Abstract--T cell receptor (TCR) repertoires encode critical immunological signatures for autoimmune diseases, yet their clinical application remains limited by sequence sparsity and low witness rates. We developed EAMil, a multi-instance deep learning framework that leverages TCR sequencing data to diagnose systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) with exceptional accuracy. By integrating Prime-Seq feature extraction with ESMonehot encoding and enhanced gate attention mechanisms, our model achieved state-of-the-art performance with AUCs of 98.95% for SLE and 97.76% for RA. EAMIL successfully identified disease-associated genes with over 90% concordance with established differential analyses and effectively distinguished disease-specific TCR genes. The model demonstrated robustness in classifying multiple disease categories, utilizing the SLEDAI score to stratify SLE patients by disease severity as well as to diagnose the site of damage in SLE patients, and effectively controlling for confounding factors such as age and gender . This interpretable framework for immune receptor analysis provides new insights for autoimmune disease detection and classification with broad potential clinical applications across immune-mediated conditions.

The disconnect between AI-generated molecules with desirable properties and their synthetic feasibility remains a critical bottleneck in computational discovery of drugs and materials. While generative AI has accelerated the proposal of candidate molecules, many of these structures prove challenging or impossible to synthesize using established chemical reactions. Here, we introduce SynTwins, a novel retrosynthesis-guided molecule design framework that finds synthetically accessible molecular analogs by emulating expert chemists' strategies in three steps: retrosynthesis, searching similar building blocks, and virtual synthesis. Using a search algorithm instead of a stochastic data-driven generator, SynTwins outperforms state-of-the-art machine learning models at exploring synthetically accessible analogs while maintaining high structural similarity to original target molecules. Furthermore, when integrated into existing molecular property-optimization frameworks, our hybrid approach produces synthetically feasible analogs with minimal loss in property scores. Our comprehensive benchmarking across diverse molecular datasets demonstrates that SynTwins effectively bridges the gap between computational design and experimental synthesis, providing a practical solution for accelerating the discovery of synthesizable molecules with desired properties for a wide range of applications.

Surface electromyography (sEMG) signals show promise for effective human-machine interfaces, particularly in rehabilitation and prosthetics. However, challenges remain in developing systems that respond quickly to user intent, produce stable flicker-free output suitable for device control, and work across different subjects without time-consuming calibration. In this work, we propose a framework for EMG-based intent detection that addresses these challenges. We cast intent detection as per-timestep segmentation of continuous sEMG streams, assigning labels as gestures unfold in real time. We introduce a masked modeling training strategy that aligns muscle activations with their corresponding user intents, enabling rapid onset detection and stable tracking of ongoing gestures. In evaluations against baseline methods, using metrics that capture accuracy, latency and stability for device control, our approach achieves state-of-the-art performance in zero-shot conditions. These results demonstrate its potential for wearable robotics and next-generation prosthetic systems. Our project website, video, code, and dataset are available at: https://reactemg.github.io/

Background: User reviews of Telehealth and Patient Portal mobile applications (apps) hereon referred to as electronic health (eHealth) apps are a rich source of unsolicited patient feedback, revealing critical insights into patient perceptions. However, the lack of large-scale, annotated datasets specific to privacy and trust has limited the ability of researchers to systematically analyze these concerns using natural language processing (NLP) techniques. Objective: This study aims to develop and benchmark Health App Reviews for Privacy & Trust (HARPT), a large-scale annotated corpus of patient reviews from eHealth apps to advance research in patient privacy and trust. Methods: We employed a multistage data construction strategy. This integrated keyword-based filtering, iterative manual labeling with review, targeted data augmentation, and weak supervision using transformer-based classifiers. A curated subset of 7,000 reviews was manually annotated to support machine learning model development and evaluation. The resulting dataset was used to benchmark a broad range of models. Results: The HARPT corpus comprises 480,000 patient reviews annotated across seven categories capturing critical aspects of trust in the application (TA), trust in the provider (TP), and privacy concerns (PC). We provide comprehensive benchmark performance for a range of machine learning models on the manually annotated subset, establishing a baseline for future research. Conclusions: The HARPT corpus is a significant resource for advancing the study of privacy and trust in the eHealth domain. By providing a large-scale, annotated dataset and initial benchmarks, this work supports reproducible research in usable privacy and trust within health informatics. HARPT is released under an open resource license.

Accurate typhoon track forecasting is crucial for early system warning and disaster response. While Transformer-based models have demonstrated strong performance in modeling the temporal dynamics of dense trajectories of humans and vehicles in smart cities, they usually lack access to broader contextual knowledge that enhances the forecasting reliability of sparse meteorological trajectories, such as typhoon tracks. To address this challenge, we propose TyphoFormer, a novel framework that incorporates natural language descriptions as auxiliary prompts to improve typhoon trajectory forecasting. For each time step, we use Large Language Model (LLM) to generate concise textual descriptions based on the numerical attributes recorded in the North Atlantic hurricane database. The language descriptions capture high-level meteorological semantics and are embedded as auxiliary special tokens prepended to the numerical time series input. By integrating both textual and sequential information within a unified Transformer encoder, TyphoFormer enables the model to leverage contextual cues that are otherwise inaccessible through numerical features alone. Extensive experiments are conducted on HURDAT2 benchmark, results show that TyphoFormer consistently outperforms other state-of-the-art baseline methods, particularly under challenging scenarios involving nonlinear path shifts and limited historical observations.

Abstract--Time series forecasting requires architectures that simultaneously achieve three competing objectives: (1) strict temporal causality for reliable predictions, (2) sub-quadratic complexity for practical scalability, and (3) multi-scale pattern recognition for accurate long-horizon forecasting. We introduce AutoHFormer, a hierarchical autoregressive transformer that addresses these challenges through three key innovations: 1) Hierarchical Temporal Modeling: Our architecture decomposes predictions into segment-level blocks processed in parallel, followed by intra-segment sequential refinement. This dual-scale approach maintains temporal coherence while enabling efficient computation. This design avoids both the anti-causal violations of standard transformers and the sequential bottlenecks of RNN hybrids. It combines fixed oscillating patterns for short-term variations with learnable decay rates for long-term trends. Comprehensive experiments demonstrate that AutoHFormer 10.76 faster training and 6.06 memory reduction compared to PatchTST on PEMS08, while maintaining consistent accuracy across 96-720 step horizons in most of cases. These breakthroughs establish new benchmarks for efficient and precise time series modeling. I. Introduction Time series forecasting [1, 2, 3, 4, 5] stands as a fundamental pillar of modern predictive analytics, enabling data-driven decision making across numerous mission-critical domains. As demonstrated in recent literature [6, 7], this task has become increasingly vital in our data-rich era.

Purpose: Accurate intraoperative X-ray/CT registration is essential for surgical navigation in orthopedic procedures. However, existing methods struggle with consistently achieving sub-millimeter accuracy, robustness under broad initial pose estimates or need manual key-point annotations. This work aims to address these challenges by proposing a novel multi-view X-ray/CT registration method for intraoperative bone registration. Methods: The proposed registration method consists of a multi-view, contour-based iterative closest point (ICP) optimization. Unlike previous methods, which attempt to match bone contours across the entire silhouette in both imaging modalities, we focus on matching specific subcategories of contours corresponding to bone substructures. This leads to reduced ambiguity in the ICP matches, resulting in a more robust and accurate registration solution. This approach requires only two X-ray images and operates fully automatically. Additionally, we contribute a dataset of 5 cadaveric specimens, including real X-ray images, X-ray image poses and the corresponding CT scans. Results: The proposed registration method is evaluated on real X-ray images using mean reprojection error (mRPD). The method consistently achieves sub-millimeter accuracy with a mRPD 0.67mm compared to 5.35mm by a commercial solution requiring manual intervention. Furthermore, the method offers improved practical applicability, being fully automatic. Conclusion: Our method offers a practical, accurate, and efficient solution for multi-view X-ray/CT registration in orthopedic surgeries, which can be easily combined with tracking systems. By improving registration accuracy and minimizing manual intervention, it enhances intraoperative navigation, contributing to more accurate and effective surgical outcomes in computer-assisted surgery (CAS).

As large language models (LLMs) are progressively deployed in various real-world applications, personalization of LLMs has become increasingly important. While various approaches to LLM personalization such as prompt-based and training-based methods have been actively explored, the development of effective decoding-time algorithms remains largely overlooked, despite their demonstrated potential. In this paper, we propose CoPe (Contrasting Personal Preference), a novel decoding-time approach applied after performing parameter-efficient fine-tuning (PEFT) on user-specific data. Our core idea is to leverage reward-guided decoding specifically for personalization by maximizing each user's implicit reward signal. We evaluate CoPe across five open-ended personalized text generation tasks. Our empirical results demonstrate that CoPe achieves strong performance, improving personalization by an average of 10.57% in ROUGE-L, without relying on external reward models or additional training procedures.

LLMs have demonstrated unprecedented capabilities in natural language processing, yet their practical deployment remains hindered by persistent factuality and faithfulness hallucinations. While existing methods address these hallucination types independently, they inadvertently induce performance trade-offs, as interventions targeting one type often exacerbate the other. Through empirical and theoretical analysis of activation space dynamics in LLMs, we reveal that these hallucination categories share overlapping subspaces within neural representations, presenting an opportunity for concurrent mitigation. To harness this insight, we propose SPACE, a unified framework that jointly enhances factuality and faithfulness by editing shared activation subspaces. SPACE establishes a geometric foundation for shared subspace existence through dual-task feature modeling, then identifies and edits these subspaces via a hybrid probe strategy combining spectral clustering and attention head saliency scoring. Experimental results across multiple benchmark datasets demonstrate the superiority of our approach.

Multimodal Generative Models (MGMs) have rapidly evolved beyond text generation, now spanning diverse output modalities including images, music, video, human motion, and 3D objects, by integrating language with other sensory modalities under unified architectures. This survey categorises six primary generative modalities and examines how foundational techniques, namely Self-Supervised Learning (SSL), Mixture of Experts (MoE), Reinforcement Learning from Human Feedback (RLHF), and Chain-of-Thought (CoT) prompting, enable cross-modal capabilities. We analyze key models, architectural trends, and emergent cross-modal synergies, while highlighting transferable techniques and unresolved challenges. Building on a common taxonomy of models and training recipes, we propose a unified evaluation framework centred on faithfulness, compositionality, and robustness, and synthesise evidence from benchmarks and human studies across modalities. We further analyse trustworthiness, safety, and ethical risks, including multimodal bias, privacy leakage, and the misuse of high-fidelity media generation for deepfakes, disinformation, and copyright infringement in music and 3D assets, together with emerging mitigation strategies. Finally, we discuss how architectural trends, evaluation protocols, and governance mechanisms can be co-designed to close current capability and safety gaps, outlining critical paths toward more general-purpose, controllable, and accountable multimodal generative systems.