, especially in low label regimes.

Model merging aims to consolidate multiple task-specific models fine-tuned on different datasets into a unified architecture that performs cross-domain proficiency. Current data-free model merging methods often struggle to scale as they rely on simple parameter-level heuristics that ignore inter-layer dependencies and non-uniform distribution of expertise. This work proposes SA-Merging, which is built upon connectivity-based saliency formulations from structural pruning (e.g., SynFlow) and extends them to the data-free model merging setting. We define a saliency score over task vectors relative to a shared base model, and further introduce merge-aware modulation that incorporates agreement across experts to mitigate task interference. Based on this formulation, an iterative saliency-aware merging procedure progressively removes non-informative updates while preserving end-to-end connectivity. Furthermore, we extend SA-Merging to introduce rank-wise saliency decomposition for LoRAs without compromising their structural integrity. Extensive experiments on vision and language tasks demonstrate the effectiveness of our saliency-based approach, further reducing the gap between data-free and test-time adaptation methods.

Energy consumption prediction is essential for efficient grid management, demand-side optimization, and sustainable energy planning. Although advanced machine learning methods have been employed for better prediction performance, existing works have two key limitations: (1) they usually formulate this task as a purely time-series prediction problem without explicitly modeling the spatial dependencies among different regions, and (2) they fail to provide reliable predictions with uncertainty estimates under abnormal situations such as extreme weather events. To advance existing research, we propose EnergyMamba, an uncertainty-aware spatiotemporal learning framework for accurate and reliable energy consumption prediction, which comprises two key components: (i) a novel Graph-Enhanced Selective State Space Model (GE-Mamba) that injects spatial context learned from the grid topology into the temporal dynamics, enabling coupled spatiotemporal modeling, and (ii) an Adaptive Sequential Conformalized Quantile Regression (AS-CQR) module, which includes locally adaptive normalization and an online feedback mechanism to dynamically calibrate prediction intervals under potential distribution shifts. We evaluate EnergyMamba on four large-scale real-world datasets from Florida, New York, and California. Results show EnergyMamba achieves around 5% improvement in prediction accuracy and 6% improvement in uncertainty quantification over 15 state-of-the-art baselines.

Modifying an attribute in tabular data often introduces an unnatural instance by breaking its relationships with other attributes. The modified instance must be both natural and minimally changed from the original instance. This paper addresses the challenge of generating such a modified instance. We identify key limitations in existing approaches: generative models either don't support instance-level attribute editing or, in the case of methods like CVAE, retain attribute information in the latent space, leading to unnecessary modifications. To solve this, we propose TabChange, an approach that analyzes the relationship between the attribute of interest and other attributes in the dataset. If the relationship is weak, it simply flips the attribute; if it is strong, it uses an adversarial framework that removes information about the attribute in the latent space representation. This removal enables precise modifications, making only the necessary adjustments to maintain naturalness. Our experiments across seven datasets show that TabChange generates counterfactuals in attributes that are comparable in naturalness and are more proximal to their original instances. This leads to a higher number of valid counterfactuals and a lower number of invalid counterfactuals compared to the baselines.

We present a simple and efficient algorithm for robust approximate message passing (AMP) in the spiked matrix setting. In particular, let $\varepsilon$ be a sufficiently small constant, and suppose that $X \in \mathbb R^{n \times n}$ is a Gaussian matrix with a planted rank-$1$ spike, and $E \in \mathbb R^{n \times n}$ is an adversarially chosen matrix supported on an $\varepsilon n \times \varepsilon n$ principal minor. Let $v_{\mathrm{AMP}}(X)$ be the output of an AMP iteration on the uncorrupted matrix $X$. We give a procedure that, given access only to the corrupted matrix $Y = X + E$, computes a vector $v_{\mathrm{ALG}}(Y)$ which is $\tilde{O}(\sqrt{\varepsilon})$-close to $v_{\mathrm{AMP}}(X)$, for any of a class of AMP iterations which includes sparse Principal Component Analysis (PCA), non-negative PCA, and $\mathbb Z_2$ synchronization. Our algorithm consists of a spectral pre-processing step combined with a robust spectral initialization procedure; given these inputs, we prove that (perhaps surprisingly) AMP is robust out-of-the-box.

Oscillatory neural signals such as electroencephalography (EEG) and local field potentials (LFPs) show phase relationships that coordinate communication across brain regions. Modern recordings capture hundreds of channels across many frequency bins, yet standard phase analyses are restricted to only a few variables. The Torus Graph (TG) model, an exponential-family distribution over phases whose univariate and pairwise potentials generalize von Mises distributions, infers principled structure among oscillations but models only static, undirected dependencies and is limited to $\sim \! 100$ variables because its score matching inference scales as $\mathcal{O}(d^{6})$. We introduce a stochastic score matching procedure that reduces the per-iteration cost to $\mathcal{O}(d^{2})$, enabling inference on datasets with thousands of variables. This scalable foundation supports analyses of 1,860 frequency-phase features from multi-electrode LFPs and enables two extensions previously inaccessible to TGs or classical circular statistics: (i) a TG Hidden Markov Model capturing state-dependent phase-coupling changes (e.g., spindle-related states during sleep) and (ii) an autoregressive TG inferring directional interactions via transfer-entropy estimation. Applied to LFP recordings, these models reveal state-dependent phase-interaction patterns between wakefulness and NREM sleep. Together, they enable systematic, large-scale mapping of dynamic and directional phase relationships across brain and cognitive states.

Post-Training Quantization (PTQ) and Low-Rank Adaptation (LoRA) constitute the standard pipeline for efficient Large Language Model (LLM) deployment. However, applying them sequentially poses a problem: PTQ often leaves behind random noise that is spread out (across the model's weights) in a way LoRA can't easily fix, meaning that LoRA ends up wasting its limited capacity trying to fix uncorrectable noise instead of improving task performance. In this paper, we propose ProjQ, a novel framework for constraining quantization noise to the low-rank manifold via orthogonal subspace projection. We derive an efficient alternating algorithm that shapes the quantization noise into a low-rank structure, effectively offloading dominant error components to the subsequent adapter while minimizing the residual error in the orthogonal "uncorrectable" subspace. Our theoretical analysis demonstrates that ProjQ preserves strictly greater model plasticity for downstream tasks compared to standard PTQ. Extensive experiments on LLaMA-2, Qwen2.5 and Qwen3 confirm that ProjQ consistently outperforms existing methods in both quantization error compensation and downstream task fine-tuning, achieving up to $2\times$ lower evaluation loss for compensation and matching the performance of standard 4-bit baselines on language modeling tasks with only 3 bits. The code is available on https://github.com/yy9301/ProjQ .

Genotype-based cis-expression prediction depends on accurately modeling local regulatory architecture. We present block-sparse Bayesian sparse linear mixed model (bsBSLMM), an extension of Bayesian sparse linear mixed model (BSLMM) that incorporates linkage disequilibrium (LD)-block spike-and-slab sparsity and a transcription start site (TSS)-informed SNP inclusion prior. Across 23,098 genes from GEUVADIS European-ancestry lymphoblastoid cell lines, bsBSLMM retained more predictable genes than BSLMM, LASSO, BLUP, TIGAR elastic net, and TIGAR Dirichlet-process regression under matched evaluation criteria. Compared with BSLMM, bsBSLMM improved held-out prediction performance for most shared genes, with gains driven primarily by LD-block sparsity and further enhanced by the TSS-informed prior. Variants selected by bsBSLMM showed stronger enrichment in GM12878 DNase and H3K27ac regulatory regions than variants selected by BSLMM. In transcriptome-wide association study (TWAS) analysis, bsBSLMM recovered established inflammatory bowel disease signals, including IL23R, and identified additional genome-wide significant genes not detected by BSLMM. Independent validation in the Louisiana Osteoporosis Study reproduced the increased prediction yield across ancestries and recovered biologically relevant bone mineral density pathways in downstream TWAS and gene set enrichment analyses. These results demonstrate that incorporating LD-block structure and biologically informed SNP priors improves cis-expression prediction and enhances downstream TWAS discovery.

Conventional tissue image analysis software provides foundational capabilities for cellular analysis, including segmentation, basic morphological feature extraction, and spatial organization analysis. However, these tools often require manual intervention and are not well integrated with code-driven automation, limiting efficiency and scalability for complex spatial tissue studies. In addition, they offer limited flexibility for custom analyses, as they typically support only a fixed set of pre-implemented spatial cellular features. To address these limitations, we propose CodeCytos, a coding-based reasoning agent framework that enables dynamic, programmable interaction with spatial molecular imaging data to improve automation and customization. CodeCytos is designed to streamline the exploration of custom spatial cellular features and adapt to diverse research needs. We demonstrate its utility through case studies on four expert-curated datasets from distinct tissue types: frontal cortex, non-small-cell lung cancer, pancreas, and tonsil. We evaluate CodeCytos under a realistic minimal prompt setting, where bioscientists pose simple questions without task-specific instructions or contextual information about spatial cellular analysis, and benchmark multiple LLM backbones with strong coding capabilities. We further show that incorporating tailored, domain-agnostic few-shot in-context coding-reasoning examples (randomly sampled demonstrations outside the spatial analysis domain) can substantially improve performance without requiring costly, expert-crafted in-domain demonstrations. Overall, CodeCytos outperforms baseline approaches, highlighting the potential of code-action agents to assist with custom feature exploration in spatial molecular imaging and to accelerate biomarker discovery.

Large Language Models (LLMs) are increasingly used for zero-shot annotation and LLM-as-a-judge tasks, yet their reliability hinges on how model-internalized priors interact with user-provided instructions. We investigate three dimensions of this interaction: (1) how an LLM's familiarity with data and task definitions relates to performance, (2) whether additional information in prompts can correct zero-shot errors ("decision stickiness"), and (3) model susceptibility to misaligned task definitions. We introduce Definition-Specific Familiarity (DSF), which measures alignment between a model's elicited concept and the target definition. Across nine LLMs and six toxicity datasets (five primary datasets plus an additional robustness dataset), DSF predicts annotation performance after controlling for dataset identity (partial $r=+0.41$). This association remains positive across all prompting conditions tested. In contrast, three common text-memorization metrics show no positive association. We show that prompting has limited corrective power: only 34.8% of zero-shot errors are corrected by additional instructions or examples, with high-confidence errors especially persistent. Misaligned definitions systematically shift predictions without reducing reported confidence, making confidence unreliable for detecting definition-policy mismatch. Together, these findings establish definition alignment as a practical model-selection criterion and show that better prompting alone cannot substitute for validating model-policy fit.

Short-form text rewriting is a constrained variant of paraphrasing in which limited context and high semantic density leave little room for variation. While large language models perform well on general paraphrasing, small language models (SLMs) often struggle with semantic fidelity and hallucination robustness in short-form settings. In this work, we present an empirical study of adapting an SLM, Phi Silica, for short-form rewrite through dataset curation, prompt distillation, parameter-efficient fine-tuning, and evaluation. We curate a dataset of short presentation-style text from public slide decks and use GPT-5-chat both to generate rewrite supervision and to conduct LLM-as-a-judge evaluation. Our results show that finetuning improves semantic fidelity, reduces hallucinations, and increases preference win rate against GPT-5-chat rewrites. The findings suggest that targeted adaptation for SLMs can substantially narrow the gap to cloud models and provide practical guidance for adapting SLMs to precision-critical rewrite tasks.

Dark vessel detection requires fusing what vessels report through AIS with what satellites observe through radar and optical sensors. DarkVesselNet is a multi-modal remote sensing stack that combines Sentinel-1 SAR, Sentinel-2 optical imagery, geospatial foundation model backbones, AIS trajectory reasoning, TGARD-style gap detection, and a Pi-DPM-inspired anomaly head. The repository exposes the system as a tested Python package and a public Hugging Face Space. The paper presents the sensor stack, backbone abstraction, fusion path, anomaly head, and current validation. The evidence currently available is software-grounded: tests for SAR speckle filtering, optical band ratios, Haversine distance, TGARD gap emission, sensor coregistration, backbone token shapes, and differentiable anomaly scoring.

Many machine learning techniques rely on approximating a loss function's curvature, but this is notoriously hard to do at the scale of modern deep networks. Surprisingly, no previous work has exploited the curvature constraints that arise from well known weight-space symmetries in loss landscapes. By analytically averaging over group actions that leave the loss invariant, we construct structured Hessian approximations from single gradients that can be tractably estimated, stored, and inverted. The choice of user-specified symmetry group directly governs the trade-off between approximation accuracy and computational cost. Moreover, our framework provides a unifying theoretical lens for viewing existing methods; in particular, a specific choice of symmetry group recovers Shampoo/Muon-like curvature estimates. We validate our method on a range of network architectures, and deploy it to second-order optimization benchmarks, including a small language model. Our curvature estimation framework might find applications in other machine learning problems such as uncertainty estimation, continual learning, compression/pruning, training data attribution, and more.

Process reward models (PRMs) are widely used in language-model training with dense step-level supervision. They assume PRM scores are stable proxies for step correctness under label-preserving transformations. These transformations change reasoning structure but preserve final answers. We argue this assumption is not well validated. Such transformations can change how PRM scores relate to correctness signals, leading to different failure modes across models.To address this gap, we introduce EST-PRM, a stress-testing framework for dense process rewards. It applies three transformations: (1) step inflation, (2) dependency-aware step reordering, and (3) confidence markers. A vulnerability decomposition is defined that separates reward inflation from loss of correctness sensitivity. Five PRM-style models are evaluated on 4,687 reasoning chains from MATH-500, GSM8K, and PRMBench.The results indicate clear differences in vulnerability patterns across models. Math-Shepherd shows the strongest sensitivity to position perturbations, with a Pearson correlation drop of $0.152 \pm 0.038$ and a $32.8 \pm 4.9\%$ score inflation rate. Qwen2.5-Math-PRM is most affected by step inflation, reaching a $47.6 \pm 4.3\%$ inflation rate. Confidence-based perturbations also distort reward calibration, revealing inconsistencies in correctness estimation. Three mitigation strategies are evaluated, highlighting trade-offs between robustness coverage and false-positive rates.