arXiv subjects

Siyuan Zhao

Publications and source records attributed to Siyuan Zhao.

15 recordsLinked to original sources

arXiv2026

Loom: Multi-Region Analysis of Spatial Transcriptomics with Local Neighborhoods and Global Trajectories

We present Loom, a spatial transcriptomics (ST) visual computing system to support the analysis of pseudo-temporal trajectories, comparative investigation across samples and regions of interest, and the examination of spatially structured processes within local microenvironments. ST is a molecular profiling technology that measures gene expression directly within a thin tissue section while preserving its spatial organization. For practical application-driven analyses, the ST local microenvironment data needs to be integrated with cell reference datasets and temporal simulations of cell behavior. This integration is challenging due to multi-modal registration issues and the complexity of the pseudo-temporal patterns, spatial enrichment data, and gene expression dynamics. Loom leverages a novel glyph coupled with a computational backbone to facilitate the detailed pseudo-temporal exploration of local microenvironments, cross-sample comparisons, and investigation of spatiotemporal biological mechanisms. We evaluate Loom through two case studies developed with experts in tissue pathology and oncologists and through an external usability study. The results demonstrate that Loom supports effectively the discovery of cellular transitions and spatiotemporal expression dynamics.

q-bio.QM↗

arXiv2026

Dysphagia Risk Stratification in Head and Neck Cancer via Two-Stage PRO-Clinical Stacking

Dysphagia is a debilitating late effect of head and neck cancer (HNC) treatment, yet timely identification of at-risk patients remains challenging in survivorship care. Definitive assessment relies on videofluoroscopic imaging, as captured by the Dynamic Imaging Grade of Swallowing Toxicity (CTCAE-DIGEST), which, while validated, requires specialized equipment, trained personnel, and significant patient burden, limiting its routine use in surveillance. Patient-reported outcomes (PROs), by contrast, are low-cost, scalable, and easily collected at any clinical encounter, making them an attractive alternative signal for identifying patients who may warrant further evaluation. However, a clear clinical framework for translating PRO responses into actionable interventions is still evolving. In particular, uncertainty remains regarding when a patient's self-reported symptom burden should prompt escalation of care. This study addresses this gap by formulating a single-visit PRO-clinical prediction framework and introducing a clinically interpretable two-stage stacking model to predict swallowing impairment risk using PRO responses and structured clinical variables, without requiring videofluoroscopic imaging. The proposed framework quantifies the independent contributions of patient-reported symptoms and clinical factors within a unified and interpretable risk assessment model. Our findings demonstrate that individual MDADI responses contain predictive information beyond that captured by composite or global summary scores, while interpretability analyses reveal symptom patterns and clinical risk factors associated with swallowing impairment. Together, these results support the use of structured PRO-clinical integration as a practical, imaging-free approach for dysphagia risk stratification in HNC survivorship.

cs.LG↗

arXiv2026

EVLA: An Electro-Aware Multimodal Assistant for Physically-Grounded Driving Reasoning and Control

Modern vision-language models (VLMs) for driving assistants typically treat vehicle dynamics as a black box, resulting in decisions that lack awareness of the vehicle's real-time electro-mechanical state. To bridge this gap, we introduce the Electro-Visual-Language Assistant (EVLA) -- a novel framework that combines multi-modal scene understanding with real-time perception of the electrified powertrain state (e.g., motor torque, battery SOC). Our approach features two key innovations: first, a Unified Co-State Encoder (UCSE) that fuses visual, textual, and vehicle-state inputs into a shared latent representation, augmented with an Energy-Efficiency Field to model spatial energy costs; and second, an Electro-aware Structured Reasoning Chain (ESRC), which replaces external chain-of-thought prompting with an internal, deterministic reasoning process grounded in physical constraints and optimization objectives. Trained end-to-end with a physics-guided joint loss, EVLA learns to generate context-aware and energy-optimal driving decisions. Extensive evaluations on a driving QA benchmark demonstrate that EVLA substantially outperforms strong fine-tuned VLM baselines, improving the final score by +0.0871 and accuracy by +5.6\%. Ablation studies validate the necessity of each component, and efficiency analyses show that EVLA achieves 36\% faster inference than multi-stage pipelines. This work underscores that integrating vehicle-state awareness and structured physical reasoning is crucial for developing next-generation, physically-grounded driving assistants.

cs.CL↗

arXiv2026

Test-Time Deep Thinking to Explore Implicit Rules

With the continuous advancement of Large Language Models (LLMs), intelligent agents are becoming increasingly vital. However, these agents often fail in environments governed by implicit rules--hidden constraints that cannot be observed directly and must be inferred through interaction. This causes agents to fall into repetitive trial-and-error loops, ultimately leading to task failure. To address this challenge, we propose Test-Time Exploration (TTExplore), a framework where a thinker component analyzes interaction history to infer these implicit rules and guide an actor. Effective exploration in this setting critically depends on the reasoning ability of the thinker. However, evaluating deep reasoning trajectories is inherently unstable and difficult, which poses a major obstacle to effective training. To overcome this issue, we introduce a novel and stable reinforcement learning pipeline. The core idea is to use accurate task-level scores as indirect rewards to bypass the difficulty of evaluating intermediate reasoning, and to retain only a single thinking node per trajectory to alleviate reward sparsity. Using this pipeline, we train a specialized 7B model, Exp-Thinker. Experiments on five text-based embodied tasks show that TTExplore equipped with Exp-Thinker improves baseline agent performance by an average of $14$-$19$ points, demonstrating the effectiveness of explicitly reasoning about implicit rules.

cs.AI↗

arXiv2026

Super Research: Answering Highly Complex Questions with Large Language Models through Super Deep and Super Wide Research

While Large Language Models (LLMs) have demonstrated proficiency in Deep Research or Wide Search, their capacity to solve highly complex questions-those requiring long-horizon planning, massive evidence gathering, and synthesis across heterogeneous sources-remains largely unexplored. We introduce Super Research, a task for complex autonomous research tasks that integrates (i) structured decomposition into a research plan, (ii) super wide retrieval for diverse perspectives, and (iii) super deep investigation to resolve uncertainties through iterative queries. To evaluate this capability, we curated a benchmark of 300 expert-written questions across diverse domains, each requiring up to 100+ retrieval steps and 1,000+ web pages to reconcile conflicting evidence. Super Research produces verifiable reports with fine-grained citations and intermediate artifacts (e.g., outlines and tables) to ensure traceable reasoning. Furthermore, we present a graph-anchored auditing protocol that evaluates Super Research along five dimensions: Coverage, Logical Consistency, Report Utility, Objectivity and Citation Health. While super-complex questions may be infrequent in standard applications, Super Research serves as a critical ceiling evaluation and stress test for LLM capabilities. A model's proficiency within Super Research acts as a powerful proxy for its general research competence; success here suggests the robustness necessary to navigate nearly any subordinate research task. Leaderboard is available at: https://cnsdqd-dyb.github.io/Super-Research-Benchmark/

cs.CL↗

arXiv2025

Attention-based ROI Discovery in 3D Tissue Images

High-dimensional tissue imaging generates highly complex 3D data containing multiple biomarkers, making it challenging to identify biologically relevant regions without an expert user specifying manual labels for regions of interest. We introduce an approach to automatically identifying regions of interest (ROIs) in the 3D microscopy data. Our approach is based on a novel self-supervised multi-layer graph attention network (SSGAT), coupled with a React interactive interface wrapped around Vitessce. SSGAT employs an adversarial self-supervised learning objective to identify meaningful immune microenvironments through marker interactions. Our method reveals complex spatial bioreactions that can be visually assessed to assess their distribution across tissue. Index Terms: Biomedical visualization, graph attention networks,self-supervised learning, spatial interaction analysis.

q-bio.QM↗

arXiv2025

SelectiveFinetuning: Enhancing Transfer Learning in Sleep Staging through Selective Domain Alignment

In practical sleep stage classification, a key challenge is the variability of EEG data across different subjects and environments. Differences in physiology, age, health status, and recording conditions can lead to domain shifts between data. These domain shifts often result in decreased model accuracy and reliability, particularly when the model is applied to new data with characteristics different from those it was originally trained on, which is a typical manifestation of negative transfer. To address this, we propose SelectiveFinetuning in this paper. Our method utilizes a pretrained Multi Resolution Convolutional Neural Network (MRCNN) to extract EEG features, capturing the distinctive characteristics of different sleep stages. To mitigate the effect of domain shifts, we introduce a domain aligning mechanism that employs Earth Mover Distance (EMD) to evaluate and select source domain data closely matching the target domain. By finetuning the model with selective source data, our SelectiveFinetuning enhances the model's performance on target domain that exhibits domain shifts compared to the data used for training. Experimental results show that our method outperforms existing baselines, offering greater robustness and adaptability in practical scenarios where data distributions are often unpredictable.

eess.SP↗

arXiv2024

DiM-Gestor: Co-Speech Gesture Generation with Adaptive Layer Normalization Mamba-2

Speech-driven gesture generation using transformer-based generative models represents a rapidly advancing area within virtual human creation. However, existing models face significant challenges due to their quadratic time and space complexities, limiting scalability and efficiency. To address these limitations, we introduce DiM-Gestor, an innovative end-to-end generative model leveraging the Mamba-2 architecture. DiM-Gestor features a dual-component framework: (1) a fuzzy feature extractor and (2) a speech-to-gesture mapping module, both built on the Mamba-2. The fuzzy feature extractor, integrated with a Chinese Pre-trained Model and Mamba-2, autonomously extracts implicit, continuous speech features. These features are synthesized into a unified latent representation and then processed by the speech-to-gesture mapping module. This module employs an Adaptive Layer Normalization (AdaLN)-enhanced Mamba-2 mechanism to uniformly apply transformations across all sequence tokens. This enables precise modeling of the nuanced interplay between speech features and gesture dynamics. We utilize a diffusion model to train and infer diverse gesture outputs. Extensive subjective and objective evaluations conducted on the newly released Chinese Co-Speech Gestures dataset corroborate the efficacy of our proposed model. Compared with Transformer-based architecture, the assessments reveal that our approach delivers competitive results and significantly reduces memory usage, approximately 2.4 times, and enhances inference speeds by 2 to 4 times. Additionally, we released the CCG dataset, a Chinese Co-Speech Gestures dataset, comprising 15.97 hours (six styles across five scenarios) of 3D full-body skeleton gesture motion performed by professional Chinese TV broadcasters.

cs.SD↗

arXiv2024

A Part-to-Whole Circular Cell Explorer

Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the tissue image with pie charts for the cell distribution. We design an interactive visual analysis system that addresses perceptual problems in the state of the art, while adding filtering, drilling, and clustering analysis capabilities. Our approach can help researchers gain deeper insights into the molecular mechanisms underlying complex biological processes within tissues.

q-bio.QM↗

arXiv2024

DCS Chain: A Flexible Private Blockchain System

Blockchain technology has seen tremendous development over the past few years. Despite the emergence of numerous blockchain systems, they all suffer from various limitations, which can all be attributed to the fundamental issue posed by the DCS trilemma. In light of this, this work introduces a novel private blockchain system named DCS Chain. The core idea is to quantify the DCS metrics and dynamically adjust the blockchain's performance across these three dimensions, to achieve theoretically optimal system performance. Overall, our system provides a comprehensive suite of blockchain essentials, including DCS quantification, consensus protocol adjustment, and communication network simulation.

cs.CR↗

arXiv2024

Audio is all in one: speech-driven gesture synthetics using WavLM pre-trained model

The generation of co-speech gestures for digital humans is an emerging area in the field of virtual human creation. Prior research has made progress by using acoustic and semantic information as input and adopting classify method to identify the person's ID and emotion for driving co-speech gesture generation. However, this endeavour still faces significant challenges. These challenges go beyond the intricate interplay between co-speech gestures, speech acoustic, and semantics; they also encompass the complexities associated with personality, emotion, and other obscure but important factors. This paper introduces "diffmotion-v2," a speech-conditional diffusion-based and non-autoregressive transformer-based generative model with WavLM pre-trained model. It can produce individual and stylized full-body co-speech gestures only using raw speech audio, eliminating the need for complex multimodal processing and manually annotated. Firstly, considering that speech audio not only contains acoustic and semantic features but also conveys personality traits, emotions, and more subtle information related to accompanying gestures, we pioneer the adaptation of WavLM, a large-scale pre-trained model, to extract low-level and high-level audio information. Secondly, we introduce an adaptive layer norm architecture in the transformer-based layer to learn the relationship between speech information and accompanying gestures. Extensive subjective evaluation experiments are conducted on the Trinity, ZEGGS, and BEAT datasets to confirm the WavLM and the model's ability to synthesize natural co-speech gestures with various styles.

cs.SD↗

arXiv2024

HotStuff-2 vs. HotStuff: The Difference and Advantage

Byzantine consensus protocols are essential in blockchain technology. The widely recognized HotStuff protocol uses cryptographic measures for efficient view changes and reduced communication complexity. Recently, the main authors of HotStuff introduced an advanced iteration named HotStuff-2. This paper aims to compare the principles and analyze the effectiveness of both protocols, hoping to depict their key differences and assess the potential enhancements offered by HotStuff-2.

cs.CR↗

arXiv2024

Speech-driven Personalized Gesture Synthetics: Harnessing Automatic Fuzzy Feature Inference

Speech-driven gesture generation is an emerging field within virtual human creation. However, a significant challenge lies in accurately determining and processing the multitude of input features (such as acoustic, semantic, emotional, personality, and even subtle unknown features). Traditional approaches, reliant on various explicit feature inputs and complex multimodal processing, constrain the expressiveness of resulting gestures and limit their applicability. To address these challenges, we present Persona-Gestor, a novel end-to-end generative model designed to generate highly personalized 3D full-body gestures solely relying on raw speech audio. The model combines a fuzzy feature extractor and a non-autoregressive Adaptive Layer Normalization (AdaLN) transformer diffusion architecture. The fuzzy feature extractor harnesses a fuzzy inference strategy that automatically infers implicit, continuous fuzzy features. These fuzzy features, represented as a unified latent feature, are fed into the AdaLN transformer. The AdaLN transformer introduces a conditional mechanism that applies a uniform function across all tokens, thereby effectively modeling the correlation between the fuzzy features and the gesture sequence. This module ensures a high level of gesture-speech synchronization while preserving naturalness. Finally, we employ the diffusion model to train and infer various gestures. Extensive subjective and objective evaluations on the Trinity, ZEGGS, and BEAT datasets confirm our model's superior performance to the current state-of-the-art approaches. Persona-Gestor improves the system's usability and generalization capabilities, setting a new benchmark in speech-driven gesture synthesis and broadening the horizon for virtual human technology. Supplementary videos and code can be accessed at https://zf223669.github.io/Diffmotion-v2-website/

cs.SD↗

arXiv2018

Towards Accurate Deceptive Opinion Spam Detection based on Word Order-preserving CNN

Nowadays, deep learning has been widely used. In natural language learning, the analysis of complex semantics has been achieved because of its high degree of flexibility. The deceptive opinions detection is an important application area in deep learning model, and related mechanisms have been given attention and researched. On-line opinions are quite short, varied types and content. In order to effectively identify deceptive opinions, we need to comprehensively study the characteristics of deceptive opinions, and explore novel characteristics besides the textual semantics and emotional polarity that have been widely used in text analysis. The detection mechanism based on deep learning has better self-adaptability and can effectively identify all kinds of deceptive opinions. In this paper, we optimize the convolution neural network model by embedding the word order characteristics in its convolution layer and pooling layer, which makes convolution neural network more suitable for various text classification and deceptive opinions detection. The TensorFlow-based experiments demonstrate that the detection mechanism proposed in this paper achieve more accurate deceptive opinion detection results.

cs.CL↗

arXiv2017

Condensed Memory Networks for Clinical Diagnostic Inferencing

Diagnosis of a clinical condition is a challenging task, which often requires significant medical investigation. Previous work related to diagnostic inferencing problems mostly consider multivariate observational data (e.g. physiological signals, lab tests etc.). In contrast, we explore the problem using free-text medical notes recorded in an electronic health record (EHR). Complex tasks like these can benefit from structured knowledge bases, but those are not scalable. We instead exploit raw text from Wikipedia as a knowledge source. Memory networks have been demonstrated to be effective in tasks which require comprehension of free-form text. They use the final iteration of the learned representation to predict probable classes. We introduce condensed memory neural networks (C-MemNNs), a novel model with iterative condensation of memory representations that preserves the hierarchy of features in the memory. Experiments on the MIMIC-III dataset show that the proposed model outperforms other variants of memory networks to predict the most probable diagnoses given a complex clinical scenario.

cs.CL↗