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Xiuli Ma

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4 papers

2 author rows

ECAI Conference 2023 Conference Paper

Attention Based Models for Cell Type Classification on Single-Cell RNA-Seq Data

Tianxu Wang
Yue Fan
Xiuli Ma

Cell type classification serves as one of the most fundamental analyses in bioinformatics. It helps recognizing various cells in cancer microenvironment, discovering new cell types and facilitating other downstream tasks. Single-cell RNA-sequencing (scRNA-seq) technology can profile the whole transcriptome of each cell, thus enabling cell type classification. However, high-dimensional scRNA-seq data pose serious challenges on cell type classification. Existing methods either classify the cells with reliance on the prior knowledge or by using neural networks whose massive parameters are hard to interpret. In this paper, we propose two novel attention-based models for cell type classification on single-cell RNA-seq data. The first model, Cell Feature Attention Network (CFAN), captures the features of a cell and performs attention model on them. To further improve interpretation, the second model, Cell-Gene Representation Attention Network (CGRAN), directly concretizes tokens as cells and genes and uses the cell representation renewed by self-attention over the cell and the genes to predict cell type. Both models show excellent performance in cell type classification; additionally, the key genes with high attention weights in CGRAN indicate and identify the marker genes of the cell types, thus proving the model’s biological interpretation.

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IJCAI Conference 2022 Conference Paper

Multi-Vector Embedding on Networks with Taxonomies

Yue Fan
Xiuli Ma

A network can effectively depict close relationships among its nodes, with labels in a taxonomy describing the nodes' rich attributes. Network embedding aims at learning a representation vector for each node and label to preserve their proximity, while most existing methods suffer from serious underfitting when dealing with datasets with dense node-label links. For instance, a node could have dozens of labels describing its diverse properties, causing the single node vector overloaded and hard to fit all the labels. We propose HIerarchical Multi-vector Embedding (HIME), which solves the underfitting problem by adaptively learning multiple 'branch vectors' for each node to dynamically fit separate sets of labels in a hierarchy-aware embedding space. Moreover, a 'root vector' is learned for each node based on its branch vectors to better predict the sparse but valuable node-node links with the knowledge of its labels. Experiments reveal HIME’s comprehensive advantages over existing methods on tasks such as proximity search, link prediction and hierarchical classification.

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AAAI Conference 2021 Conference Paper

Gene Regulatory Network Inference using 3D Convolutional Neural Network

Yue Fan
Xiuli Ma

Gene regulatory networks (GRNs) consist of gene regulations between transcription factors (TFs) and their target genes. Single-cell RNA sequencing (scRNA-seq) brings both opportunities and challenges to the inference of GRNs. On the one hand, scRNA-seq data reveals statistic information of gene expressions at the single-cell resolution, which is conducive to the construction of GRNs; on the other hand, noises and dropouts pose great difficulties on the analysis of scRNA-seq data, causing low prediction accuracy by traditional methods. In this paper, we propose 3D Co-Expression Matrix Analysis (3DCEMA), which predicts regulatory relationships by classifying 3D co-expression matrices of gene triplets using a 3D convolutional neural network. We found that by introducing a third gene as a comparison factor, our method can avoid the disturbance of noises and dropouts, and significantly increase the prediction accuracy of regulations between gene pairs. Compared with other existing GRN inference algorithms on both in-silico datasets and scRNA-Seq datasets, our algorithm based on deep learning shows higher stability and accuracy in the task of GRN inference.

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AAAI Conference 2016 Conference Paper

EKNOT: Event Knowledge from News and Opinions in Twitter

Min Li
Jingjing Wang
Wenzhu Tong
Hongkun Yu
Xiuli Ma
Yucheng Chen
Haoyan Cai
Jiawei Han

We present the EKNOT system that automatically discovers major events from online news articles, connects each event to its discussion in Twitter, and provides a comprehensive summary of the events from both news media and social media’s point of view. EKNOT takes a time period as input and outputs a complete picture of the events within the given time range along with the public opinions. For each event, EKNOT provides multi-dimensional summaries: a) a summary from news for an objective description; b) a summary from tweets containing opinions/sentiments; c) an entity graph which illustrates the major players involved and their correlations; d) the time span of the event; and e) an opinion (sentiment) distribution. Also, if a user is interested in a particular event, he/she can zoom into this event to investigate its aspects (subevents) summarized in the same manner. EKNOT is built on real-time crawled news articles and tweets, allowing users to explore the dynamics of major events with minimal delays.

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