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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
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Posts
Future Blog Post
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Blog Post number 4
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
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Blog Post number 2
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Blog Post number 1
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portfolio
Portfolio item number 1
Short description of portfolio item number 1
Portfolio item number 2
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publications
Supervised learning is an accurate method for network-based gene classification
Published in Bioinformatics, 2020
Renming Liu*, Christopher A Mancuso*, Anna Yannakopoulos, Kayla A Johnson, Arjun Krishnan
Paper / GitHub
PecanPy: a fast, efficient and parallelized Python implementation of node2vec
Published in Bioinformatics, 2021
GenePlexus: a web-server for gene discovery using network-based machine learning
Published in Nucleic Acids Research, 2022
Christopher A Mancuso, Patrick S Bills, Douglas Krum, Jacob Newsted, Renming Liu, Arjun Krishnan
Paper / GitHub / WebServer
Applications of an Association Activity Coefficient Model, NRTL-PA, to Alcohol-Containing Mixtures
Published in Industrial & Engineering Chemistry Research, 2022
Aseel M Bala, Renming Liu, Lars Peereboom, Carl T Lira
Paper
Taxonomy of Benchmarks in Graph Representation Learning
Published in LoG'22: Learning on Graphs Conference, 2022
Renming Liu*, Semih Cantürk*, Frederik Wenkel, Sarah McGuire, Xinyi Wang, Anna Little, Leslie O’Bray, Michael Perlmutter, Bastian Rieck, Matthew Hirn, Guy Wolf, Ladislav Rampášek
Paper / GitHub
Accurately modeling biased random walks on weighted networks using node2vec+
Published in Bioinformatics, 2023
Renming Liu, Matthew Hirn, Arjun Krishnan
Paper / Software / Benchmark
PyGenePlexus: a Python package for gene discovery using network-based machine learning
Published in Bioinformatics, 2023
Christopher A Mancuso*, Renming Liu*, Arjun Krishnan
Paper / GitHub / PyPI
Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation
arXiv
Hongzhi Wen, Wenzhuo Tang, Wei Jin, Jiayuan Ding, Renming Liu, Feng Shi, Yuying Xie, Jiliang Tang
Paper
A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models
bioRxiv
Wenzhuo Tang*, Renming Liu*, Hongzhi Wen, Xinnan Dai, Jiayuan Ding, Hang Li, Wenqi Fan, Yuying Xie, Jiliang Tang
Paper / GitHub
Single-Cell Multimodal Prediction via Transformers
Published in CIKM'23: Proceedings of the 32nd ACM International Conference on Information and Knowledge Management, 2023
Wenzhuo Tang*, Hongzhi Wen*, Renming Liu*, Jiayuan Ding, Wei Jin, Yuying Xie, Hui Liu, Jiliang Tang
Paper / GitHub
CONE: COntext-specific Network Embedding via Contextualized Graph Attention
Submitted to MLCB’24
Renming Liu*, Hao Yuan*, Kayla A Johnson, Arjun Krishnan
Paper / GitHub
DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis
Published in Genome Biology, 2024
Jiayuan Ding*, Hongzhi Wen*, Wenzhuo Tang*, Renming Liu*, Zhaoheng Li, Julian Venegas, Runze Su, Dylan Molho, Wei Jin, Wangyang Zuo, Yixin Wang, Robert Yang, Yuying Xie, Jiliang Tang
Paper / GitHub / PyPI
Deep Learning in Single-Cell Analysis
Published in ACM Transactions on Intelligent Systems and Technology, 2024
Dylan Molho*, Jiayuan Ding*, Zhaoheng Li, Hongzhi Wen, Wenzhuo Tang, Yixin Wang, Julian Venegas, Wei Jin, Renming Liu, Runze Su, Patrick Danaher, Robert Yang, Yu Leo Lei, Yuying Xie, Jiliang Tang
Paper
Joint representation of molecular networks from multiple species improves gene classification
Published in PLOS Computational Biology, 2024
Christopher A Mancuso, Kayla A Johnson, Renming Liu, Arjun Krishnan
Paper / GitHub
Graph Positional and Structural Encoder
Published in International Conference on Machine Learning (ICML), 2024
Renming Liu*, Semih Cantürk*, Olivier Lapointe-Gagné, Vincent Létourneau, Guy Wolf, Dominique Beaini, Ladislav Rampášek
Paper / GitHub / Twitter Thread
Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks
Published in Machine Learning in Computational Biology (MLCB). PMLR., 2024
SpatialCTD: a large-scale TME spatial transcriptomic dataset to evaluate cell type deconvolution for immuno-oncology
Published in Journal of Computational Biology, 2024
Jiayuan Ding, Julian Venegas, Qiaolin Lu, Yixin Wang, Lidan Wu, Wei Jin, Hongzhi Wen, Renming Liu, Wenzhuo Tang, Zhaoheng Li, Wangyang Zuo, Yi Chang, Yu Leo Lei, View ORCID ProfilePatrick Danaher, Yuying Xie, Jiliang Tang
Paper
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.