An artificial intelligence framework for end-to-end rare disease phenotyping from clinical notes using large language models

Phenotyping is fundamental to rare disease diagnosis, but manual curation of structured phenotypes from clinical notes is labor-intensive and difficult to scale. Existing artificial intelligence approaches typically optimize individual components of phenotyping but do not operationalize the full clinical workflow of extracting features from clinical text, standardizing them to Human Phenotype Ontology (HPO) terms, and prioritizing diagnostically informative HPO terms. We developed RARE-PHENIX, an end-to-end AI framework for rare disease phenotyping that integrates large language model-based phenotype extraction, ontology-grounded standardization to HPO terms, and supervised ranking of diagnostically informative phenotypes. We trained RARE-PHENIX using data from 2,671 patients across 11 Undiagnosed Diseases Network clinical sites, and externally validated it on 16,357 real-world clinical notes from Vanderbilt University Medical Center. Using clinician-curated HPO terms as the gold standard, RARE-PHENIX consistently outperformed a state-of-the-art deep learning baseline (PhenoBERT) across ontology-based similarity and precision-recall-F1 metrics in end-to-end evaluation (i.e., ontology-based similarity of 0.70 vs. 0.58). Ablation analyses demonstrated performance improvements with the addition of each module in RARE-PHENIX (extraction, standardization, and prioritization), supporting the value of modeling the full clinical phenotyping workflow. By modeling phenotyping as a clinically aligned workflow rather than a single extraction task, RARE-PHENIX provides structured, ranked phenotypes that are more concordant with clinician curation and has the potential to support human-in-the-loop rare disease diagnosis in real-world settings.

Human-Guided Agentic AI for Multimodal Clinical Prediction: Lessons from the AgentDS Healthcare Benchmark

Agentic AI systems are increasingly capable of autonomous data science workflows, yet clinical prediction tasks demand domain expertise that purely automated approaches struggle to provide. We investigate how human guidance of agentic AI can improve multimodal clinical prediction, presenting our approach to all three AgentDS Healthcare benchmark challenges: 30-day hospital readmission prediction (Macro-F1 = 0.8986), emergency department cost forecasting (MAE = $465.13), and discharge readiness assessment (Macro-F1 = 0.7939). Across these tasks, human analysts directed the agentic workflow at key decision points, multimodal feature engineering from clinical notes, scanned PDF billing receipts, and time-series vital signs; task-appropriate model selection; and clinically informed validation strategies. Our approach ranked 5th overall in the healthcare domain, with a 3rd-place finish on the discharge readiness task. Ablation studies reveal that human-guided decisions compounded to a cumulative gain of +0.065 F1 over automated baselines, with multimodal feature extraction contributing the largest single improvement (+0.041 F1). We distill three generalizable lessons: (1) domain-informed feature engineering at each pipeline stage yields compounding gains that outperform extensive automated search; (2) multimodal data integration requires task-specific human judgment that no single extraction strategy generalizes across clinical text, PDFs, and time-series; and (3) deliberate ensemble diversity with clinically motivated model configurations outperforms random hyperparameter search. These findings offer practical guidance for teams deploying agentic AI in healthcare settings where interpretability, reproducibility, and clinical validity are essential.

RADE-Net: Robust Attention Network for Radar-Only Object Detection in Adverse Weather

Automotive perception systems are obligated to meet high requirements. While optical sensors such as Camera and Lidar struggle in adverse weather conditions, Radar provides a more robust perception performance, effectively penetrating fog, rain, and snow. Since full Radar tensors have large data sizes and very few datasets provide them, most Radar-based approaches work with sparse point clouds or 2D projections, which can result in information loss. Additionally, deep learning methods show potential to extract richer and more dense features from low level Radar data and therefore significantly increase the perception performance. Therefore, we propose a 3D projection method for fast-Fourier-transformed 4D Range-Azimuth-Doppler-Elevation (RADE) tensors. Our method preserves rich Doppler and Elevation features while reducing the required data size for a single frame by 91.9% compared to a full tensor, thus achieving higher training and inference speed as well as lower model complexity. We introduce RADE-Net, a lightweight model tailored to 3D projections of the RADE tensor. The backbone enables exploitation of low-level and high-level cues of Radar tensors with spatial and channel-attention. The decoupled detection heads predict object center-points directly in the Range-Azimuth domain and regress rotated 3D bounding boxes from rich feature maps in the cartesian scene. We evaluate the model on scenes with multiple different road users and under various weather conditions on the large-scale K-Radar dataset and achieve a 16.7% improvement compared to their baseline, as well as 6.5% improvement over current Radar-only models. Additionally, we outperform several Lidar approaches in scenarios with adverse weather conditions. The code is available under https://github.com/chr-is-tof/RADE-Net.

GrIT: Group Informed Transformer for Sequential Recommendation

Sequential recommender systems aim to predict a user's future interests by extracting temporal patterns from their behavioral history. Existing approaches typically employ transformer-based architectures to process long sequences of user interactions, capturing preference shifts by modeling temporal relationships between items. However, these methods often overlook the influence of group-level features that capture the collective behavior of similar users. We hypothesize that explicitly modeling temporally evolving group features alongside individual user histories can significantly enhance next-item recommendation. Our approach introduces latent group representations, where each user's affiliation to these groups is modeled through learnable, time-varying membership weights. The membership weights at each timestep are computed by modeling shifts in user preferences through their interaction history, where we incorporate both short-term and long-term user preferences. We extract a set of statistical features that capture the dynamics of user behavior and further refine them through a series of transformations to produce the final drift-aware membership weights. A group-based representation is derived by weighting latent group embeddings with the learned membership scores. This representation is integrated with the user's sequential representation within the transformer block to jointly capture personal and group-level temporal dynamics, producing richer embeddings that lead to more accurate, context-aware recommendations. We validate the effectiveness of our approach through extensive experiments on five benchmark datasets, where it consistently outperforms state-of-the-art sequential recommendation methods.

Deep Sequence Modeling with Quantum Dynamics: Language as a Wave Function

We introduce a sequence modeling framework in which the latent state is a complex-valued wave function evolving on a finite-dimensional Hilbert space under a learned, time-dependent Hamiltonian. Unlike standard recurrent architectures that rely on gating mechanisms to suppress competing hypotheses, our framework utilizes quantum interference: the Hamiltonian steers the phases of complex amplitudes so that conflicting interpretations cancel while compatible ones reinforce. The dynamics are strictly unitary, ensuring that the state norm is preserved exactly at every time step via a Cayley (Crank--Nicolson) discretization. Token probabilities are extracted using the Born rule, a quadratic measurement operator that couples magnitudes and relative phases. Our primary theoretical contribution is a separation theorem characterizing the representational advantage of this readout: we define a family of disambiguation tasks that a complex unitary model of dimension $N$ solves exactly, but which requires a state dimension of $Ω(N^2)$ for any real-valued orthogonal model equipped with a standard affine-softmax readout. This quadratic gap arises because the Born rule implicitly lifts the $N$-dimensional state into the space of rank-one Hermitian matrices, accessing pairwise phase correlations that are inaccessible to linear projections. Finally, we derive a continuity equation for the latent probability mass, yielding conserved pairwise currents that serve as a built-in diagnostic for tracing information flow between dimensions.

PIS: A Physics-Informed System for Accurate State Partitioning of $Aβ_{42}$ Protein Trajectories

Understanding the conformational evolution of $β$-amyloid ($Aβ$), particularly the $Aβ_{42}$ isoform, is fundamental to elucidating the pathogenic mechanisms underlying Alzheimer's disease. However, existing end-to-end deep learning models often struggle to capture subtle state transitions in protein trajectories due to a lack of explicit physical constraints. In this work, we introduce PIS, a Physics-Informed System designed for robust metastable state partitioning. By integrating pre-computed physical priors, such as the radius of gyration and solvent-accessible surface area, into the extraction of topological features, our model achieves superior performance on the $Aβ_{42}$ dataset. Furthermore, PIS provides an interactive platform that features dynamic monitoring of physical characteristics and multi-dimensional result validation. This system offers biological researchers a powerful set of analytical tools with physically grounded interpretability. A demonstration video of PIS is available on https://youtu.be/AJHGzUtRCg0.

Vision-Language Models for Ergonomic Assessment of Manual Lifting Tasks: Estimating Horizontal and Vertical Hand Distances from RGB Video

Manual lifting tasks are a major contributor to work-related musculoskeletal disorders, and effective ergonomic risk assessment is essential for quantifying physical exposure and informing ergonomic interventions. The Revised NIOSH Lifting Equation (RNLE) is a widely used ergonomic risk assessment tool for lifting tasks that relies on six task variables, including horizontal (H) and vertical (V) hand distances; such distances are typically obtained through manual measurement or specialized sensing systems and are difficult to use in real-world environments. We evaluated the feasibility of using innovative vision-language models (VLMs) to non-invasively estimate H and V from RGB video streams. Two multi-stage VLM-based pipelines were developed: a text-guided detection-only pipeline and a detection-plus-segmentation pipeline. Both pipelines used text-guided localization of task-relevant regions of interest, visual feature extraction from those regions, and transformer-based temporal regression to estimate H and V at the start and end of a lift. For a range of lifting tasks, estimation performance was evaluated using leave-one-subject-out validation across the two pipelines and seven camera view conditions. Results varied significantly across pipelines and camera view conditions, with the segmentation-based, multi-view pipeline consistently yielding the smallest errors, achieving mean absolute errors of approximately 6-8 cm when estimating H and 5-8 cm when estimating V. Across pipelines and camera view configurations, pixel-level segmentation reduced estimation error by approximately 20-30% for H and 35-40% for V relative to the detection-only pipeline. These findings support the feasibility of VLM-based pipelines for video-based estimation of RNLE distance parameters.

BigMaQ: A Big Macaque Motion and Animation Dataset Bridging Image and 3D Pose Representations

The recognition of dynamic and social behavior in animals is fundamental for advancing ethology, ecology, medicine and neuroscience. Recent progress in deep learning has enabled automated behavior recognition from video, yet an accurate reconstruction of the three-dimensional (3D) pose and shape has not been integrated into this process. Especially for non-human primates, mesh-based tracking efforts lag behind those for other species, leaving pose descriptions restricted to sparse keypoints that are unable to fully capture the richness of action dynamics. To address this gap, we introduce the $\textbf{Big Ma}$ca$\textbf{Q}$ue 3D Motion and Animation Dataset ($\texttt{BigMaQ}$), a large-scale dataset comprising more than 750 scenes of interacting rhesus macaques with detailed 3D pose descriptions. Extending previous surface-based animal tracking methods, we construct subject-specific textured avatars by adapting a high-quality macaque template mesh to individual monkeys. This allows us to provide pose descriptions that are more accurate than previous state-of-the-art surface-based animal tracking methods. From the original dataset, we derive BigMaQ500, an action recognition benchmark that links surface-based pose vectors to single frames across multiple individual monkeys. By pairing features extracted from established image and video encoders with and without our pose descriptors, we demonstrate substantial improvements in mean average precision (mAP) when pose information is included. With these contributions, $\texttt{BigMaQ}$ establishes the first dataset that both integrates dynamic 3D pose-shape representations into the learning task of animal action recognition and provides a rich resource to advance the study of visual appearance, posture, and social interaction in non-human primates. The code and data are publicly available at https://martinivis.github.io/BigMaQ/ .

CREDIT: Certified Ownership Verification of Deep Neural Networks Against Model Extraction Attacks

Machine Learning as a Service (MLaaS) has emerged as a widely adopted paradigm for providing access to deep neural network (DNN) models, enabling users to conveniently leverage these models through standardized APIs. However, such services are highly vulnerable to Model Extraction Attacks (MEAs), where an adversary repeatedly queries a target model to collect input-output pairs and uses them to train a surrogate model that closely replicates its functionality. While numerous defense strategies have been proposed, verifying the ownership of a suspicious model with strict theoretical guarantees remains a challenging task. To address this gap, we introduce CREDIT, a certified ownership verification against MEAs. Specifically, we employ mutual information to quantify the similarity between DNN models, propose a practical verification threshold, and provide rigorous theoretical guarantees for ownership verification based on this threshold. We extensively evaluate our approach on several mainstream datasets across different domains and tasks, achieving state-of-the-art performance. Our implementation is publicly available at: https://github.com/LabRAI/CREDIT.

A data-driven model-free physical-informed deep operator network for solving nonlinear dynamic system

The existing physical-informed Deep Operator Networks are mostly based on either the well-known mathematical formula of the system or huge amounts of data for different scenarios. However, in some cases, it is difficult to get the exact mathematical formula and vast amounts of data in some dynamic systems, we can only get a few experimental data or limited mathematical information. To address the cases, we propose a data-driven model-free physical-informed Deep Operator Network (DeepOnet) framework to learn the nonlinear dynamic systems from few available data. We first explore the short-term dependence of the available data and use a surrogate machine learning model to extract the short-term dependence. Then, the surrogate machine learning model is incorporated into the DeepOnet as the physical information part. Then, the constructed DeepOnet is trained to simulate the system's dynamic response for given control inputs and initial conditions. Numerical experiments on different systems confirm that our DeepOnet framework learns to approximate the dynamic response of some nonlinear dynamic systems effectively.