OpenRaiser/Intern-Atlas huggingface dataset:
A medical coding language model trained on clinical narratives from a population-wide cohort of 1.8 million patients
Venue: arXiv cs.LG 2026
Year: 2026

Medical coding translates clinical documentation into standardized codes for billing, research, and public health, but manual coding is time-consuming and error-prone. Existing automation efforts rely on small datasets that poorly represent real-world patient heterogeneity. We trained a language model on 5.8 million electronic health records from 1.8 million patients across nearly all specialties in Eastern Denmark (2006--2016) to predict ICD-10 codes from clinical notes, medications, and laboratory results. Evaluated on 270,000 held-out patients, the model achieved a micro F1 of 71.8% and a top-10 recall of 95.5%. Performance varied by specialty (F1: 53--91%), with higher scores in specialties with well-defined diagnostic criteria. Codes appearing predominantly as secondary diagnoses had markedly lower F1 scores. For three such codes (suicide-related behaviors, weight disorders, and hypertension), the model identified thousands of uncoded cases, of which 76-86% were confirmed valid upon manual review, suggesting systematic under-coding rather than model error. These findings suggest under-coding of secondary diagnoses in Eastern Denmark during this period, with potential implications for epidemiological research, public health surveillance, and understanding of multimorbidity. Similar time constraints and reimbursement structures in other healthcare systems suggest this may not be isolated to this dataset. The model can automate coding for approximately 50% of cases and provide accurate suggestions for most others, and may offer a practical solution to help capture missed secondary conditions.
Pretty Good Measurement for Radiomics: A Quantum-Inspired Multi-Class Classifier for Lung Cancer Subtyping and Prostate Cancer Risk Stratification
Venue: arXiv cs.CV 2026
Year: 2026

We investigate a quantum-inspired approach to supervised multi-class classification based on the \emph{Pretty Good Measurement} (PGM), viewed as an operator-valued decision rule derived from quantum state discrimination. The method associates each class with an encoded mixed state and performs classification through a single POVM construction, thus providing a genuinely multi-class strategy without reduction to pairwise or one-vs-rest schemes. In this perspective, classification is reformulated as the discrimination of a finite ensemble of class-dependent density operators, with performance governed by the geometry induced by the encoding map and by the overlap structure among classes. To assess the practical scope of this framework, we apply the PGM-based classifier to two biomedical radiomics case studies: histopathological subtyping of non-small-cell lung carcinoma (NSCLC) and prostate cancer (PCa) risk stratification. The evaluation is conducted under protocols aligned with previously reported radiomics studies, enabling direct comparison with established classical baselines. The results show that the PGM-based classifier is consistently competitive and, in several settings, improves upon standard methods. In particular, the method performs especially well in the NSCLC binary and three-class tasks, while remaining competitive in the four-class case, where increased class overlap yields a more demanding discrimination geometry. In the PCa study, the PGM classifier remains close to the strongest ensemble baseline and exhibits clinically relevant sensitivity--specificity trade-offs across feature-selection scenarios.
CoPeP: Benchmarking Continual Pretraining for Protein Language Models
Venue: arXiv cs.LG 2026
Year: 2026

Protein language models (pLMs) have recently gained significant attention for their ability to uncover relationships between sequence, structure, and function from evolutionary statistics, thereby accelerating therapeutic drug discovery. These models learn from large protein databases that are continuously updated by the biology community and whose dynamic nature motivates the application of continual learning, not only to keep up with the ever-growing data, but also as an opportunity to take advantage of the temporal meta-information that is created during this process. As a result, we introduce the Continual Pretraining of Protein Language Models (CoPeP) benchmark, a novel benchmark for evaluating continual learning approaches on pLMs. Specifically, we curate a sequence of protein datasets derived from the UniProt Knowledgebase spanning a decade and define metrics to assess pLM performance across 31 protein understanding tasks. We evaluate several methods from the continual learning literature, including replay, unlearning, and plasticity-based methods, some of which have never been applied to models and data of this scale. Our findings reveal that incorporating temporal meta-information improves perplexity by up to 7% even when compared to training on data from all tasks jointly. Moreover, even at scale, several continual learning methods outperform naive continual pretraining. The CoPeP benchmark offers an exciting opportunity to study these methods at scale in an impactful real-world application.
Seeking Necessary and Sufficient Information from Multimodal Medical Data
Venue: arXiv cs.CV 2026
Year: 2026

Learning multimodal representations from medical images and other data sources can provide richer information for decision-making. While various multimodal models have been developed for this, they overlook learning features that are both necessary (must be present for the outcome to occur) and sufficient (enough to determine the outcome). We argue learning such features is crucial as they can improve model performance by capturing essential predictive information, and enhance model robustness to missing modalities as each modality can provide adequate predictive signals. Such features can be learned by leveraging the Probability of Necessity and Sufficiency (PNS) as a learning objective, an approach that has proven effective in unimodal settings. However, extending PNS to multimodal scenarios remains underexplored and is non-trivial as key conditions of PNS estimation are violated. We address this by decomposing multimodal representations into modality-invariant and modality-specific components, then deriving tractable PNS objectives for each. Experiments on synthetic and real-world medical datasets demonstrate our method's effectiveness. Code will be available on GitHub.
Ray Tracing using HIP
Venue: arXiv cs.GR 2026
Year: 2026

In this technical report, we introduce the basics of ray tracing and explain how to accelerate the computation of the rendering algorithm in HIP. We also show how to use a HIP ray tracing framework - HIPRT, leveraging hardware ray tracing features of AMD GPUs. We conclude this technical report with a list of references for further reading.
Stepwise Penalization for Length-Efficient Chain-of-Thought Reasoning
Venue: arXiv cs.CL 2026
Year: 2026

Large reasoning models improve with more test-time computation, but often overthink, producing unnecessarily long chains-of-thought that raise cost without improving accuracy. Prior reinforcement learning approaches typically rely on a single outcome reward with trajectory-level length penalties, which cannot distinguish essential from redundant reasoning steps and therefore yield blunt compression. Although recent work incorporates step-level signals, such as offline pruning, supervised data construction, or verifier-based intermediate rewards, reasoning length is rarely treated as an explicit step-level optimization objective during RL. We propose Step-wise Adaptive Penalization (SWAP), a fine-grained framework that allocates length reduction across steps based on intrinsic contribution. We estimate step importance from the model's on-policy log-probability improvement toward the correct answer, then treat excess length as a penalty mass redistributed to penalize low-importance steps more heavily while preserving high-importance reasoning. We optimize with a unified outcome-process advantage within group-relative policy optimization. Extensive experiments demonstrate that SWAP reduces reasoning length by 64.3% on average while improving accuracy by 5.7% relative to the base model.
When does Chain-of-Thought Help: A Markovian Perspective
Venue: arXiv cs.LG 2026
Year: 2026

Chain-of-Thought (CoT) prompting is a widely used inference-time technique for improving reasoning, yet its gains are uneven across tasks. We analyze when and why CoT helps by modeling the step-wise reasoning trajectory as a Markov chain. Each intermediate step is a state and the dependence between steps is captured by a transition kernel. Our theory identifies transition alignment, whether instances share a common step-wise transition kernel, as the key determinant of CoT's effectiveness. When transitions are identical across steps, CoT reduces inference-time sample complexity: fewer context sample trajectories suffice to recover the final decision. In contrast, when transitions differ across steps, these gains can vanish. We further quantify how noise in intermediate steps modulates CoT's benefit. Beyond theory, we design synthetic benchmarks that isolate these factors to complement prior results on real-world tasks and to empirically validate our predictions.
DIG to Heal: Scaling General-purpose Agent Collaboration via Explainable Dynamic Decision Paths
Venue: arXiv cs.AI 2026
Year: 2026

The increasingly popular agentic AI paradigm promises to harness the power of multiple, general-purpose large language model (LLM) agents to collaboratively complete complex tasks. While many agentic AI systems utilize predefined workflows or agent roles in order to reduce complexity, ideally these agents would be truly autonomous, able to achieve emergent collaboration even as the number of collaborating agents increases. Yet in practice, such unstructured interactions can lead to redundant work and cascading failures that are difficult to interpret or correct. In this work, we study multi-agent systems composed of general-purpose LLM agents that operate without predefined roles, control flow, or communication constraints, relying instead on emergent collaboration to solve problems. We introduce the Dynamic Interaction Graph (DIG), which captures emergent collaboration as a time-evolving causal network of agent activations and interactions. DIG makes emergent collaboration observable and explainable for the first time, enabling real-time identification, explanation, and correction of collaboration-induced error patterns directly from agents' collaboration paths. Thus, DIG fills a critical gap in understanding how general LLM agents solve problems together in truly agentic multi-agent systems. The project webpage can be found at: https://happyeureka.github.io/dig.
Geometric Look-Angle Shaping Strategy for Enclosed Inspection
Venue: arXiv cs.RO 2026
Year: 2026

This paper introduces inspection through GLASS, a Geometric Look-Angle Shaping Strategy for enclosed regions using unmanned aerial vehicles. In doing so, the vehicles guidance command is constructed through a bounded, geometry-consistent shaping of the look angle relative to a desired standoff path. By embedding a smooth, hyperbolic-tangent-type shaping function within a polar geometric framework, GLASS ensures global existence of the guidance dynamics. It avoids the far-field limitations inherent to conventional formulations. Lyapunov stability analysis establishes asymptotic convergence to a prescribed inspection standoff under explicit curvature feasibility conditions, along with analytical settling-time characteristics. The proposed strategy incorporates maximum turn-rate constraints without inducing singularities throughout the workspace. High-fidelity six-degree-of-freedom quadrotor simulations demonstrate the effectiveness of GLASS in representative enclosed inspection scenarios, highlighting a practically viable guidance framework for autonomous enclosed inspection missions.
Detecting Transportation Mode Using Dense Smartphone GPS Trajectories and Transformer Models
Venue: arXiv cs.LG 2026
Year: 2026

Transportation mode detection is an important topic within GeoAI and transportation research. In this study, we introduce SpeedTransformer, a novel Transformer-based model that relies solely on speed inputs to infer transportation modes from dense smartphone GPS trajectories. In benchmark experiments, SpeedTransformer outperformed traditional deep learning models, such as the Long Short-Term Memory (LSTM) network. Moreover, the model demonstrated strong flexibility in transfer learning, achieving high accuracy across geographical regions after fine-tuning with small datasets. Finally, we deployed the model in a real-world experiment, where it consistently outperformed baseline models under complex built environments and high data uncertainty. These findings suggest that Transformer architectures, when combined with dense GPS trajectories, hold substantial potential for advancing transportation mode detection and broader mobility-related research.
Acoustic Sensing for Universal Jamming Grippers
Venue: arXiv cs.RO 2026
Year: 2026

Universal jamming grippers excel at grasping unknown objects due to their compliant bodies. Traditional tactile sensors can compromise this compliance, reducing grasping performance. We present acoustic sensing as a form of morphological sensing, where the gripper's soft body itself becomes the sensor. A speaker and microphone are placed inside the gripper cavity, away from the deformable membrane, fully preserving compliance. Sound propagates through the gripper and object, encoding object properties, which are then reconstructed via machine learning. Our sensor achieves high spatial resolution in sensing object size (2.6 mm error) and orientation (0.6 deg error), remains robust to external noise levels of 80 dBA, and discriminates object materials (up to 100% accuracy) and 16 everyday objects (85.6% accuracy). We validate the sensor in a realistic tactile object sorting task, achieving 53 minutes of uninterrupted grasping and sensing, confirming the preserved grasping performance. Finally, we demonstrate that disentangled acoustic representations can be learned, improving robustness to irrelevant acoustic variations.
How Large Language Models Get Stuck: Early structure with persistent errors
Venue: arXiv cs.CL 2026
Year: 2026

Linguistic insights may help make Large Language Model (LLM) training more efficient. We trained Meta's OPT model on the 100M word BabyLM dataset, and evaluated it on the BLiMP benchmark, which consists of 67 classes, each defined by sentence pairs that differ in a targeted syntactic or semantic rule violation. We tested the model's preference for grammatical over ungrammatical sentences across training iterations and grammatical types. In nearly one-third of the BLiMP classes, OPT fails to consistently assign a higher likelihood to grammatical sentences, even after extensive training. When it fails, it often establishes a clear (erroneous) separation of the likelihoods at an early stage of processing and sustains this to the end of our training phase. We hypothesize that this mis-categorization is costly because it creates entrenched biases that must, eventually, be reversed in order for the model to perform well. We probe this phenomenon using a mixture of qualitative (based on linguistic theory and the theory of Deep Learning) and quantitative (based on numerical testing) assessments. Our qualitative assessments indicate that only some BLiMP tests are meaningful guides. We conclude by articulating a hypothesis, the Bigram Hypothesis, which claims that the learning process will exhibit erroneous entrenchment if bigram statistics bias the model toward wrong distinctions early in training, and we describe a method of testing the hypothesis on appropriately selected BLiMP classes.
Conservative Equilibrium Discovery in Offline Game-Theoretic Multiagent Reinforcement Learning
Venue: arXiv cs.AI 2026
Year: 2026

Offline learning of strategies takes data efficiency to its extreme by restricting algorithms to a fixed dataset of state-action trajectories. We consider the problem in a mixed-motive multiagent setting, where the goal is to solve a game under the offline learning constraint. We first frame this problem in terms of selecting among candidate equilibria. Since datasets may inform only a small fraction of game dynamics, it is generally infeasible in offline game-solving to even verify a proposed solution is a true equilibrium. Therefore, we consider the relative probability of low regret (i.e., closeness to equilibrium) across candidates based on the information available. Specifically, we extend Policy Space Response Oracles (PSRO), an online game-solving approach, by quantifying game dynamics uncertainty and modifying the RL objective to skew towards solutions more likely to have low regret in the true game. We further propose a novel meta-strategy solver, tailored for the offline setting, to guide strategy exploration in PSRO. Our incorporation of Conservatism principles from Offline reinforcement learning approaches for strategy Exploration gives our approach its name: COffeE-PSRO. Experiments demonstrate COffeE-PSRO's ability to extract lower-regret solutions than state-of-the-art offline approaches and reveal relationships between algorithmic components empirical game fidelity, and overall performance.
DiffSOS: Acoustic Conditional Diffusion Model for Speed-of-Sound Reconstruction in Ultrasound Computed Tomography
Venue: arXiv cs.CV 2026
Year: 2026

Accurate Speed-of-Sound (SoS) reconstruction from acoustic waveforms is a cornerstone of ultrasound computed tomography (USCT), enabling quantitative velocity mapping that reveals subtle anatomical details and pathological variations often invisible in conventional imaging. However, practical utility is hindered by the limitations of existing algorithms; traditional Full Waveform Inversion (FWI) is computationally intensive, while current deep learning approaches tend to produce oversmoothed results lacking fine details. We propose DiffSOS, a conditional diffusion model that directly maps acoustic waveforms to SoS maps. Our framework employs a specialized acoustic ControlNet to strictly ground the denoising process in physical wave measurements. To ensure structural consistency, we optimize a hybrid loss function that integrates noise prediction, spatial reconstruction, and noise frequency content. To accelerate inference, we employ stochastic Denoising Diffusion Implicit Model (DDIM) sampling, achieving near real-time reconstruction with only 10 steps. Crucially, we exploit the stochastic generative nature of our framework to estimate pixel-wise uncertainty, providing a measure of reliability that is often absent in deterministic approaches. Evaluated on the OpenPros USCT benchmark, DiffSOS significantly outperforms state-of-the-art networks, achieving an average Multi-scale Structural Similarity of 0.957. Our approach provides high-fidelity SoS maps with a principled measure of confidence, facilitating safer and faster clinical interpretation.
PointAlign: Feature-Level Alignment Regularization for 3D Vision-Language Models
Venue: arXiv cs.CV 2026
Year: 2026

The development of 3D Vision-Language Models (VLMs), crucial for applications in robotics, autonomous driving, and augmented reality, is severely constrained by the scarcity of paired 3D-text data. Existing methods rely solely on next-token prediction loss, using only language tokens for supervision. This results in inefficient utilization of limited 3D data and leads to a significant degradation and loss of valuable geometric information in intermediate representations. To address these limitations, we propose {\mname}, a novel feature-level alignment regularization method. {\mname} explicitly supervises intermediate point cloud tokens to preserve fine-grained 3D geometric-semantic information throughout the language modeling process. Specifically, we constrain the intermediate point cloud tokens within the LLM to align with visual input tokens via a consistency loss. By training only a lightweight alignment projector and LoRA adapters, {\mname} achieves explicit feature-level supervision with minimal computational overhead, effectively preventing geometric degradation. Extensive experiments on ModelNet40 and Objaverse datasets demonstrate that our method achieves \textbf{2.08} pp improvement on average for classification tasks, with a substantial \textbf{7.50} pp gain on the challenging open-vocabulary Objaverse classification task and \textbf{4.88} pp improvement on 3D object captioning evaluated by Qwen2-72B-Instruct, validating the effectiveness of {\mname}. Code is publicly available at \href{https://github.com/yharoldsu0627/PointAlign}{https://github.com/yharoldsu0627/PointAlign}.
LLM-Bootstrapped Targeted Finding Guidance for Factual MLLM-based Medical Report Generation
Venue: arXiv cs.CL 2026
Year: 2026

The automatic generation of medical reports utilizing Multimodal Large Language Models (MLLMs) frequently encounters challenges related to factual instability, which may manifest as the omission of findings or the incorporation of inaccurate information, thereby constraining their applicability in clinical settings. Current methodologies typically produce reports based directly on image features, which inherently lack a definitive factual basis. In response to this limitation, we introduce Fact-Flow, an innovative framework that separates the process of visual fact identification from the generation of reports. This is achieved by initially predicting clinical findings from the image, which subsequently directs the MLLM to produce a report that is factually precise. A pivotal advancement of our approach is a pipeline that leverages a Large Language Model (LLM) to autonomously create a dataset of labeled medical findings, effectively eliminating the need for expensive manual annotation. Extensive experimental evaluations conducted on two disease-focused medical datasets validate the efficacy of our method, demonstrating a significant enhancement in factual accuracy compared to state-of-the-art models, while concurrently preserving high standards of text quality.
Self-Correction Inside the Model: Leveraging Layer Attention to Mitigate Hallucinations in Large Vision Language Models
Venue: arXiv cs.CV 2026
Year: 2026

Although Large Vision-Language Models (LVLMs) have made substantial progress, hallucination, where generated text is not grounded in the visual input, remains a challenge. As LVLMs become stronger, previously reported hallucination patterns, such as linguistic bias and overthinking phenomenon, become far less consistent, making the corresponding mitigation techniques substantially less effective. In this paper, we introduce an Internal self-Correction mechanism utilizing Layer Attention (ICLA) that operates directly on hidden states during generation. Each layer selectively retrieves information from all preceding layers through a diagonal cross-layer attention mechanism, enabling self-refinement without any external correction signals. With introducing and training only 0.2M and 0.1M additional parameters on LLaVA1.5-7B and Qwen2.5-VL-7B, \ours consistently improves visual grounding across multiple hallucination benchmarks, demonstrating its effectiveness for more advanced LVLMs.