OpenRaiser/Intern-Atlas huggingface dataset:
Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
Venue: arXiv cs.LG 2026
Year: 2026

We report the discovery and extraction of a compact hematopoietic algorithm from the single-cell foundation model scGPT, to our knowledge the first biologically useful, competitive algorithm extracted from a foundation model via mechanistic interpretability. We show that scGPT internally encodes a compact hematopoietic manifold with significant developmental branch structure, validated on a strict non-overlap Tabula Sapiens external panel and confirmed via frozen-head zero-shot transfer to an independent multi-donor immune panel. To isolate this geometry, we introduce a general three-stage extraction method consisting of direct operator export from frozen attention weights, a lightweight learned adaptor, and a task-specific readout, producing a standalone algorithm without target-dataset retraining. In 88-split donor-holdout benchmarks against scVI, Palantir, DPT, CellTypist, PCA, and raw-expression baselines, the extracted algorithm achieves the strongest pseudotime-depth ordering and leads on key subtype endpoints (CD4/CD8 AUROC 0.867, mono/macro AUROC 0.951). Compared to standard probing of frozen scGPT embeddings with a 3-layer MLP, the extracted head is BH-significantly better on 6/8 classification endpoints while completing a full 12-split evaluation campaign 34.5x faster with approximately 1000x fewer trainable parameters. The exported operator compresses from three pooled attention heads to a single head without statistically significant loss, and further to a rank-64 surrogate. Mechanistic interpretability of the compact operator reveals a concentrated four-factor core explaining 66.2% of ablation impact, with factors resolving into explicit T/lymphoid, B/plasma, granulocytic, and monocyte/macrophage gene programs. A supplementary second-manifold validation (intercellular communication geometry) confirms that the extraction method generalizes beyond hematopoiesis.
How to make the most of your masked language model for protein engineering
Venue: arXiv cs.LG 2026
Year: 2026

A plethora of protein language models have been released in recent years. Yet comparatively little work has addressed how to best sample from them to optimize desired biological properties. We fill this gap by proposing a flexible, effective sampling method for masked language models (MLMs), and by systematically evaluating models and methods both in silico and in vitro on actual antibody therapeutics campaigns. Firstly, we propose sampling with stochastic beam search, exploiting the fact that MLMs are remarkably efficient at evaluating the pseudo-perplexity of the entire 1-edit neighborhood of a sequence. Reframing generation in terms of entire-sequence evaluation enables flexible guidance with multiple optimization objectives. Secondly, we report results from our extensive in vitro head-to-head evaluation for the antibody engineering setting. This reveals that choice of sampling method is at least as impactful as the model used, motivating future research into this under-explored area.
Data-Driven Integration Kernels for Interpretable Nonlocal Operator Learning
Venue: arXiv cs.LG 2026
Year: 2026

Machine learning models can represent climate processes that are nonlocal in horizontal space, height, and time, often by combining information across these dimensions in highly nonlinear ways. While this can improve predictive skill, it makes learned relationships difficult to interpret and prone to overfitting as the extent of nonlocal information grows. We address this challenge by introducing data-driven integration kernels, a framework that adds structure to nonlocal operator learning by explicitly separating nonlocal information aggregation from local nonlinear prediction. Each spatiotemporal predictor field is first integrated using learnable kernels (defined as continuous weighting functions over horizontal space, height, and/or time), after which a local nonlinear mapping is applied only to the resulting kernel-integrated features and any optional local inputs. This design confines nonlinear interactions to a small set of integrated features and makes each kernel directly interpretable as a weighting pattern that reveals which horizontal locations, vertical levels, and past timesteps contribute most to the prediction. We demonstrate the framework for South Asian monsoon precipitation using a hierarchy of neural network models with increasing structure, including baseline, nonparametric kernel, and parametric kernel models. Across this hierarchy, kernel-based models achieve near-baseline performance with far fewer trainable parameters, showing that much of the relevant nonlocal information can be captured through a small set of interpretable integrations when appropriate structural constraints are imposed.
Towards Modeling Situational Awareness Through Visual Attention in Clinical Simulations
Venue: arXiv cs.HC 2026
Year: 2026

Situational awareness (SA) is essential for effective team performance in time-critical clinical environments, yet its dynamic and distributed nature remains difficult to characterize. In this preliminary study, we apply Transition Network Analysis (TNA) to model visual attention in multiperson VR-based cardiac arrest simulations. Using eye-tracking data from 40 clinicians assigned to four standardized roles (Airway, CPR, Defib, TeamLead), we construct gaze transition networks between clinically meaningful areas of interest (AOIs) and extract metrics such as entropy and self-loop rate to quantify attentional structure and flow. Our findings reveal that individual and team's visual attention is dynamically and adaptively redistributed across roles and scenario phases, with those in CPR roles narrowing their focus to execution-critical tasks and those in the TeamLead role concentrating on global monitoring as clinical demands evolve. TNA thus provides a powerful lens for mapping functional differentiation of team cognition and may support the development of phase-sensitive analytics and targeted instructional interventions in acute care training.
Large language models can disambiguate opioid slang on social media
Venue: arXiv cs.CL 2026
Year: 2026

Social media text shows promise for monitoring trends in the opioid overdose crisis; however, the overwhelming majority of social media text is unrelated to opioids. When leveraging social media text to monitor trends in the ongoing opioid overdose crisis, a common strategy for identifying relevant content is to use a lexicon of opioid-related terms as inclusion criteria. However, many slang terms for opioids, such as "smack" or "blues," have common non-opioid meanings, making them ambiguous. The advanced textual reasoning capability of large language models (LLMs) presents an opportunity to disambiguate these slang terms at scale. We present three tasks on which to evaluate four state-of-the-art LLMs (GPT-4, GPT-5, Gemini 2.5 Pro, and Claude Sonnet 4.5): a lexicon-based setting, in which the LLM must disambiguate a specific term within the context of a given post; a lexicon-free setting, in which the LLM must identify opioid-related posts from context without a lexicon; and an emergent slang setting, in which the LLM must identify opioid-related posts with simulated new slang terms. All four LLMs showed excellent performance across all tasks. In both subtasks of the lexicon-based setting, LLM F1 scores ("fenty" subtask: 0.824-0.972; "smack" subtask: 0.540-0.862) far exceeded those of the best lexicon strategy (0.126 and 0.009, respectively). In the lexicon-free task, LLM F1 scores (0.544-0.769) surpassed those of lexicons (0.080-0.540), and LLMs demonstrated uniformly higher recall. On emergent slang, all LLMs had higher accuracy (average: 0.784), F1 score (average: 0.712), precision (average: 0.981), and recall (average: 0.587) than the two lexicons assessed. Our results show that LLMs can be used to identify relevant content for low-prevalence topics, including but not limited to opioid references, enhancing data provided to downstream analyses and predictive models.
PC-Diffuser: Path-Consistent Capsule CBF Safety Filtering for Diffusion-Based Trajectory Planner
Venue: arXiv cs.RO 2026
Year: 2026

Autonomous driving in complex traffic requires planners that generalize beyond hand-crafted rules, motivating data-driven approaches that learn behavior from expert demonstrations. Diffusion-based trajectory planners have recently shown strong closed-loop performance by iteratively denoising a full-horizon plan, but they remain difficult to certify and can fail catastrophically in rare or out-of-distribution scenarios. To address this challenge, we present PC-Diffuser, a safety augmentation framework that embeds a certifiable, path-consistent barrier-function structure directly into the denoising loop of diffusion planning. The key idea is to make safety an intrinsic part of trajectory generation rather than a post-hoc fix: we enforce forward invariance along the rollout while preserving the diffusion model's intended path geometry. Specifically, PC-Diffuser (i) evaluates collision risk using a capsule-distance barrier function that better reflects vehicle geometry and reduces unnecessary conservativeness, (ii) converts denoised waypoints into dynamically feasible motion under a kinematic bicycle model, and (iii) applies a path-consistent safety filter that eliminates residual constraint violations without geometric distortion, so the corrected plan remains close to the learned distribution. By injecting these safety-consistent corrections at every denoising step and feeding the refined trajectory back into the diffusion process, PC-Diffuser enables iterative, context-aware safeguarding instead of post-hoc repair...
Overcoming Visual Clutter in Vision Language Action Models via Concept-Gated Visual Distillation
Venue: arXiv cs.CV 2026
Year: 2026

Vision-Language-Action (VLA) models demonstrate impressive zero-shot generalization but frequently suffer from a "Precision-Reasoning Gap" in cluttered environments. This failure is driven by background-induced feature dilution, where high-frequency semantic noise corrupts the geometric grounding required for precise manipulation. To bridge this gap, we propose Concept-Gated Visual Distillation (CGVD), a training-free, model-agnostic inference framework that stabilizes VLA policies. CGVD operates by parsing instructions into safe and distractor sets, utilizing a two-layer target refinement process--combining cross-validation and spatial disambiguation--to explicitly penalize false positives and isolate genuine manipulation targets. We then process the scene via Fourier-based inpainting, generating a clean observation that actively suppresses semantic distractors while preserving critical spatial geometry and visual proprioception. Extensive evaluations in highly cluttered manipulation tasks demonstrate that CGVD prevents performance collapse. In environments with dense semantic distractors, our method significantly outperforms state-of-the-art baselines, achieving a 77.5% success rate compared to the baseline's 43.0%. By enforcing strict attribute adherence, CGVD establishes inference-time visual distillation as a critical prerequisite for robust robotic manipulation in the clutter.
HEAL: Hindsight Entropy-Assisted Learning for Reasoning Distillation
Venue: arXiv cs.AI 2026
Year: 2026

Distilling reasoning capabilities from Large Reasoning Models (LRMs) into smaller models is typically constrained by the limitation of rejection sampling. Standard methods treat the teacher as a static filter, discarding complex "corner-case" problems where the teacher fails to explore valid solutions independently, thereby creating an artificial "Teacher Ceiling" for the student. In this work, we propose Hindsight Entropy-Assisted Learning (HEAL), an RL-free framework designed to bridge this reasoning gap. Drawing on the educational theory of the Zone of Proximal Development(ZPD), HEAL synergizes three core modules: (1) Guided Entropy-Assisted Repair (GEAR), an active intervention mechanism that detects critical reasoning breakpoints via entropy dynamics and injects targeted hindsight hints to repair broken trajectories; (2) Perplexity-Uncertainty Ratio Estimator (PURE), a rigorous filtering protocol that decouples genuine cognitive breakthroughs from spurious shortcuts; and (3) Progressive Answer-guided Curriculum Evolution (PACE), a three-stage distillation strategy that organizes training from foundational alignment to frontier breakthrough. Extensive experiments on multiple benchmarks demonstrate that HEAL significantly outperforms traditional SFT distillation and other baselines.
Causal Concept Graphs in LLM Latent Space for Stepwise Reasoning
Venue: arXiv cs.LG 2026
Year: 2026

Sparse autoencoders can localize where concepts live in language models, but not how they interact during multi-step reasoning. We propose Causal Concept Graphs (CCG): a directed acyclic graph over sparse, interpretable latent features, where edges capture learned causal dependencies between concepts. We combine task-conditioned sparse autoencoders for concept discovery with DAGMA-style differentiable structure learning for graph recovery and introduce the Causal Fidelity Score (CFS) to evaluate whether graph-guided interventions induce larger downstream effects than random ones. On ARC-Challenge, StrategyQA, and LogiQA with GPT-2 Medium, across five seeds ($n{=}15$ paired runs), CCG achieves $\CFS=5.654\pm0.625$, outperforming ROME-style tracing ($3.382\pm0.233$), SAE-only ranking ($2.479\pm0.196$), and a random baseline ($1.032\pm0.034$), with $p<0.0001$ after Bonferroni correction. Learned graphs are sparse (5-6\% edge density), domain-specific, and stable across seeds.
Silent Subversion: Sensor Spoofing Attacks via Supply Chain Implants in Satellite Systems
Venue: arXiv cs.CR 2026
Year: 2026

Spoofing attacks are among the most destructive cyber threats to terrestrial systems, and they become even more dangerous in space, where satellites cannot be easily serviced, and operators depend on accurate telemetry to ensure mission success. When telemetry is compromised, entire spaceborne missions are placed at risk. Prior work on spoofing has largely focused on attacks from Earth, such as injecting falsified uplinks or overpowering downlinks with stronger radios. In contrast, onboard spoofing originating from within the satellite itself remains an underexplored and underanalyzed threat. This vector is particularly concerning given that modern satellites, especially small satellites, rely on modular architectures and globalized supply chains that reduce cost and accelerate development but also introduce hidden risks. This paper presents an end-to-end demonstration of an internal satellite spoofing attack delivered through a compromised vendor-supplied component implemented in NASA's NOS3 simulation environment. Our rogue Core Flight Software application passed integration and generated packets in the correct format and cadence that the COSMOS ground station accepted as legitimate. By undermining both onboard estimators and ground operator views, the attack directly threatens mission integrity and availability, as corrupted telemetry can bias navigation, conceal subsystem failures, and mislead operators into executing harmful maneuvers. These results expose component-level telemetry spoofing as an overlooked supply-chain vector distinct from jamming or external signal injection. We conclude by discussing practical countermeasures-including authenticated telemetry, component attestation, provenance tracking, and lightweight runtime monitoring-and highlight the trade-offs required to secure resource-constrained small satellites.
Multi-Person Pose Estimation Evaluation Using Optimal Transportation and Improved Pose Matching
Venue: arXiv cs.CV 2026
Year: 2026

In Multi-Person Pose Estimation, many metrics place importance on ranking of pose detection confidence scores. Current metrics tend to disregard false-positive poses with low confidence, focusing primarily on a larger number of high-confidence poses. Consequently, these metrics may yield high scores even when many false-positive poses with low confidence are detected. For fair evaluation taking into account a tradeoff between true-positive and false-positive poses, this paper proposes Optimal Correction Cost for pose (OCpose), which evaluates detected poses against pose annotations as an optimal transportation. For the fair tradeoff between true-positive and false-positive poses, OCpose equally evaluates all the detected poses regardless of their confidence scores. In OCpose, on the other hand, the confidence score of each pose is utilized to improve the reliability of matching scores between the estimated pose and pose annotations. As a result, OCpose provides a different perspective assessment than other confidence ranking-based metrics.
Shape Control of a Planar Hyper-Redundant Robot via Hybrid Kinematics-Informed and Learning-based Approach
Venue: arXiv cs.RO 2026
Year: 2026

Hyper-redundant robots offer high dexterity, making them good at operating in confined and unstructured environments. To extend the reachable workspace, we built a multi-segment flexible rack actuated planar robot. However, the compliance of the flexible mechanism introduces instability, rendering it sensitive to external and internal uncertainties. To address these limitations, we propose a hybrid kinematics-informed and learning-based shape control method, named SpatioCoupledNet. The neural network adopts a hierarchical design that explicitly captures bidirectional spatial coupling between segments while modeling local disturbance along the robot body. A confidence-gating mechanism integrates prior kinematic knowledge, allowing the controller to adaptively balance model-based and learned components for improved convergence and fidelity. The framework is validated on a five-segment planar hyper-redundant robot under three representative shape configurations. Experimental results demonstrate that the proposed method consistently outperforms both analytical and purely neural controllers. In complex scenarios, it reduces steady-state error by up to 75.5% against the analytical model, and accelerates convergence by up to 20.5% compared to the data-driven baseline. Furthermore, gating analysis reveals a state-dependent authority fusion, shifting toward data-driven predictions in unstable states, while relying on physical priors in the remaining cases. Finally, we demonstrate robust performance in a dynamic task where the robot maintains a fixed end-effector position while avoiding moving obstacles, achieving a precise tip-positioning accuracy with a mean error of 10.47 mm.
Motion Forcing: A Decoupled Framework for Robust Video Generation in Motion Dynamics
Venue: arXiv cs.CV 2026
Year: 2026

The ultimate goal of video generation is to satisfy a fundamental trilemma: achieving high visual quality, maintaining rigorous physical consistency, and enabling precise controllability. While recent models can maintain this balance in simple, isolated scenarios, we observe that this equilibrium is fragile and often breaks down as scene complexity increases (e.g., involving collisions or dense traffic). To address this, we introduce \textbf{Motion Forcing}, a framework designed to stabilize this trilemma even in complex generative tasks. Our key insight is to explicitly decouple physical reasoning from visual synthesis via a hierarchical \textbf{``Point-Shape-Appearance''} paradigm. This approach decomposes generation into verifiable stages: modeling complex dynamics as sparse geometric anchors (\textbf{Point}), expanding them into dynamic depth maps that explicitly resolve 3D geometry (\textbf{Shape}), and finally rendering high-fidelity textures (\textbf{Appearance}). Furthermore, to foster robust physical understanding, we employ a \textbf{Masked Point Recovery} strategy. By randomly masking input anchors during training and enforcing the reconstruction of complete dynamic depth, the model is compelled to move beyond passive pattern matching and learn latent physical laws (e.g., inertia) to infer missing trajectories. Extensive experiments on autonomous driving benchmarks show that Motion Forcing significantly outperforms state-of-the-art baselines, maintaining trilemma stability across complex scenes. Evaluations on physics and robotics further confirm our framework's generality.
World2Act: Latent Action Post-Training via Skill-Compositional World Models
Venue: arXiv cs.CV 2026
Year: 2026

World Models (WMs) have emerged as a promising approach for post-training Vision-Language-Action (VLA) policies to improve robustness and generalization under environmental changes. However, most WM-based post-training methods rely on pixel-space supervision, making policies sensitive to pixel-level artifacts and hallucination from imperfect WM rollouts. We introduce World2Act, a post-training framework that aligns VLA actions directly with WM video-dynamics latents using a contrastive matching objective, reducing dependence on pixels. Post-training performance is tied to rollout quality, yet current WMs struggle with arbitrary-length video generation as they are mostly trained on fixed-length clips while robotic execution durations vary widely. To address this, we propose an automatic LLM-based skill-decomposition pipeline that segments high-level instructions into low-level prompts. Our pipeline produces RoboCasa-Skill and LIBERO-Skill, supporting skill-compositional WMs that remain temporally consistent across diverse task horizons. Empirically, applying World2Act to VLAs like GR00T-N1.6 and Cosmos Policy achieves state-of-the-art results on RoboCasa and LIBERO, and improves real-world performance by 6.7%, enhancing embodied agent generalization.
COHORT: Hybrid RL for Collaborative Large DNN Inference on Multi-Robot Systems Under Real-Time Constraints
Venue: arXiv cs.RO 2026
Year: 2026

Large deep neural networks (DNNs), especially transformer-based and multimodal architectures, are computationally demanding and challenging to deploy on resource-constrained edge platforms like field robots. These challenges intensify in mission-critical scenarios (e.g., disaster response), where robots must collaborate under tight constraints on bandwidth, latency, and battery life, often without infrastructure or server support. To address these limitations, we present COHORT, a collaborative DNN inference and task-execution framework for multi-robot systems built on the Robotic Operating System (ROS). COHORT employs a hybrid offline-online reinforcement learning (RL) strategy to dynamically schedule and distribute DNN module execution across robots. Our key contributions are threefold: (a) Offline RL policy learning combined with Advantage-Weighted Regression (AWR), trained on auction-based task allocation data from heterogeneous DNN workloads across distributed robots, (b) Online policy adaptation via Multi-Agent PPO (MAPPO), initialized from the offline policy and fine-tuned in real time, and (c) comprehensive evaluation of COHORT on vision-language model (VLM) inference tasks such as CLIP and SAM, analyzing scalability with increasing robot/workload and robustness under . We benchmark COHORT against genetic algorithms and multiple RL baselines. Experimental results demonstrate that COHORT reduces battery consumption by 15.4% and increases GPU utilization by 51.67%, while satisfying frame-rate and deadline constraints 2.55 times of the time.