arXiv subjects

Yaoyun Zhang

Publications and source records attributed to Yaoyun Zhang.

9 recordsLinked to original sources

arXiv2025

UniFlow-Audio: Unified Flow Matching for Audio Generation from Omni-Modalities

Audio generation, including speech, music and sound effects, has advanced rapidly in recent years. These tasks can be divided into two categories: time-aligned (TA) tasks, where each input unit corresponds to a specific segment of the output audio (e.g., phonemes aligned with frames in speech synthesis); and non-time-aligned (NTA) tasks, where such alignment is not available. Since modeling paradigms for the two types are typically different, research on different audio generation tasks has traditionally followed separate trajectories. However, audio is not inherently divided into such categories, making a unified model a natural and necessary goal for general audio generation. Previous unified audio generation works have adopted autoregressive architectures, while unified non-autoregressive approaches remain largely unexplored. In this work, we propose UniFlow-Audio, a universal audio generation framework based on flow matching. We propose a dual-fusion mechanism that temporally aligns audio latents with TA features and integrates NTA features via cross-attention in each model block. Task-balanced data sampling is employed to maintain strong performance across both TA and NTA tasks. UniFlow-Audio supports omni-modalities, including text, audio, and video. By leveraging the advantage of multi-task learning and the generative modeling capabilities of flow matching, UniFlow-Audio achieves strong results across 7 tasks using fewer than 8K hours of public training data and under 1B trainable parameters. Even the small variant with only ~200M trainable parameters shows competitive performance, highlighting UniFlow-Audio as a potential non-auto-regressive foundation model for audio generation. Code and models will be available at https://wsntxxn.github.io/uniflow_audio.

cs.SD↗

arXiv2025

FakeSound2: A Benchmark for Explainable and Generalizable Deepfake Sound Detection

The rapid development of generative audio raises ethical and security concerns stemming from forged data, making deepfake sound detection an important safeguard against the malicious use of such technologies. Although prior studies have explored this task, existing methods largely focus on binary classification and fall short in explaining how manipulations occur, tracing where the sources originated, or generalizing to unseen sources-thereby limiting the explainability and reliability of detection. To address these limitations, we present FakeSound2, a benchmark designed to advance deepfake sound detection beyond binary accuracy. FakeSound2 evaluates models across three dimensions: localization, traceability, and generalization, covering 6 manipulation types and 12 diverse sources. Experimental results show that although current systems achieve high classification accuracy, they struggle to recognize forged pattern distributions and provide reliable explanations. By highlighting these gaps, FakeSound2 establishes a comprehensive benchmark that reveals key challenges and aims to foster robust, explainable, and generalizable approaches for trustworthy audio authentication.

cs.SD↗

arXiv2025

A Study of Large Language Models for Patient Information Extraction: Model Architecture, Fine-Tuning Strategy, and Multi-task Instruction Tuning

Natural language processing (NLP) is a key technology to extract important patient information from clinical narratives to support healthcare applications. The rapid development of large language models (LLMs) has revolutionized many NLP tasks in the clinical domain, yet their optimal use in patient information extraction tasks requires further exploration. This study examines LLMs' effectiveness in patient information extraction, focusing on LLM architectures, fine-tuning strategies, and multi-task instruction tuning techniques for developing robust and generalizable patient information extraction systems. This study aims to explore key concepts of using LLMs for clinical concept and relation extraction tasks, including: (1) encoder-only or decoder-only LLMs, (2) prompt-based parameter-efficient fine-tuning (PEFT) algorithms, and (3) multi-task instruction tuning on few-shot learning performance. We benchmarked a suite of LLMs, including encoder-based LLMs (BERT, GatorTron) and decoder-based LLMs (GatorTronGPT, Llama 3.1, GatorTronLlama), across five datasets. We compared traditional full-size fine-tuning and prompt-based PEFT. We explored a multi-task instruction tuning framework that combines both tasks across four datasets to evaluate the zero-shot and few-shot learning performance using the leave-one-dataset-out strategy.

cs.CL↗

arXiv2024

Smooth-Foley: Creating Continuous Sound for Video-to-Audio Generation Under Semantic Guidance

The video-to-audio (V2A) generation task has drawn attention in the field of multimedia due to the practicality in producing Foley sound. Semantic and temporal conditions are fed to the generation model to indicate sound events and temporal occurrence. Recent studies on synthesizing immersive and synchronized audio are faced with challenges on videos with moving visual presence. The temporal condition is not accurate enough while low-resolution semantic condition exacerbates the problem. To tackle these challenges, we propose Smooth-Foley, a V2A generative model taking semantic guidance from the textual label across the generation to enhance both semantic and temporal alignment in audio. Two adapters are trained to leverage pre-trained text-to-audio generation models. A frame adapter integrates high-resolution frame-wise video features while a temporal adapter integrates temporal conditions obtained from similarities of visual frames and textual labels. The incorporation of semantic guidance from textual labels achieves precise audio-video alignment. We conduct extensive quantitative and qualitative experiments. Results show that Smooth-Foley performs better than existing models on both continuous sound scenarios and general scenarios. With semantic guidance, the audio generated by Smooth-Foley exhibits higher quality and better adherence to physical laws.

cs.SD↗

arXiv2023

Domain Invariant Learning for Gaussian Processes and Bayesian Exploration

Out-of-distribution (OOD) generalization has long been a challenging problem that remains largely unsolved. Gaussian processes (GP), as popular probabilistic model classes, especially in the small data regime, presume strong OOD generalization abilities. Surprisingly, their OOD generalization abilities have been under-explored before compared with other lines of GP research. In this paper, we identify that GP is not free from the problem and propose a domain invariant learning algorithm for Gaussian processes (DIL-GP) with a min-max optimization on the likelihood. DIL-GP discovers the heterogeneity in the data and forces invariance across partitioned subsets of data. We further extend the DIL-GP to improve Bayesian optimization's adaptability on changing environments. Numerical experiments demonstrate the superiority of DIL-GP for predictions on several synthetic and real-world datasets. We further demonstrate the effectiveness of the DIL-GP Bayesian optimization method on a PID parameters tuning experiment for a quadrotor. The full version and source code are available at: https://github.com/Billzxl/DIL-GP.

cs.LG↗

arXiv2023

DiffDTM: A conditional structure-free framework for bioactive molecules generation targeted for dual proteins

Advances in deep generative models shed light on de novo molecule generation with desired properties. However, molecule generation targeted for dual protein targets still faces formidable challenges including protein 3D structure data requisition for model training, auto-regressive sampling, and model generalization for unseen targets. Here, we proposed DiffDTM, a novel conditional structure-free deep generative model based on a diffusion model for dual targets based molecule generation to address the above issues. Specifically, DiffDTM receives protein sequences and molecular graphs as inputs instead of protein and molecular conformations and incorporates an information fusion module to achieve conditional generation in a one-shot manner. We have conducted comprehensive multi-view experiments to demonstrate that DiffDTM can generate drug-like, synthesis-accessible, novel, and high-binding affinity molecules targeting specific dual proteins, outperforming the state-of-the-art (SOTA) models in terms of multiple evaluation metrics. Furthermore, we utilized DiffDTM to generate molecules towards dopamine receptor D2 and 5-hydroxytryptamine receptor 1A as new antipsychotics. The experimental results indicate that DiffDTM can be easily plugged into unseen dual targets to generate bioactive molecules, addressing the issues of requiring insufficient active molecule data for training as well as the need to retrain when encountering new targets.

cs.LG↗

arXiv2023

Revisiting Automatic Question Summarization Evaluation in the Biomedical Domain

Automatic evaluation metrics have been facilitating the rapid development of automatic summarization methods by providing instant and fair assessments of the quality of summaries. Most metrics have been developed for the general domain, especially news and meeting notes, or other language-generation tasks. However, these metrics are applied to evaluate summarization systems in different domains, such as biomedical question summarization. To better understand whether commonly used evaluation metrics are capable of evaluating automatic summarization in the biomedical domain, we conduct human evaluations of summarization quality from four different aspects of a biomedical question summarization task. Based on human judgments, we identify different noteworthy features for current automatic metrics and summarization systems as well. We also release a dataset of our human annotations to aid the research of summarization evaluation metrics in the biomedical domain.

cs.CL↗

arXiv2023

Molecular Geometry-aware Transformer for accurate 3D Atomic System modeling

Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT calculations. Molecular energy is at least related to atoms, bonds, bond angles, torsion angles, and nonbonding atom pairs. Previous Transformer models only use atoms as inputs which lack explicit modeling of the aforementioned factors. To alleviate this limitation, we propose Moleformer, a novel Transformer architecture that takes nodes (atoms) and edges (bonds and nonbonding atom pairs) as inputs and models the interactions among them using rotational and translational invariant geometry-aware spatial encoding. Proposed spatial encoding calculates relative position information including distances and angles among nodes and edges. We benchmark Moleformer on OC20 and QM9 datasets, and our model achieves state-of-the-art on the initial state to relaxed energy prediction of OC20 and is very competitive in QM9 on predicting quantum chemical properties compared to other Transformer and Graph Neural Network (GNN) methods which proves the effectiveness of the proposed geometry-aware spatial encoding in Moleformer.

q-bio.MN↗

arXiv2021

COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.

cs.CL↗