OpenRaiser/Intern-Atlas huggingface dataset:
Prototype-Based Knowledge Guidance for Fine-Grained Structured Radiology Reporting
Venue: arXiv cs.AI 2026
Year: 2026

Structured radiology reporting promises faster, more consistent communication than free text, but automation remains difficult as models must make many fine-grained, discrete decisions about rare findings and attributes from limited structured supervision. In contrast, free-text reports are produced at scale in routine care and implicitly encode fine-grained, image-linked information through detailed descriptions. To leverage this unstructured knowledge, we propose ProtoSR, an approach for injecting free-text information into structured report population. First, we introduce an automatic extraction pipeline that uses an instruction-tuned LLM to mine 80k+ MIMIC-CXR studies and build a multimodal knowledge base aligned with a structured reporting template, representing each answer option with a visual prototype. Using this knowledge base, ProtoSR is trained to retrieve prototypes relevant for the current image-question pair and augment the model predictions through a prototype-conditioned residual, providing a data-driven second opinion that selectively corrects predictions. On the Rad-ReStruct benchmark, ProtoSR achieves state-of-the-art results, with the largest improvements on detailed attribute questions, demonstrating the value of integrating free-text derived signal for fine-grained image understanding.
Exhaustive Circuit Mapping of a Single-Cell Foundation Model Reveals Massive Redundancy, Heavy-Tailed Hub Architecture, and Layer-Dependent Differentiation Control
Venue: arXiv cs.LG 2026
Year: 2026

Mechanistic interpretability of biological foundation models has relied on selective feature sampling, pairwise interaction testing, and observational trajectory analysis. Each of these can introduce systematic bias. Here we present three experiments that address these limitations through exhaustive circuit tracing, higher order combinatorial ablation, and causal trajectory steering in Geneformer, a transformer based single cell foundation model. First, exhaustive tracing of all 4065 active sparse autoencoder features at layer 5 yields 1393850 significant downstream edges, a 27 fold expansion over selective sampling. This reveals a heavy tailed hub distribution in which 1.8 percent of features account for disproportionate connectivity and 40 percent of the top 20 hubs lack biological annotation. These results indicate systematic annotation bias in prior selective analyses. Second, three way combinatorial ablation across 8 feature triplets shows that redundancy deepens monotonically with interaction order, with a three way ratio of 0.59 versus a pairwise ratio of 0.74, and with zero synergy. This confirms that the model architecture is subadditive at all tested orders. Third, trajectory guided feature steering establishes a causal link between layer position and differentiation directionality. Late layer features at L17 consistently push cell states toward maturity, with fraction positive equal to 1.0. Early and mid layer features at L0 and L11 mostly push away from maturity, with fraction positive ranging from 0.00 to 0.58. Together these results move from correlation toward causal evidence for layer dependent control of cell state.
Learning Transferable Sensor Models via Language-Informed Pretraining
Venue: arXiv cs.AI 2026
Year: 2026

Modern sensing systems generate large volumes of unlabeled multivariate time-series data. This abundance of unlabeled data makes self-supervised learning (SSL) a natural approach for learning transferable representations. However, most existing approaches are optimized for reconstruction or forecasting objectives and often fail to capture the semantic structure required for downstream classification and reasoning tasks. While recent sensor-language alignment methods improve semantic generalization through captioning and zero-shot transfer, they are limited to fixed sensor configurations, such as predefined channel sets, signal lengths, or temporal resolutions, which hinders cross-domain applicability. To address these gaps, we introduce \textbf{SLIP} (\textbf{S}ensor \textbf{L}anguage-\textbf{I}nformed \textbf{P}retraining), an open-source framework for learning language-aligned representations that generalize across diverse sensor setups. SLIP integrates contrastive alignment with sensor-conditioned captioning, facilitating both discriminative understanding and generative reasoning. By repurposing a pretrained decoder-only language model via cross-attention and introducing an elegant, flexible patch-embedder, SLIP supports different temporal resolutions and variable-length input at inference time without additional retraining. Across 11 datasets, SLIP demonstrates superior performance in zero-shot transfer, signal captioning, and question answering. It achieves a 77.14% average linear-probing accuracy, a 5.93% relative improvement over strong baselines, and reaches 64.83% accuracy in sensor-based question answering.
Preliminary analysis of RGB-NIR Image Registration techniques for off-road forestry environments
Venue: arXiv cs.CV 2026
Year: 2026

RGB-NIR image registration plays an important role in sensor-fusion, image enhancement and off-road autonomy. In this work, we evaluate both classical and Deep Learning (DL) based image registration techniques to access their suitability for off-road forestry applications. NeMAR, trained under 6 different configurations, demonstrates partial success however, its GAN loss instability suggests challenges in preserving geometric consistency. MURF, when tested on off-road forestry data shows promising large scale feature alignment during shared information extraction but struggles with fine details in dense vegetation. Even though this is just a preliminary evaluation, our study necessitates further refinements for robust, multi-scale registration for off-road forest applications.
Design Exploration of Lightweight Interactions for Awareness-Supporting Technologies in Hybrid Work
Venue: arXiv cs.HC 2026
Year: 2026

Hybrid work settings often lack the informal communication that naturally emerges from spontaneous encounters and ambient awareness of coworkers' activities, potentially hindering team collaboration. To address this challenge, we explored how lightweight interactions can be integrated into awareness-supporting technologies for fostering informal communication. Our experiential design approach focused on how information is perceived and processed rather than explicit content exchange. Through brainstorming, speculating, and prototyping, we explored the design space for small hybrid teams. By annotating and analyzing design concepts, speculative scenarios, and prototypes, we developed a framework that identified design options for lightweight interactions and methods for integrating them with information displays.
Deep Learning-Based Metamodeling of Nonlinear Stochastic Dynamic Systems under Parametric and Predictive Uncertainty
Venue: arXiv cs.LG 2026
Year: 2026

Modeling high-dimensional, nonlinear dynamic structural systems under natural hazards presents formidable computational challenges, especially when simultaneously accounting for uncertainties in external loads and structural parameters. Studies have successfully incorporated uncertainties related to external loads from natural hazards, but few have simultaneously addressed loading and parameter uncertainties within structural systems while accounting for prediction uncertainty of neural networks. To address these gaps, three metamodeling frameworks were formulated, each coupling a feature-extraction module implemented through a multi-layer perceptron (MLP), a message-passing neural network (MPNN), or an autoencoder (AE) with a long short-term memory (LSTM) network using Monte Carlo dropout and a negative log-likelihood loss. The resulting architectures (MLP-LSTM, MPNN-LSTM, and AE-LSTM) were validated on two case studies: a multi-degree-of-freedom Bouc-Wen system and a 37-story fiber-discretized nonlinear steel moment-resisting frame, both subjected to stochastic seismic excitation and structural parameter uncertainty. All three approaches achieved low prediction errors: the MLP-LSTM yielded the most accurate results for the lower-dimensional Bouc-Wen system, whereas the MPNN-LSTM and AE-LSTM provided superior performance on the more complex steel-frame model. Moreover, a consistent correlation between predictive variance and actual error confirms the suitability of these frameworks for active-learning strategies and for assessing model confidence in structural response predictions.
Sim-to-reality adaptation for Deep Reinforcement Learning applied to an underwater docking application
Venue: arXiv cs.RO 2026
Year: 2026

Deep Reinforcement Learning (DRL) offers a robust alternative to traditional control methods for autonomous underwater docking, particularly in adapting to unpredictable environmental conditions. However, bridging the "sim-to-real" gap and managing high training latencies remain significant bottlenecks for practical deployment. This paper presents a systematic approach for autonomous docking using the Girona Autonomous Underwater Vehicle (AUV) by leveraging a high-fidelity digital twin environment. We adapted the Stonefish simulator into a multiprocessing RL framework to significantly accelerate the learning process while incorporating realistic AUV dynamics, collision models, and sensor noise. Using the Proximal Policy Optimization (PPO) algorithm, we developed a 6-DoF control policy trained in a headless environment with randomized starting positions to ensure generalized performance. Our reward structure accounts for distance, orientation, action smoothness, and adaptive collision penalties to facilitate soft docking. Experimental results demonstrate that the agent achieved a success rate of over 90% in simulation. Furthermore, successful validation in a physical test tank confirmed the efficacy of the sim-to-reality adaptation, with the DRL controller exhibiting emergent behaviors such as pitch-based braking and yaw oscillations to assist in mechanical alignment.
HPC Containers for EBRAINS: Towards Portable Cross-Domain Software Environment
Venue: arXiv cs.DC 2026
Year: 2026

Deploying complex, distributed scientific workflows across diverse HPC sites is often hindered by site-specific dependencies and complex build environments. This paper investigates the design and performance of portable HPC container images capable of encapsulating MPI- and CUDA-enabled software stacks without sacrificing bare-metal performance. This work is part of recent work performed within the EBRAINS Research Infrastructure, to evaluate the implementation of portable HPC (Apptainer-based) container images targeting the EBRAINS Software Distribution (ESD) -- a Spack-based software ecosystem comprising approximately 80 top-level packages (and 800 dependencies). We evaluate a hybrid, PMIx-based containerization strategy using Apptainer that seamlessly bypasses the need for site-specific builds by dynamically leveraging host-level specialized hardware, such as network interfaces and GPUs, on two production HPC clusters: Karolina and Jureca-DC. We demonstrate the feasibility of building portable, MPI- and CUDA-enabled scientific software into container images that correctly leverage site-installed drivers and hardware to reproduce bare-metal communication behavior. Using communication microbenchmarks (e.g., OSU and NCCL) alongside performance metrics of applications from neuroscience, we measure and verify their performance against bare-metal deployments. Crucially, our verification approach extends beyond top-level runtime measurements; we highlight the analysis of underlying debug logs to actively detect misbehavior and misconfigurations, such as suboptimal transport pathways. Ultimately, this investigation demonstrates the feasibility of a simple and reproducible methodology for decoupling software environments from underlying infrastructures, paving the way for automated pipelines that ensure optimized, performance-verified execution across varied HPC architectures.
Chemical Reaction Networks Learn Better than Spiking Neural Networks
Venue: arXiv cs.LG 2026
Year: 2026

We mathematically prove that chemical reaction networks without hidden layers can solve tasks for which spiking neural networks require hidden layers. Our proof uses the deterministic mass-action kinetics formulation of chemical reaction networks. Specifically, we prove that a certain reaction network without hidden layers can learn a classification task previously proved to be achievable by a spiking neural network with hidden layers. We provide analytical regret bounds for the global behavior of the network and analyze its asymptotic behavior and Vapnik-Chervonenkis dimension. In a numerical experiment, we confirm the learning capacity of the proposed chemical reaction network for classifying handwritten digits in pixel images, and we show that it solves the task more accurately and efficiently than a spiking neural network with hidden layers. This provides a motivation for machine learning in chemical computers and a mathematical explanation for how biological cells might exhibit more efficient learning behavior within biochemical reaction networks than neuronal networks.
NBAvatar: Neural Billboards Avatars with Realistic Hand-Face Interaction
Venue: arXiv cs.CV 2026
Year: 2026

We present NBAvatar - a method for realistic rendering of head avatars handling non-rigid deformations caused by hand-face interaction. We introduce a novel representation for animated avatars by combining the training of oriented planar primitives with neural rendering. Such a combination of explicit and implicit representations enables NBAvatar to handle temporally and pose-consistent geometry, along with fine-grained appearance details provided by the neural rendering technique. In our experiments, we demonstrate that NBAvatar implicitly learns color transformations caused by face-hand interactions and surpasses existing approaches in terms of novel-view and novel-pose rendering quality. Specifically, NBAvatar achieves up to 30% LPIPS reduction under high-resolution megapixel rendering compared to Gaussian-based avatar methods, while also improving PSNR and SSIM, and achieves higher structural similarity compared to the state-of-the-art hand-face interaction method InteractAvatar.
A Multi-Label Temporal Convolutional Framework for Transcription Factor Binding Characterization
Venue: arXiv cs.LG 2026
Year: 2026

Transcription factors (TFs) regulate gene expression through complex and co-operative mechanisms. While many TFs act together, the logic underlying TFs binding and their interactions is not fully understood yet. Most current approaches for TF binding site prediction focus on individual TFs and binary classification tasks, without a full analysis of the possible interactions among various TFs. In this paper we investigate DNA TF binding site recognition as a multi-label classification problem, achieving reliable predictions for multiple TFs on DNA sequences retrieved in public repositories. Our deep learning models are based on Temporal Convolutional Networks (TCNs), which are able to predict multiple TF binding profiles, capturing correlations among TFs andtheir cooperative regulatory mechanisms. Our results suggest that multi-label learning leading to reliable predictive performances can reveal biologically meaningful motifs and co-binding patterns consistent with known TF interactions, while also suggesting novel relationships and cooperation among TFs.
Decentralized Cooperative Localization for Multi-Robot Systems with Asynchronous Sensor Fusion
Venue: arXiv cs.RO 2026
Year: 2026

Decentralized cooperative localization (DCL) is a promising approach for nonholonomic mobile robots operating in GPS-denied environments with limited communication infrastructure. This paper presents a DCL framework in which each robot performs localization locally using an Extended Kalman Filter, while sharing measurement information during update stages only when communication links are available and companion robots are successfully detected by LiDAR. The framework preserves cross-correlation consistency among robot state estimates while handling asynchronous sensor data with heterogeneous sampling rates and accommodating accelerations during dynamic maneuvers. Unlike methods that require pre-aligned coordinate systems, the proposed approach allows robots to initialize with arbitrary reference-frame orientations and achieves automatic alignment through transformation matrices in both the prediction and update stages. To improve robustness in feature-sparse environments, we introduce a dual-landmark evaluation framework that exploits both static environmental features and mobile robots as dynamic landmarks. The proposed framework enables reliable detection and feature extraction during sharp turns, while prediction accuracy is improved through information sharing from mutual observations. Experimental results in both Gazebo simulation and real-world basement environments show that DCL outperforms centralized cooperative localization (CCL), achieving a 34% reduction in RMSE, while the dual-landmark variant yields an improvement of 56%. These results demonstrate the applicability of DCL to challenging domains such as enclosed spaces, underwater environments, and feature-sparse terrains where conventional localization methods are ineffective.
Towards Dynamic Model Identification and Gravity Compensation for the dVRK-Si Patient Side Manipulator
Venue: arXiv cs.RO 2026
Year: 2026

The da Vinci Research Kit (dVRK) is widely used for research in robot-assisted surgery, but most modeling and control methods target the first-generation dVRK Classic. The recently introduced dVRK-Si, built from da Vinci Si hardware, features a redesigned Patient Side Manipulator (PSM) with substantially larger gravity loading, which can degrade control if unmodeled. This paper presents the first complete kinematic and dynamic modeling framework for the dVRK-Si PSM. We derive a modified DH kinematic model that captures the closed-chain parallelogram mechanism, formulate dynamics via the Euler-Lagrange method, and express inverse dynamics in a linear-in-parameters regressor form. Dynamic parameters are identified from data collected on a periodic excitation trajectory optimized for numerical conditioning and estimated by convex optimization with physical feasibility constraints. Using the identified model, we implement real-time gravity compensation and computed-torque feedforward in the dVRK control stack. Experiments on a physical dVRK-Si show that the gravity compensation reduces steady-state joint errors by 68-84% and decreases end-effector tip drift during static holds from 4.2 mm to 0.7 mm. Computed-torque feedforward further improves transient and position tracking accuracy. For sinusoidal trajectory tracking, computed-torque feedforward reduces position errors by 35% versus gravity-only feedforward and by 40% versus PID-only. The proposed pipeline supports reliable control, high-fidelity simulation, and learning-based automation on the dVRK-Si.
To Words and Beyond: Probing Large Language Models for Sentence-Level Psycholinguistic Norms of Memorability and Reading Times
Venue: arXiv cs.CL 2026
Year: 2026

Large Language Models (LLMs) have recently been shown to produce estimates of psycholinguistic norms, such as valence, arousal, or concreteness, for words and multiword expressions, that correlate with human judgments. These estimates are obtained by prompting an LLM, in zero-shot fashion, with a question similar to those used in human studies. Meanwhile, for other norms such as lexical decision time or age of acquisition, LLMs require supervised fine-tuning to obtain results that align with ground-truth values. In this paper, we extend this approach to the previously unstudied features of sentence memorability and reading times, which involve the relationship between multiple words in a sentence-level context. Our results show that via fine-tuning, models can provide estimates that correlate with human-derived norms and exceed the predictive power of interpretable baseline predictors, demonstrating that LLMs contain useful information about sentence-level features. At the same time, our results show very mixed zero-shot and few-shot performance, providing further evidence that care is needed when using LLM-prompting as a proxy for human cognitive measures.
On Information Self-Locking in Reinforcement Learning for Active Reasoning of LLM agents
Venue: arXiv cs.AI 2026
Year: 2026

Reinforcement learning (RL) with outcome-based rewards has achieved significant success in training large language model (LLM) agents for complex reasoning tasks. However, in active reasoning where agents need to strategically ask questions to acquire task-relevant information, we find that LLM agents trained with RL often suffer from information self-locking: the agent ceases to ask informative questions and struggles to internalize already-obtained information. To understand the phenomenon, we decompose active reasoning into two core capabilities: Action Selection (AS), which determines the observation stream through queries, and Belief Tracking (BT), which updates the agent's belief based on collected evidence. We show that deficient AS and BT capabilities will limit the information exploration during RL training. Furthermore, insufficient exploration in turn hinders the improvement of AS and BT, creating a feedback loop that locks the agent in a low-information regime. To resolve the issue, we propose a simple yet effective approach that reallocates the learning signal by injecting easy- to-obtain directional critiques to help the agent escape self-locking. Extensive experiments with 7 datasets show that our approach significantly mitigates the information self-locking, bringing up to 60% improvements.
TopoBench: Benchmarking LLMs on Hard Topological Reasoning
Venue: arXiv cs.AI 2026
Year: 2026

Solving topological grid puzzles requires reasoning over global spatial invariants such as connectivity, loop closure, and region symmetry and remains challenging for even the most powerful large language models (LLMs). To study these abilities under controlled settings, we introduce TopoBench, a benchmark of six puzzle families across three difficulty levels. We evaluate strong reasoning LLMs on TopoBench and find that even frontier models solve fewer than one quarter of hard instances, with two families nearly unsolved. To investigate whether these failures stem from reasoning limitations or from difficulty extracting and maintaining spatial constraints, we annotate 750 chain of thought traces with an error taxonomy that surfaces four candidate causal failure modes, then test them with targeted interventions simulating each error type. These interventions show that certain error patterns like premature commitment and constraint forgetting have a direct impact on the ability to solve the puzzle, while repeated reasoning is a benign effect of search. Finally we study mitigation strategies including prompt guidance, cell-aligned grid representations and tool-based constraint checking, finding that the bottleneck lies in extracting constraints from spatial representations and not in reasoning over them. Code and data are available at github.com/mayug/topobench-benchmark.