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Ziyang Song

Publications and source records attributed to Ziyang Song.

At least 19 recordsLinked to original sources
arXiv2026

DoctorAgents: an agentic framework to iteratively refine AutoML pipeline for small clinical temporal data

Clinical machine learning (ML) has the potential to support high-stakes medical decision-making, but reliable deployment is often constrained by scarce, heterogeneous, and temporal complexity. Developing effective ML pipelines for such data remains time-consuming and error-prone, while existing automated machine learning (AutoML) systems only partially address this challenge because they largely rely on brute-force search over predefined spaces and lack explicit reasoning and memory. We therefore reformulate AutoML for small clinical data from exhaustive search to reasoning-driven refinement. We propose DoctorAgents, an agentic AI framework that autonomously constructs and optimizes end-to-end ML pipelines through specialized large language model (LLM) agents for generation, validation, and refinement. DoctorAgents backpropagates natural-language feedback through textual gradient descent to perform targeted updates without exhaustive search. Experiments across diverse clinical tasks show that DoctorAgents consistently outperforms established AutoML baselines while producing more interpretable task-specific representations.

cs.AI↗
arXiv2026

Patients-like-me: A Variational LM--GNN Framework for Explainable Clinical Prediction

Language models (LMs) offer strong textual representations for electronic health records (EHRs), but they encode patient sequences in isolation and provide limited explainability. Graph neural networks (GNNs) complement LMs by incorporating inter-patient relationships and enabling reference-patient attribution, yet they rely on high-quality patient representations. We propose Patients-like-me (PLM), a unified LM--GNN framework that integrates local patient semantics with global cohort structure. To train PLM efficiently, we introduce a Variational Expectation-Maximization algorithm that alternates LM and GNN updates under a supervised variational objective. Extensive experiments on MIMIC-III and MIMIC-IV show that PLM consistently outperforms state-of-the-art methods, with improvements generalizing across encoder-only and decoder-only LM backbones. These gains are achieved with only modest additional computational overhead. PLM also provides reference-patient explanations by retrieving influential similar patients, while edge-masking experiments confirm that the highest-ranked references have the greatest impact on model predictions.

cs.CL↗
arXiv2026

FedAgentKE: Federated Semantic Knowledge Evolution for Heterogeneous Agents

Large language model (LLM)-based agents increasingly rely on reasoning, tool use, and iterative execution, yet existing agent frameworks still operate largely in isolation. While recent memory-based agent systems improve individual agents through local retrieval and workflow reuse, local experiences remain fragmented across isolated agent frameworks, limiting cross-framework knowledge transfer and collaborative reasoning evolution. We propose FedAgentKE, a lightweight framework for Federated Semantic Knowledge Evolution across heterogeneous agents. FedAgentKE enables distributed agent frameworks to collaboratively evolve transferable reasoning abstractions through iterative semantic knowledge distillation, aggregation, and adaptation without sharing raw reasoning trajectories. Experiments demonstrate consistent improvements under both cross-framework and cross-task settings, highlighting the potential of federated semantic knowledge evolution for future collaborative agent ecosystems.

cs.MA↗
arXiv2026

ChatHealthAI: Aligning Electronic Health Record Representations with Large Language Models for Grounded Clinical Reasoning

Large language models (LLMs) exhibit strong natural-language reasoning abilities for clinical decision support, but struggle to effectively model structured longitudinal electronic health records (EHRs). In contrast, EHR foundation models can learn predictive patient representations, yet lack interpretable language-based reasoning. To bridge this gap, we propose ChatHealthAI, a multimodal reasoning framework that aligns structured EHR representations from a pretrained EHR foundation model with the semantic space of a frozen LLM through a task-aware resampler. By integrating longitudinal patient representations with refined clinical event descriptions, ChatHealthAI enables clinically grounded natural-language reasoning while maintaining accurate patient prediction. We evaluated ChatHealthAI on three clinical predictive tasks from the EHRSHOT benchmark. Results show that ChatHealthAI improves reasoning quality and interpretability while preserving competitive predictive performance. These findings highlight the potential of integrating EHR foundation models with pretrained LLMs for interpretable clinical prediction.

cs.AI↗
arXiv2026

FedEHR-Gen: Federated Synthetic Time-Series EHR Generation via Latent Space Alignment and Distribution-Aware Aggregation

Synthetic Electronic Health Record (EHR) generation provides a promising avenue for data augmentation and cross-hospital modeling in privacy-constrained healthcare settings. However, most existing EHR generative models are centralized and require pooling data across hospitals, which is often infeasible when real-world data sharing is restricted. While federated EHR generation offers a natural solution, direct federated modeling often collapses or diverges due to the high dimensionality, sparsity, and cross-hospital heterogeneity of EHR data. In this work, we propose FedEHR-Gen, the first federated framework for synthetic time-series EHR generation across distributed hospitals. FedEHR-Gen uses a two-stage learning paradigm. First, we introduce a federated autoencoder that projects high-dimensional and sparse EHR features onto a compact latent space. To ensure semantic consistency across hospitals, we develop a layer-wise matching aggregation mechanism that aligns local encoders into a unified global latent space. Second, operating on this aligned latent space, we train a federated temporal conditional variational autoencoder (TCVAE) with distribution-aware aggregation, enabling stable temporal generative modeling under severe cross-hospital heterogeneity. Extensive experiments on the eICU and MIMIC-III datasets demonstrate that FedEHR-Gen achieves generation fidelity, downstream utility, and privacy risk comparable to centralized training, while consistently outperforming the standard federated baseline.

cs.LG↗
arXiv2026

SafeRx-Agent: A Knowledge-Grounded Multi-Agent Framework for Safe and Explainable Medication Recommendation

Medication recommendation predicts medications for patient visits, but existing methods still face two key challenges. At the model level, traditional drug recommendation methods only predict structured drug codes with limited evidence grounding, while LLM agents can use richer clinical context but may lack safety verification and traceability. At the task level, existing benchmarks often use broad medication categories, which ignore subgroup-level safety differences and can lead to risk overestimation. We introduce the first fine-grained medication recommendation setting based on fourth-level ATC code generation. We propose Safe Prescription Agent (SafeRx-Agent), a knowledge-grounded multi-agent framework that uses patient context, external clinical knowledge, and safety verification to recommend traceable medication sets. Experimental results on MIMIC-III and MIMIC-IV datasets show that SafeRx-Agent improves fine-grained medication prediction accuracy while controlling drug interactions, contraindications, and medication set size.

cs.CL↗
arXiv2026

MV-S2V: Multi-View Subject-Consistent Video Generation

Existing Subject-to-Video Generation (S2V) methods have achieved high-fidelity and subject-consistent video generation, yet remain constrained to single-view subject references. This limitation renders the S2V task reducible to an S2I + I2V pipeline, failing to exploit the full potential of video subject control. In this work, we propose and address the challenging Multi-View S2V (MV-S2V) task, which synthesizes videos from multiple reference views to enforce 3D-level subject consistency. Regarding the scarcity of training data, we first develop a synthetic data curation pipeline to generate highly customized synthetic data, complemented by a small-scale real-world captured dataset to boost the training of MV-S2V. Another key issue lies in the potential confusion between cross-subject and cross-view references in conditional generation. To overcome this, we further introduce Temporally Shifted RoPE (TS-RoPE) to distinguish between different subjects and distinct views of the same subject in reference conditioning. Our framework achieves superior 3D subject consistency w.r.t. multi-view reference images and high-quality visual outputs, establishing a new meaningful direction for subject-driven video generation. Code and data are available at: https://szy-young.github.io/mv-s2v

cs.CV↗
arXiv2025

Depth Anything in $360^\circ$: Towards Scale Invariance in the Wild

Panoramic depth estimation provides a comprehensive solution for capturing complete $360^\circ$ environmental structural information, offering significant benefits for robotics and AR/VR applications. However, while extensively studied in indoor settings, its zero-shot generalization to open-world domains lags far behind perspective images, which benefit from abundant training data. This disparity makes transferring capabilities from the perspective domain an attractive solution. To bridge this gap, we present Depth Anything in $360^\circ$ (DA360), a panoramic-adapted version of Depth Anything V2. Our key innovation involves learning a shift parameter from the ViT backbone, transforming the model's scale- and shift-invariant output into a scale-invariant estimate that directly yields well-formed 3D point clouds. This is complemented by integrating circular padding into the DPT decoder to eliminate seam artifacts, ensuring spatially coherent depth maps that respect spherical continuity. Evaluated on standard indoor benchmarks and our newly curated outdoor dataset, Metropolis, DA360 shows substantial gains over its base model, achieving over 50\% and 10\% relative depth error reduction on indoor and outdoor benchmarks, respectively. Furthermore, DA360 significantly outperforms robust panoramic depth estimation methods, achieving about 30\% relative error improvement compared to PanDA across all three test datasets and establishing new state-of-the-art performance for zero-shot panoramic depth estimation.

cs.CV↗
arXiv2025

ByteLoom: Weaving Geometry-Consistent Human-Object Interactions through Progressive Curriculum Learning

Human-object interaction (HOI) video generation has garnered increasing attention due to its promising applications in digital humans, e-commerce, advertising, and robotics imitation learning. However, existing methods face two critical limitations: (1) a lack of effective mechanisms to inject multi-view information of the object into the model, leading to poor cross-view consistency, and (2) heavy reliance on fine-grained hand mesh annotations for modeling interaction occlusions. To address these challenges, we introduce ByteLoom, a Diffusion Transformer (DiT)-based framework that generates realistic HOI videos with geometrically consistent object illustration, using simplified human conditioning and 3D object inputs. We first propose an RCM-cache mechanism that leverages Relative Coordinate Maps (RCM) as a universal representation to maintain object's geometry consistency and precisely control 6-DoF object transformations in the meantime. To compensate HOI dataset scarcity and leverage existing datasets, we further design a training curriculum that enhances model capabilities in a progressive style and relaxes the demand of hand mesh. Extensive experiments demonstrate that our method faithfully preserves human identity and the object's multi-view geometry, while maintaining smooth motion and object manipulation.

cs.CV↗
arXiv2025

CETCAM: Camera-Controllable Video Generation via Consistent and Extensible Tokenization

Achieving precise camera control in video generation remains challenging, as existing methods often rely on camera pose annotations that are difficult to scale to large and dynamic datasets and are frequently inconsistent with depth estimation, leading to train-test discrepancies. We introduce CETCAM, a camera-controllable video generation framework that eliminates the need for camera annotations through a consistent and extensible tokenization scheme. CETCAM leverages recent advances in geometry foundation models, such as VGGT, to estimate depth and camera parameters and converts them into unified, geometry-aware tokens. These tokens are seamlessly integrated into a pretrained video diffusion backbone via lightweight context blocks. Trained in two progressive stages, CETCAM first learns robust camera controllability from diverse raw video data and then refines fine-grained visual quality using curated high-fidelity datasets. Extensive experiments across multiple benchmarks demonstrate state-of-the-art geometric consistency, temporal stability, and visual realism. Moreover, CETCAM exhibits strong adaptability to additional control modalities, including inpainting and layout control, highlighting its flexibility beyond camera control. The project page is available at https://sjtuytc.github.io/CETCam_project_page.github.io/.

cs.CV↗
arXiv2025

Anatomy-R1: Enhancing Anatomy Reasoning in Multimodal Large Language Models via Anatomical Similarity Curriculum and Group Diversity Augmentation

Multimodal Large Language Models (MLLMs) have achieved impressive progress in natural image reasoning, yet their potential in medical imaging remains underexplored, especially in clinical anatomical surgical images. Anatomy understanding tasks demand precise understanding and clinically coherent answers, which are difficult to achieve due to the complexity of medical data and the scarcity of high-quality expert annotations. These challenges limit the effectiveness of conventional Supervised Fine-Tuning (SFT) strategies. While recent work has demonstrated that Group Relative Policy Optimization (GRPO) can enhance reasoning in MLLMs without relying on large amounts of data, we find two weaknesses that hinder GRPO's reasoning performance in anatomy recognition: 1) knowledge cannot be effectively shared between different anatomical structures, resulting in uneven information gain and preventing the model from converging, and 2) the model quickly converges to a single reasoning path, suppressing the exploration of diverse strategies. To overcome these challenges, we propose two novel methods. First, we implement a progressive learning strategy called Anatomical Similarity Curriculum Learning by controlling question difficulty via the similarity of answer choices, enabling the model to master complex problems incrementally. Second, we utilize question augmentation referred to as Group Diversity Question Augmentation to expand the model's search space for difficult queries, mitigating the tendency to produce uniform responses. Comprehensive experiments on the SGG-VQA and OmniMedVQA benchmarks show our method achieves a significant improvement across the two benchmarks, demonstrating its effectiveness in enhancing the medical reasoning capabilities of MLLMs. The code can be found in https://github.com/tomato996/Anatomy-R1

cs.CV↗
arXiv2025

Cross-modal Retrieval Models for Stripped Binary Analysis

Retrieving binary code via natural language queries is a pivotal capability for downstream tasks in the software security domain, such as vulnerability detection and malware analysis. However, it is challenging to identify binary functions semantically relevant to the user query from thousands of candidates, as the absence of symbolic information distinguishes this task from source code retrieval. In this paper, we introduce, BinSeek, a two-stage cross-modal retrieval framework for stripped binary code analysis. It consists of two models: BinSeek-Embedding is trained on large-scale dataset to learn the semantic relevance of the binary code and the natural language description, furthermore, BinSeek-Reranker learns to carefully judge the relevance of the candidate code to the description with context augmentation. To this end, we built an LLM-based data synthesis pipeline to automate training construction, also deriving a domain benchmark for future research. Our evaluation results show that BinSeek achieved the state-of-the-art performance, surpassing the the same scale models by 31.42% in Rec@3 and 27.17% in MRR@3, as well as leading the advanced general-purpose models that have 16 times larger parameters.

cs.SE↗
arXiv2025

NeuroABench: A Multimodal Evaluation Benchmark for Neurosurgical Anatomy Identification

Multimodal Large Language Models (MLLMs) have shown significant potential in surgical video understanding. With improved zero-shot performance and more effective human-machine interaction, they provide a strong foundation for advancing surgical education and assistance. However, existing research and datasets primarily focus on understanding surgical procedures and workflows, while paying limited attention to the critical role of anatomical comprehension. In clinical practice, surgeons rely heavily on precise anatomical understanding to interpret, review, and learn from surgical videos. To fill this gap, we introduce the Neurosurgical Anatomy Benchmark (NeuroABench), the first multimodal benchmark explicitly created to evaluate anatomical understanding in the neurosurgical domain. NeuroABench consists of 9 hours of annotated neurosurgical videos covering 89 distinct procedures and is developed using a novel multimodal annotation pipeline with multiple review cycles. The benchmark evaluates the identification of 68 clinical anatomical structures, providing a rigorous and standardized framework for assessing model performance. Experiments on over 10 state-of-the-art MLLMs reveal significant limitations, with the best-performing model achieving only 40.87% accuracy in anatomical identification tasks. To further evaluate the benchmark, we extract a subset of the dataset and conduct an informative test with four neurosurgical trainees. The results show that the best-performing student achieves 56% accuracy, with the lowest scores of 28% and an average score of 46.5%. While the best MLLM performs comparably to the lowest-scoring student, it still lags significantly behind the group's average performance. This comparison underscores both the progress of MLLMs in anatomical understanding and the substantial gap that remains in achieving human-level performance.

cs.CV↗
arXiv2025

TRACE: Learning 3D Gaussian Physical Dynamics from Multi-view Videos

In this paper, we aim to model 3D scene geometry, appearance, and physical information just from dynamic multi-view videos in the absence of any human labels. By leveraging physics-informed losses as soft constraints or integrating simple physics models into neural nets, existing works often fail to learn complex motion physics, or doing so requires additional labels such as object types or masks. We propose a new framework named TRACE to model the motion physics of complex dynamic 3D scenes. The key novelty of our method is that, by formulating each 3D point as a rigid particle with size and orientation in space, we directly learn a translation rotation dynamics system for each particle, explicitly estimating a complete set of physical parameters to govern the particle's motion over time. Extensive experiments on three existing dynamic datasets and one newly created challenging synthetic datasets demonstrate the extraordinary performance of our method over baselines in the task of future frame extrapolation. A nice property of our framework is that multiple objects or parts can be easily segmented just by clustering the learned physical parameters.

cs.CV↗
arXiv2025

Multimodal Causal-Driven Representation Learning for Generalizable Medical Image Segmentation

Vision-Language Models (VLMs), such as CLIP, have demonstrated remarkable zero-shot capabilities in various computer vision tasks. However, their application to medical imaging remains challenging due to the high variability and complexity of medical data. Specifically, medical images often exhibit significant domain shifts caused by various confounders, including equipment differences, procedure artifacts, and imaging modes, which can lead to poor generalization when models are applied to unseen domains. To address this limitation, we propose Multimodal Causal-Driven Representation Learning (MCDRL), a novel framework that integrates causal inference with the VLM to tackle domain generalization in medical image segmentation. MCDRL is implemented in two steps: first, it leverages CLIP's cross-modal capabilities to identify candidate lesion regions and construct a confounder dictionary through text prompts, specifically designed to represent domain-specific variations; second, it trains a causal intervention network that utilizes this dictionary to identify and eliminate the influence of these domain-specific variations while preserving the anatomical structural information critical for segmentation tasks. Extensive experiments demonstrate that MCDRL consistently outperforms competing methods, yielding superior segmentation accuracy and exhibiting robust generalizability.

cs.CV↗
arXiv2025

FreeGave: 3D Physics Learning from Dynamic Videos by Gaussian Velocity

In this paper, we aim to model 3D scene geometry, appearance, and the underlying physics purely from multi-view videos. By applying various governing PDEs as PINN losses or incorporating physics simulation into neural networks, existing works often fail to learn complex physical motions at boundaries or require object priors such as masks or types. In this paper, we propose FreeGave to learn the physics of complex dynamic 3D scenes without needing any object priors. The key to our approach is to introduce a physics code followed by a carefully designed divergence-free module for estimating a per-Gaussian velocity field, without relying on the inefficient PINN losses. Extensive experiments on three public datasets and a newly collected challenging real-world dataset demonstrate the superior performance of our method for future frame extrapolation and motion segmentation. Most notably, our investigation into the learned physics codes reveals that they truly learn meaningful 3D physical motion patterns in the absence of any human labels in training.

cs.CV↗
arXiv2025

DepthMaster: Taming Diffusion Models for Monocular Depth Estimation

Monocular depth estimation within the diffusion-denoising paradigm demonstrates impressive generalization ability but suffers from low inference speed. Recent methods adopt a single-step deterministic paradigm to improve inference efficiency while maintaining comparable performance. However, they overlook the gap between generative and discriminative features, leading to suboptimal results. In this work, we propose DepthMaster, a single-step diffusion model designed to adapt generative features for the discriminative depth estimation task. First, to mitigate overfitting to texture details introduced by generative features, we propose a Feature Alignment module, which incorporates high-quality semantic features to enhance the denoising network's representation capability. Second, to address the lack of fine-grained details in the single-step deterministic framework, we propose a Fourier Enhancement module to adaptively balance low-frequency structure and high-frequency details. We adopt a two-stage training strategy to fully leverage the potential of the two modules. In the first stage, we focus on learning the global scene structure with the Feature Alignment module, while in the second stage, we exploit the Fourier Enhancement module to improve the visual quality. Through these efforts, our model achieves state-of-the-art performance in terms of generalization and detail preservation, outperforming other diffusion-based methods across various datasets. Our project page can be found at https://indu1ge.github.io/DepthMaster_page.

cs.CV↗
arXiv2024

P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

physics.bio-ph↗