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01.
arXiv (CS.CV) 2026-06-15

HiLo-Token: Input-Adaptive High-Low Frequency Token Compression for Efficient Image Editing

Creative image editing tools, such as Photoshop's Remove or Generative Fill buttons, are central to everyday customer use and account for a major share of traffic in Photoshop and Lightroom. However, current generative AI models face significant latency challenges, which become even more pronounced when transitioning from convolution-based U-Nets to Diffusion Transformers (DiTs). In our evaluation on hundreds of representative image editing samples spanning a wide range of mask ratios, the DiT module alone accounts for an average of 73% of the total model latency, even after being distilled from 50 timesteps down to 8 timesteps. To tackle this challenge, we propose $HiLo-Token$, an input-adaptive token compression framework that allocates more token budget to high-frequency, rich-context regions while assigning fewer tokens to low-frequency areas. Specifically, for the editing region specified by the user mask, we retain all tokens within a dilated mask to preserve strong locality and contextual relevance. Outside the editing region, we introduce a simple yet effective high-frequency token selection strategy based on spatial frequency to capture important local details, while using tokens from a 16x downsampled image to represent low-frequency components and preserve the blurry but global structure. Extensive experiments on production-level evaluation data validate the effectiveness of the proposed method, achieving 3.13x, 2.59x, and 1.67x DiT speedups on A100-80GB for image editing tasks across small, medium, and large mask ratio categories with average ratios of 6.38%, 15.92%, and 35.36%, respectively, without any regression in generation quality.

02.
bioRxiv (Bioinfo) 2026-06-11

Calibrated Uncertainty Quantification for Patient-Level AML Drug Sensitivity Prediction Using Split Conformal Prediction

Accurate prediction of ex vivo drug sensitivity in acute myeloid leukemia (AML) patients from transcriptomic data is a critical challenge for precision oncology. Existing computational approaches have explored uncertainty quantification in cancer drug response prediction primarily using cell line data, while patient-level AML models typically rely on heuristic confidence measures rather than statistically calibrated uncertainty estimates. Here, we present a framework applying split conformal prediction to patient-level AML drug response modeling using the BeatAML 2.0 cohort. We trained Elastic Net and XGBoost regressors on bulk RNA-seq gene expression profiles from 318 AML patients, analyzing 34,764 patient-drug observations across 122 compounds. Baseline models achieved median Pearson R values of 0.291 (Elastic Net) and 0.281 (XGBoost) across 122 drugs. Wrapping these models with split conformal prediction yielded well-calibrated prediction intervals across three confidence levels: empirical coverages of 81.4%, 90.7%, and 95.5% against nominal targets of 80%, 90%, and 95%, respectively. Analysis of prediction interval widths revealed substantial drug-class-specific uncertainty patterns, with HDAC and BCL-2 inhibitors exhibiting markedly higher uncertainty than MDM2 inhibitors, suggesting a potential association between transcriptomic predictability and drug mechanism of action, although several drug classes were represented by only a small number of compounds. Predictive uncertainty was not significantly associated with ELN2017 molecular risk classification (Kruskal-Wallis p=0.395) or NPM1 mutation status (p=0.788). These results demonstrate that statistically valid uncertainty quantification can be achieved for patient-level AML drug response prediction despite substantial biological heterogeneity. to the best of our knowledge, no published study has applied split conformal prediction to patient-level ex vivo drug sensitivity prediction in the BeatAML cohort, providing a principled alternative to heuristic confidence scoring approaches. Keywords: Acute myeloid leukemia (AML); Ex vivo drug sensitivity; Conformal prediction; Uncertainty quantification; Precision oncology; BeatAML; Transcriptomic biomarkers; Machine learning.

03.
arXiv (CS.CV) 2026-06-11

How Auxiliary Reasoning Unleashes GUI Grounding in VLMs

Graphical user interface (GUI) grounding is a fundamental task for building GUI agents. However, general vision-language models (VLMs) struggle with this task due to a lack of specific optimization. We identify a key gap in this paper: while VLMs exhibit significant latent grounding potential, as demonstrated by their performance measured by Pointing Game, they underperform when tasked with outputting explicit coordinates. To address this discrepancy and bypass the high data and annotation costs of current fine-tuning approaches, we propose three zero-shot auxiliary reasoning methods. By providing explicit spatial cues such as axes, grids and labeled intersections as part of the input image, these methods enable VLMs to better articulate their implicit spatial understanding capabilities. We evaluate these methods on four GUI grounding benchmarks across seven open-source and proprietary VLMs. Experimental results show substantial gains from auxiliary reasoning. Mark-Grid Scaffold boosts Gemini-3.1-Pro from 11.72\% under direct inference to 95.20\% on ScreenSpot-v2, achieves state-of-the-art performance on ScreenSpot, and approaches the strongest fine-tuned methods on ScreenSpot-v2 and UI-I2E-Bench. Our code is available at https://github.com/liweim/AuxiliaryReasoning.

04.
arXiv (CS.CL) 2026-06-16

CAF-Gen: A Multi-Agent System for Enriching Argumentation Structures

Formalizing complex reasoning from natural text is one of the central challenges in computational linguistics. It requires systems to understand not just keywords but also the context and complex reasoning embedded in a text. Current Argument Mining (AM) techniques identify basic claims and premises, yet they often struggle to capture the richer structural information required by advanced schemas such as the Carneades Argumentation Framework (CAF), which incorporates features such as premise types, proof standards, and argument schemes. We address this limitation by introducing CAF-Gen, an automated multi-agent framework designed to enrich shallow argument structures into CAF-compliant argument models. By employing an iterative Creator-Reviewer pipeline, a creator agent's output is validated by a critical agent to ensure structural integrity. This multi-agent collaboration is crucial for mitigating the structural instability typical of single-pass generative models. Our experiments demonstrate that the iterative feedback loop improves the quality of the resulting data and achieves strong alignment with the original annotations, while producing structurally richer models. Our findings show that the multi-agent system can overcome the limitations of single-pass generation, providing a robust methodology for the automated modeling of formal argumentation.

05.
arXiv (CS.LG) 2026-06-16

Whole-Brain Connectomic Graph Model Enables Whole-Body Locomotion Control in Fruit Fly

arXiv:2602.17997v3 Announce Type: replace Abstract: Animals perform coordinated whole-body movements under the control of neural systems shaped by brain-wide connectivity. The mapping of the whole-brain neural connections, or the connectomes, provides a natural graph for modeling sensorimotor information flow, yet its potential as a neural controller for embodied agents remains largely unexplored. Here, we introduce the Fly-connectomic Graph Model, which directly instantiates the whole-brain connectome of an adult Drosophila as a graph-structured neural controller for movements of a simulated biomechanical fruit fly via deep reinforcement learning. We achieve stable performance across diverse locomotion tasks, as well as better sample efficiency compared to both graph and non-graph baselines. Our results demonstrate a biologically informed way towards effective control policy design by translating whole-brain wiring principles into actionable architectural priors, while also improving the interpretability through dynamic information flow. This work also highlights the potential to bridge neuromechanics with embodied intelligence by providing a computational platform for investigating the sensorimotor transformation underlying animal behavior and a paradigm to advance the development of more nature-aligned intelligent systems.

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

ArogyaSutra: A Multi-Agent Framework for Multimodal Medical Reasoning in Indic Languages

Multimodal Large Language Models (MLLMs) have shown promising reasoning capabilities in general domains, yet their performance remains limited in specialized settings such as healthcare, especially in multilingual and low-resource scenarios. This gap is critical in regions like rural India, where patients often express complex medical queries in native Indic languages and rely on multimodal inputs such as medical images. Existing English-centric MLLMs struggle to support such use cases, limiting equitable access to AI-driven healthcare assistance. To address this challenge, we introduce ArogyaBodha, a large-scale multilingual multimodal medical question-answer dataset constructed from eight heterogeneous sources, covering 31 body systems, six imaging modalities, and 21 clinical domains across English and seven major Indian languages. We further propose ArogyaSutra, an actor-critic-based multi-agent framework that integrates tool grounding with dual-memory mechanisms for step-wise, reasoning-aware decision making, and uses stored actor-critic simulation trajectories for distillation. Experiments show that our dataset and framework improve multilingual medical reasoning accuracy across all Indic languages, with ablations validating the contribution of each component. The source code and dataset are available at: https://iitp-cse.github.io/ ArogyaSutra/

07.
arXiv (CS.CV) 2026-06-12

Perceive, Interact, Reason: Building Tool-Augmented Visual Agents for Spatial Reasoning

While recent vision-language models (VLMs) demonstrate strong multimodal understanding, they remain limited in spatial reasoning tasks that require active evidence acquisition and multi-step visual interaction. This limitation suggests that relying solely on implicit visual representations from vision encoders is insufficient for recovering fine-grained spatial evidence. We introduce PERception-Interaction-reason Agent (PERIA), a tool-augmented visual agent for spatial reasoning tasks across map reasoning, visual probing, and vision reconstruction. PERIA uses two lightweight tool families: vision perception tools for exposing textual, symbolic, and spatial evidence, and vision interaction tools for manipulating visual context, tracing paths, and verifying spatial relations. To train PERIA, we develop a unified recipe that combines supervised tool-use trajectory synthesis, composite rewards, and Observation-Relaxed Group-in-Group Policy Optimization (OR-GIGPO) for effective multi-tool behavior. Experiments on 13 benchmarks from 8 datasets show that PERIA-8B improves over the Qwen3-8B backbone by 10.0% on in-distribution benchmarks and 4.4% on out-of-distribution benchmarks, while outperforming previous state-of-the-art baselines of similar size by 7.0%-14.8%. It also achieves performance comparable to much larger models such as Qwen3-VL-235B-A22B-Thinking and GPT-5, demonstrating the effectiveness of PERIA in enhancing spatial reasoning capabilities.

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

Something from Nothing: Data Augmentation for Robust Severity Level Estimation of Dysarthric Speech

arXiv:2603.15988v3 Announce Type: replace-cross Abstract: Dysarthric speech quality assessment (DSQA) is critical for clinical diagnostics and inclusive speech technologies. However, subjective evaluation is costly and difficult to scale, and the scarcity of labeled data limits robust objective modeling. To address this, we propose a three-stage framework that leverages unlabeled dysarthric speech and large-scale typical speech datasets to scale training. A teacher model first generates pseudo-labels for unlabeled samples, followed by weakly supervised pretraining using a label-aware contrastive learning strategy that exposes the model to diverse speakers and acoustic conditions. The pretrained model is then fine-tuned for the downstream DSQA task. Experiments on five unseen datasets spanning multiple etiologies and languages demonstrate the robustness of our approach. Our Whisper-based baseline significantly outperforms SOTA DSQA predictors such as SpICE, and the full framework achieves an average SRCC of 0.761 across unseen test datasets.

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

LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks

Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig

11.
arXiv (CS.CL) 2026-06-12

From Tokens to Faces: Investigating Discrete Speech Representations for 3D Facial Animation

The choice of speech representation is critical in speech-driven 3D facial animation. Representations differ in what they encode: SSL features emphasize segmental and semantic cues, neural codecs yield latents optimized for acoustic reconstruction, and ASR-style objectives produce label-based spaces. We evaluate four speech representation families for 3D facial synthesis, comparing their facial reconstruction quality across two facial decoders using objective metrics and a perceptual evaluation. We additionally conduct probing analyses that relate tokenized representations to phonetic units and to articulatory deformations. We found that encoding phonetic classes is beneficial for accurate facial animation prediction on both semantic and label-based representations with comparable facial animation quality. From the latter, we introduce an Audio Visual Text-to-Speech (AVTTS) pipeline that leverages, as a shared space, discrete representations to decode speech and 3D facial motion.

12.
arXiv (CS.CV) 2026-06-18

Low-Rank Tensor Completion Based on Fractional Regularization with Ky Fan p-k Norm

This paper addresses low-rank tensor completion (LRTC) by proposing a novel nonconvex surrogate, namely the ratio of the tensor nuclear norm to the tensor Ky Fan p-k norm (TNPK), to accurately approximate the tensor tubal rank. The TNPK possesses appealing properties, including scale invariance, parameter flexibility, and the existence of closed-form solutions under specific choices of p and k. With specific parameter settings of p and k, it reduces to the ratio of the tensor nuclear norm to the tensor Ky Fan k norm (TNK) or the ratio of the tensor nuclear norm to the tensor Frobenius norm (TNF). We construct a LRTC model and, under the tensor null space property (NSP), prove that low-rank tensors are local minimizers of the proposed model. Moreover, we derive the proximal operator of the Ky Fan p-k inverse-norm and further develop an efficient alternating direction method of multipliers (ADMM) algorithm with guaranteed subsequential convergence under mild conditions. Extensive experiments on synthetic and real-world datasets validate the superior performance of our method against state-of-the-art competitors.

13.
arXiv (CS.AI) 2026-06-12

MARS: Margin-Adversarial Risk-controlled Stopping for Parallel LLM Test-time Scaling

arXiv:2606.12935v1 Announce Type: new Abstract: Parallel test-time scaling samples many reasoning traces and majority-votes their answers, improving LLM accuracy but requiring traces to run to completion, incurring substantial computational overhead. We observe that probing partial traces at intermediate checkpoints can extract current answers without disrupting generation, revealing an evolving aggregate vote. Based on this observation, we introduce MARS, a margin-adversarial stopping rule that estimates which active traces are likely to change their answers and stops once the leader remains safe under a conservative bound on future vote movement. The rule separates two sources of uncertainty. It learns the trace-level switch probabilities that determine how much of the current margin is likely to be retained, while handling the harder question of where switching traces land through an adversarial bound calibrated from warmup traces. With true switch probabilities, MARS guarantees with high probability that the early-stopped answer matches the full-budget vote. In practice, a five-feature logistic model closely matches oracle switching behavior. Across three reasoning models and three competition-math benchmarks, MARS saves 25-47% of self-consistency tokens and 14-29% on top of DeepConf Online, a strong confidence-weighted baseline that already filters and truncates weak traces, while matching the accuracy of the corresponding full-budget baselines.

14.
arXiv (CS.CV) 2026-06-18

Domain Generalizable Adaptation of 3D Vision-Language Models via Regularized Fine-Tuning

Domain adaptation remains a central challenge in 3D vision, especially for multimodal foundation models that align 3D point clouds with visual and textual data. While these models demonstrate strong general capabilities, adapting them to downstream domains with limited data often leads to overfitting and catastrophic forgetting. To address this, we introduce ReFine3D, a regularized fine-tuning framework designed for domain-generalizable tuning of 3D large multimodal models (LMMs). ReFine3D combines selective layer tuning with two targeted regularization strategies: multi-view consistency across augmented point clouds and text diversity through synonym-based prompts generated by large language models. Additionally, we incorporate point-rendered vision supervision and a test-time augmentation mechanism with confidence-based aggregation to further enhance robustness. Extensive experiments across different 3D domain generalization benchmarks show that ReFine3D improves base-to-novel class generalization by 1.36%, cross-dataset transfer by 2.43%, robustness to corruption by 1.80%, and few-shot accuracy by up to 3.11%, outperforming prior state-of-the-art methods with minimal added computational overhead.

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

CausalMotion: Structured Physical Reasoning as Keyframe and Trajectory Guidance for Training-Free Video Generation

Recent advances in diffusion-based video generation have significantly improved visual quality and short-term temporal coherence. However, existing methods still struggle to produce videos with physically consistent and causally plausible dynamics, especially in scenarios involving long-horizon interactions. This limitation arises from the fact that video diffusion models primarily learn physical consistency implicitly, while vision-language models can directly model physical laws. Based on this idea, in this work, we propose CausalMotion, a training-free framework that injects explicit physical reasoning into video generation through structured intermediate representations. Our key idea is to decouple reasoning from generation by leveraging a vision-language model to decompose a text prompt into a sequence of causally consistent keyframes and object-centric motion trajectories. These representations are then aligned and integrated as soft constraints to guide a pretrained video diffusion model during inference. This design enables explicit modeling of object dynamics and causal transitions without requiring additional training or supervision. Extensive experiments show that our method consistently improves physical plausibility and temporal coherence, particularly in dynamics-intensive scenarios, while maintaining high perceptual video quality.

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

StarOR: Synergizing Tree Search and Test-Time Reinforcement Learning for Optimization Modeling

arXiv:2606.15197v1 Announce Type: cross Abstract: Optimization modeling is inherently hierarchical, requiring a precise sequence of symbolic commitments. Traditional learning-based automated optimization modeling methods improve modeling policies through large-scale annotated or curated training data, but are costly to adapt to new problem distributions. Meanwhile, one-shot generation remains brittle in hierarchical modeling, where early symbolic errors can propagate into invalid formulations. Test-time scaling offers a promising alternative by enabling structural exploration with additional instance-level computation; however, existing search-based methods typically rely on a fixed policy, causing repeated rollouts to inherit similar modeling biases and providing limited credit assignment for intermediate decisions. To address these limitations, we propose StarOR, a synergistic search-and-adaptation framework that couples MCTS with Test-Time Reinforcement Learning for optimization modeling. StarOR decomposes the modeling process into four stages and updates a transient LoRA adapter via GRPO at each non-terminal node. By using MCTS-generated siblings as local comparison sets, StarOR transforms search-time exploration into instance-specific policy refinement. Moreover, an unsupervised multi-faceted reward system provides fine-grained feedback for intermediate formulation decisions without ground-truth labels. Experiments across five optimization benchmarks show that StarOR achieves state-of-the-art performance even with a 4B backbone, outperforming existing methods and the frontier LLMs.

17.
arXiv (CS.CV) 2026-06-16

Assessing Reliability of Symbol Detection in Concept Bottleneck Models

Concept Bottleneck Models (CBMs) are a relevant tool for explainable Artificial Intelligence because they make their predictions through human-interpretable symbols. However, high task accuracy does not guarantee that these symbols are detected faithfully: jointly trained CBMs may encode task-specific shortcuts in the bottleneck, making their explanations unreliable. In this paper, we study concept-detection reliability by swapping independently trained concept detectors and classification heads that share the same symbolic vocabulary. We use the resulting performance degradation, concept-level metrics, and symbol-wise uncertainty estimates to identify concepts that are especially prone to spurious firing. Finally, we propose a reliability-aware training strategy in which a shared concept detector is optimized with multiple classification heads and penalized for relying on globally or instance-wise unreliable symbols. On CUB-200-2011 with full concept supervision, detectors and heads are almost freely interchangeable (swap drop below one accuracy point, relative retention above $99\%$, and no concept detected below chance), whereas on a controlled synthetic task we show that, as the concept-supervision weight is reduced, models keep near-perfect task accuracy while swapped accuracy and agreement with the ground-truth concepts collapse to chance. Our reliability-aware training substantially mitigates this leakage, roughly doubling swap accuracy in the leaky regime.

18.
arXiv (CS.AI) 2026-06-12

Arbor: Tree Search as a Cognition Layer for Autonomous Agents

arXiv:2606.12563v1 Announce Type: new Abstract: Arbor is a multi-agent framework that introduces structured tree search as a cognition layer for autonomous agents operating in large, stateful action spaces. Prior autonomous optimization systems operate on isolated targets with stateless evaluation. Arbor instead maintains an explicit search tree of scored hypotheses that serves as the shared working memory across agents, evolving with every measurement, treating failures as diagnostic signal that reshapes subsequent exploration, and expanding as prior successes shift the bottleneck distribution. We validate Arbor on full-stack LLM inference optimization, a domain where achieving peak performance has historically required coordinated effort from engineering teams across the application, framework, compiler, kernel, and hardware stack. Arbor pairs an Orchestrator agent, which drives optimization by delegating to Domain Specialists across the inference stack, with a Critic agent that safeguards stability through root-cause analysis, introspection, and measurement validation – a checks-and-balances architecture where neither agent can unilaterally drive the system. Agent capabilities are decomposed into hard skills (domain expertise) and soft skills (coordination protocols that determine how contributions compose), enabling fully autonomous multi-day campaigns. Arbor achieves up to 193% inference throughput-latency Pareto improvement over vendor-optimized baselines, while a single agent without the harness plateaus at +33% throughput improvement and crashes irrecoverably within hours. Arbor generalizes to multiple generations of hardware platform, and run-to-run variance is within 2 percentage points demonstrating that the method is hardware-agnostic and reproducible.

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

MET-Bench: Multimodal Entity Tracking for Evaluating the Limitations of Vision-Language and Reasoning Models

Entity state tracking is a necessary component of world modeling that requires maintaining coherent representations of entities over time. Previous work has benchmarked entity tracking performance in purely text-based tasks. We introduce MET-Bench, a multimodal entity tracking benchmark designed to evaluate the ability of vision-language models to track entity states across modalities. Using three domains, we assess how effectively current models integrate textual and image-based state updates. Our findings reveal a significant performance gap between text-based and image-based entity tracking. We empirically show this discrepancy primarily stems from deficits in visual reasoning rather than perception. We further show that explicit text-based reasoning strategies improve performance, yet limitations remain, especially in long-horizon multimodal tasks. We apply reinforcement learning to improve entity tracking in open-source VLMs. This yields substantial in-modality gains, but does not transfer robustly across input modalities. Our results highlight the need for improved multimodal representations and reasoning techniques to bridge the gap between textual and visual entity tracking.

20.
arXiv (CS.AI) 2026-06-18

A DeepLearning Framework for Dynamic Estimation of Origin-Destination Sequence

arXiv:2307.05623v2 Announce Type: replace-cross Abstract: OD matrix estimation is a critical problem in the transportation domain. The principle method uses the traffic sensor measured information such as traffic counts to estimate the traffic demand represented by the OD matrix. The problem is divided into two categories: static OD matrix estimation and dynamic OD matrices sequence(OD sequence for short) estimation. The above two face the underdetermination problem caused by abundant estimated parameters and insufficient constraint information. In addition, OD sequence estimation also faces the lag challenge: due to different traffic conditions such as congestion, identical vehicle will appear on different road sections during the same observation period, resulting in identical OD demands correspond to different trips. To this end, this paper proposes an integrated method, which uses deep learning methods to infer the structure of OD sequence and uses structural constraints to guide traditional numerical optimization. Our experiments show that the neural network(NN) can effectively infer the structure of the OD sequence and provide practical constraints for numerical optimization to obtain better results. Moreover, the experiments show that provided structural information contains not only constraints on the spatial structure of OD matrices but also provides constraints on the temporal structure of OD sequence, which solve the effect of the lagging problem well.

21.
arXiv (CS.CV) 2026-06-15

Overhead Wildlife Locator (OWL): Benchmarking Weakly Supervised Learning for Aerial Wildlife Surveys

Automated aerial wildlife surveys increasingly rely on deep learning, yet standard object detectors require bounding-box annotations, reported to be up to seven times slower and three times more expensive to produce than point-level labels. To address this bottleneck, we introduce the Overhead Wildlife Locator (OWL), a weakly supervised density-estimation framework with three variants: OWL-C, a fully convolutional model for high-throughput screening; OWL-T, a Swin-augmented hybrid for heterogeneous, cluttered scenes; and OWL-D, built on a frozen DINOv3 ViT-H+/16 encoder with a DPT-style fusion decoder. We benchmark all three against POLO, YOLOv11n, and YOLOv11l across five public aerial datasets, from sparse fixed-wing savanna surveys to dense UAV paddock imagery, and against the published HerdNet baseline on its native Delplanque split. OWL-D sets a new state of the art on Delplanque (0.934 AP vs. HerdNet's 0.840) and records the highest AP on four of the five datasets. Performance is regime-dependent: on the extreme-density SheepCounter UAV dataset the hybrid OWL-T leads (0.978 AP) and the convolutional variants attain the lowest counting error, whereas the foundation-based OWL-D degrades, indicating which variant suits which survey type. We further validate operational readiness on the Alaska Department of Fish and Game's 2022 Central Arctic Caribou census: under cross-herd and cross-temporal transfer, OWL-C fine-tuned on the 2017 Porcupine Caribou Herd split attains F1 = 0.965 on a held-out patch test set, with a signed count error of +3.1% aggregated across the released test patches. We release the OWL code, model weights, and the annotated Porcupine Caribou Herd 2017 (PCH) and Central Arctic Herd 2022 (CAH) patches, the first open patch-level datasets for large-scale caribou aerial surveys, at https://github.com/microsoft/MegaDetector-Overhead.

22.
PLOS Computational Biology 2026-06-18

scMagnifier: Resolving fine-grained cell subtypes via GRN-informed perturbations and consensus clustering

作者:

by Zhenhui He, Dong Kangning Resolving fine-grained cell subtypes in single-cell RNA sequencing (scRNA-seq) data remains challenging, as their subtle transcriptional differences are often obscured by technical noise and data sparsity. Here, we present scMagnifier, a consensus clustering framework that leverages gene regulatory network (GRN)-informed in silico perturbations to amplify subtle transcriptional differences and uncover latent cell subpopulations. scMagnifier perturbs candidate transcription factors (TFs), propagates perturbation effects through cluster-specific GRNs to simulate post-perturbation expression profiles, and integrates clustering results across multiple perturbations into stable subtype assignments. Additionally, scMagnifier introduces regulatory perturbation consensus UMAP (rpcUMAP), a perturbation-aware visualization that provides clearer separation between cell subtypes and guides the selection of the optimal number of clusters. In both single-batch and multi-batch benchmarks, scMagnifier consistently improves the resolution and accuracy of fine-grained cell type identification. Notably, when integrated with spatial clustering methods such as STAGATE, scMagnifier is compatible with spatial transcriptomics workflows and effectively reveals tumor cell subtypes and their spatial organization in ovarian cancer.

23.
arXiv (CS.LG) 2026-06-18

On the Stability of Nonlinear Dynamics in GD and SGD: Beyond Quadratic Potentials

arXiv:2602.14789v2 Announce Type: replace Abstract: The dynamical stability of the iterates during training plays a key role in determining the minima obtained by optimization algorithms. For example, stable solutions of gradient descent (GD) correspond to flat minima, which have been associated with favorable features. While prior work often relies on linearization to determine stability, it remains unclear whether linearized dynamics faithfully capture the full nonlinear behavior. Recent work has shown that GD may stably oscillate near a linearly unstable minimum and still converge once the step size decays, indicating that linear analysis can be misleading. In this work, we explicitly study the effect of nonlinear terms. Specifically, we derive an exact criterion for stable oscillations of GD near minima in the multivariate setting. Our condition depends on high-order derivatives, generalizing existing results. Extending the analysis to stochastic gradient descent (SGD), we show that nonlinear dynamics can diverge in expectation even if a single batch is unstable. This implies that stability can be dictated by a single batch that oscillates unstably, rather than an average effect, as linear analysis suggests. Finally, we prove that if all batches are linearly stable, the nonlinear dynamics of SGD are stable in expectation.

24.
bioRxiv (Bioinfo) 2026-06-17

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

Temperature is a fundamental constraint on biological systems, yet how it is reflected in genome sequence organization remains unclear. Here, we show that genome-wide distributions of short DNA sequences contain a robust signal of thermal adaptation that is largely independent of phylogeny. Using Structural Topic Modelling (STM), a machine-learning approach for identifying groups of co-occurring sequence motifs, we analyze canonical 6-mer and 9-mer frequency profiles of bacterial and archaeal genome proxies (randomly sampled genomic regions) and identify motif families systematically associated with thermophiles and psychrophiles. In bacterial thermophiles, the identified motif families are dominated by highly specific, overrepresented and co-occurring C- and G-stacked hexamers, and a distinct family of CG-periodic hexamers recurring across multiple temperature comparisons. In contrast, bacterial psychrophile-associated motifs are dominated by low-complexity A-, T-, and AT-run hexamers. Thermophilic archaea generally exhibit a distinct CTAG-centred hexamer family, suggesting that different domains may adapt to similar environmental constraints through different sequence-level solutions. However, this domain-level contrast is not absolute: in a targeted analysis of two thermophilic bacterium–archaeon pairs, we find unusually similar frequencies of all the STM-identified thermophile-associated hexamer families, suggesting that shared high-temperature environments can, in specific cases, partially override phylogenetic divergence. Notably, the identified motif families constitute only a small and highly selective subset of the vast space of possible G+C-rich or A+T-rich sequences. This indicates that thermal adaptation is associated with specific sequence architectures rather than broad shifts in nucleotide composition. Accordingly, the observed signal cannot be explained by overall base composition alone, but instead arises from structured combinations and positional arrangements of nucleotides within short sequence contexts. Related motif families are recovered at both k=6 and k=9, indicating that the signal reflects systematic shifts in genome-wide sequence organization rather than isolated sequence motifs. These patterns are consistent with known sequence-dependent DNA physical properties documented in biochemical and biophysical studies, including differences in base-stacking interactions and conformational flexibility. Together, our results suggest that genome-wide sequence organization reflects sequence-dependent DNA physical properties associated with thermal adaptation, revealing a previously underappreciated physical layer of genomic information beyond phylogenetic history.

25.
arXiv (CS.AI) 2026-06-16

Agent Economics: An Entropy-Controlled Pluralistic Alignment Framework for Preventing Artificial Hivemind in Autonomous Agents

arXiv:2606.09039v2 Announce Type: replace Abstract: This study proposes the Behavioral Protocol Framework (BPF), an entropy-controlled pluralistic alignment framework designed to address two critical challenges in autonomous agent economies: the hivemind effect arising from excessive strategic convergence among agents and the lack of transparency in autonomous decision-making processes. The proposed BPF consists of three core modules: Mentalizing-based Social Intelligence (MbSI) grounded in Theory of Mind (ToM), Pluralistic Alignment (PA), and a Verifiable Execution Kernel (VEK). These modules are organically integrated within a closed-loop architecture that governs the entire lifecycle of agent behavior, from decision-making and execution to verification and feedback. To evaluate the proposed framework, a simulation environment implemented in Python and a Streamlit-based user interface will be developed. Through empirical experimentation, the study aims to examine whether the entropy-control mechanism of the PA module can effectively preserve strategic diversity among agents and mitigate collective convergence, while the VEK module provides a comprehensive and transparent audit trail of the decision-making process. The anticipated results are expected to demonstrate that the proposed framework can simultaneously enhance the stability, efficiency, and trustworthiness of autonomous agent economies. Consequently, this research offers a practical approach for developing robust, transparent, and accountable agent-native economic systems.