Author name cluster

Cheng Chang

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5 papers

2 author rows

AAAI Conference 2025 Conference Paper

DUSTED: Dual-Attention Enhanced Spatial Transcriptomics Denoiser

Jun Zhu
Yifu Li
Zhenchao Tang
Cheng Chang

Spatially Resolved Transcriptomics (SRT) has become an indispensable tool in various fields, including tumor microenvironment identification, neurobiology, and the study of complex tissue architecture. However, the accuracy of these insights is often compromised by noise in spatial transcriptomics data due to technical limitations. While recent advancements in denoising methods have shown some promise, they frequently fall short by neglecting spatial features, overlooking the variability in noise levels among genes, and relying heavily on external histological images for supplementary information. In our study, we propose DUSTED, a Dual-Attention Enhanced Spatial Transcriptomics Denoiser, designed to address these challenges. Built on a graph autoencoder framework, DUSTED utilizes gene channel attention and graph attention mechanisms to simultaneously consider spatial features and noise variability in gene expression data. Additionally, it integrates the negative binomial distribution with or without zero-inflation, ensuring a more accurate fit for gene expression distributions. Benchmark tests using simulated datasets demonstrate that DUSTED outperforms existing methods. Furthermore, in real-world applications with the HOCWTA and DLPFC datasets, DUSTED excels in enhancing the correlation between gene and protein expression, recovering spatial gene expression patterns, and improving clustering results. These improvements underscore its potential impact on advancing our understanding of tumor microenvironments, neural tissue organization, and other biologically significant areas.

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TMLR Journal 2025 Journal Article

Is Your LLM Secretly a World Model of the Internet? Model-Based Planning for Web Agents

Yu Gu
Kai Zhang
Yuting Ning
Boyuan Zheng
Boyu Gou
Tianci Xue
Cheng Chang
Sanjari Srivastava

Language agents based on large language models (LLMs) have demonstrated great promise in automating web-based tasks. Recent work has shown that incorporating advanced planning algorithms, e.g., tree search, is advantageous over reactive planning for web agents. However, unlike simulated sandbox environments, real-world environments such as the web are rife with irreversible actions. This undermines the feasibility of backtracking, a cornerstone of (tree) search. Overly relying on test-time search also hurts efficiency. We advocate model-based planning for web agents that employs a world model to simulate and deliberate over the outcome of each candidate action before committing to one. We systematically explore this paradigm by: (1) Proposing a model-based planning framework, WebDreamer, which employs LLMs to serve as both world models and value functions; (2) Training specialized LLMs as world models with a scalable data synthesis pipeline. Empirical results demonstrate that WebDreamers achieves substantial performance improvements over reactive baselines. It is competitive, while being - times more efficient, with tree search in sandbox environments (VisualWebArena) and also works effectively on real-world websites (Online-Mind2Web and Mind2Web-Live). Furthermore, our trained world model, Dreamer-7B, performs comparable to GPT-4o, highlighting the potential of specialized world models for efficient and effective planning in complex web environments. All code, models, and data are publicly available at https://github.com/OSU-NLP-Group/WebDreamer

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AAAI Conference 2024 Conference Paper

ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing

Zhi Jin
Sheng Xu
Xiang Zhang
Tianze Ling
Nanqing Dong
Wanli Ouyang
Zhiqiang Gao
Cheng Chang

De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translation task, potentially overlooking critical nuances between spectra and peptides. In our research, we present ContraNovo, a pioneering algorithm that leverages contrastive learning to extract the relationship between spectra and peptides and incorporates the mass information into peptide decoding, aiming to address these intricacies more efficiently. Through rigorous evaluations on two benchmark datasets, ContraNovo consistently outshines contemporary state-of-the-art solutions, underscoring its promising potential in enhancing de novo peptide sequencing.

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NeurIPS Conference 2019 Conference Paper

Guided Similarity Separation for Image Retrieval

Chundi Liu
Guangwei Yu
Maksims Volkovs
Cheng Chang
Himanshu Rai
Junwei Ma
Satya Krishna Gorti

Despite recent progress in computer vision, image retrieval remains a challenging open problem. Numerous variations such as view angle, lighting and occlusion make it difficult to design models that are both robust and efficient. Many leading methods traverse the nearest neighbor graph to exploit higher order neighbor information and uncover the highly complex underlying manifold. In this work we propose a different approach where we leverage graph convolutional networks to directly encode neighbor information into image descriptors. We further leverage ideas from clustering and manifold learning, and introduce an unsupervised loss based on pairwise separation of image similarities. Empirically, we demonstrate that our model is able to successfully learn a new descriptor space that significantly improves retrieval accuracy, while still allowing efficient inner product inference. Experiments on five public benchmarks show highly competitive performance with up to 24\% relative improvement in mAP over leading baselines. Full code for this work is available here: https: //github. com/layer6ai-labs/GSS.

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ECAI Conference 2016 Conference Paper

Topic-Level Influencers Identification in the Microblog Sphere

Yakun Wang
Zhongbao Zhang
Sen Su
Cheng Chang
Muhammad Azam Zia

This paper studies the problem of identifying influencers on specific topics in the microblog sphere. Prior works usually use the cumulative number of social links to measure users' topic-level influence, which ignores the dynamics of influence. As a result, they usually find faded influencers. To address the limitations of prior methods, we propose a novel probabilistic generative model to capture the variation of influence over time. Then a influence decay method is proposed to measure users' current topic-level influence.

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