Qiao Jin

5607 Baum Boulevard · Pittsburgh, PA 15206 · (412) 628-7086 · jinqiao.andy@gmail.com

I am a fifth year M.D. candidate at School of Medicine, Tsinghua University, currently visiting Department of Biomedical Informatics, University of Pittsburgh. I am interested in deep learning for natural language processing in biomedical fields. My advisor is Prof. Xinghua Lu and I am also supervised by Prof. Lu's collaborator Prof. William Cohen at CMU. I worked with Prof. Xuegong Zhang at Tsinghua University.

My dream is to create AGI in biomedical field, which will empower human doctors and researchers with the Unreasonable Effectiveness of Data. I also dream of contributing to the revolution of medical education in the era of AI. Moreover, I have an enthusiasm for democratizing medicine, i.e., making the medical knowledge, resources and techniques available to everyone that needs them.

Qiao is currently looking for AI&Biomed research internship opportunities for summer, 2019.

News

Began my 2-year research at Pitt (as a visiting scholar)
August 2017

Education

Tsinghua University

Bachelor of Science, Doctor of Medicine
Clinical Medicine

Overall GPA 93.27/100, Rank 1/32

August 2014 - Present

Experiences

Medical Student

School of Medicine, Tsinghua University

[Video (Chinese)] [Program Intro]

Our program is aimed at cultivation of the so-called 'Physician Scientists'. Most (if not all) of the graduates from this program will practice medicine in top hospitals of China. Obviously, I might be one exception.

August 2014 - Present

Research Assistant

DBMI of UPitt, MLD of CMU
Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning [bioRxiv] [pdf]

The increasing amount of scientific literature in biological and biomedical science research has created a challenge in continuous and reliable curation of the latest knowledge discovered, and automatic biomedical text-mining has been one of the answers to this challenge. In this paper, we aim to further improve the reliability of biomedical text-mining by training the system to directly simulate the human behaviors such as querying the PubMed, selecting articles from queried results, and reading selected articles for knowledge. We take advantage of the efficiency of biomedical text-mining, the flexibility of deep reinforcement learning, and the massive amount of knowledge collected in UMLS into an integrative artificial intelligent reader that can automatically identify the authentic articles and effectively acquire the knowledge conveyed in the articles.

We construct a system, whose current primary task is to build the genetic association database between genes and complex traits of human. Our contributions in this paper are three-fold: 1) We propose to improve the reliability of text-mining by building a system that can directly simulate the behavior of a researcher, and we develop corresponding methods, such as Bi-directional LSTM for text mining and Deep Q-Network for organizing behaviors. 2) We demonstrate the effectiveness of our system with an example in constructing a genetic association database. 3) We release our implementation as a generic framework for researchers in the community to conveniently construct other databases.

AttentionMeSH: Interpretable and Scalable Automatic MeSH Indexer [pdf] [code] [slides]

There are millions of articles in PubMed database. To facilitate information retrieval, curators in the National Library of Medicine (NLM) assign a set of Medical Subject Headings (MeSH) to each article. MeSH is a hierarchically-organized vocabulary, containing about 28K different concepts, covering the fields from clinical medicine to information sciences. Several automatic MeSH indexing models have been developed to improve the time-consuming and financially expensive manual annotation, including the NLM official tool -- Medical Text Indexer, and the winner of BioASQ Task5a challenge -- DeepMeSH. However, these models are complex and not interpretable. We propose a novel end-to-end model, AttentionMeSH, which utilizes deep learning and attention mechanism to index MeSH terms to biomedical text. The attention mechanism enables the model to associate textual evidence with annotations, thus providing interpretability at the word level. The model also uses a novel masking mechanism to enhance accuracy and speed. In the final week of BioASQ Chanllenge Task6a, we ranked 2nd by average MiF using an on-construction model. After the contest, we achieve close to state-of-the-art MiF performance of ~0.684 using our final model. Human evaluations show AttentionMeSH also provides high level of interpretability, retrieving about 90% of all expert-labeled relevant words given an MeSH-article pair at 20 output.

Neural Models for Reasoning over Multiple Mentions [arXiv] [pdf] [code]

Many problems in NLP require aggregating information from multiple mentions of the same entity which may be far apart in the text. Existing Recurrent Neural Network (RNN) layers are biased towards short-term dependencies and hence not suited to such tasks. We present a recurrent layer which is instead biased towards coreferent dependencies. The layer uses coreference annotations extracted from an external system to connect entity mentions belonging to the same cluster. Incorporating this layer into a state-of-the-art reading comprehension model improves performance on three datasets -- Wikihop, LAMBADA and the bAbi AI tasks -- with large gains when training data is scarce.

October 2017 - Present

Undergraduate Research Assistant

Department of Automation, Tsinghua University
In silico re-deciphering of the genetic code [Report]

My first deep learning project performed in Jan 2017. I tried biological seq2seq (from mRNA to Protein translation) and re-deciphered the genetic code in silico.

Permutation clustering of the DNA sequence facilitates understanding of the nonlinearly organized genome [Proposal]

I tried a permutation-based clustering approach on Hi-C data and identified several interesting patterns after permutation clustering. [Slides of the proposal]

September 2016 - August 2017

Member of Tsinghua 2016 iGEM Team

School of Life Sciences, Tsinghua University
A CRISPR/Cas9-based gene surveillance system in S. cerevisiae [Project Website]

Genetic mutations are the fundation of cancer development. We propose to construct a suvCas9 system in Saccharomyces cerevisiae to function as the monitor of genomic sequence. The system has the potential to prevent carcinogenesis by killing all the mutated cells. [This video] gives an introduction of how our system works.

This project won a Gold Medal in iGEM 2016.

December 2015 - November 2016

Undergraduate Research Assistant

School of Aerospace, Tsinghua University
Building of an orthopedics surgical robot with visual servo system [Patent]

We built a robot with visual servo system that can perform fracture restoration surgery. I am in charge of the computer vision part. We had a patent in China and applied for some more Chinese and international patents.

October 2016 - August 2017

Undergraduate Research Assistant (Student Leader)

School of Medicine, Tsinghua University
Based on a sequenced pedigree: a novel TTN truncating variant related to dilated cardiomyopathy

We reported a case of DCM where genetic testing identified a novel familial truncating mutation in the TTN gene. We believe it follows an autosomal-dominant inheritance pattern with low penetrance. Genetic testing results of the family members identified his son, brother and brother’s daughter as carriers, but they are not clinically affected. We speculate that the unfavorable lifestyle of the patient may contribute to the disease. Our findings may provide some insights of prevention, diagnosis and management of DCM with similar mutations and demonstrate the importance of genetic screening of family members after finding an index patient.

January 2016 - August 2017

Xuetang Talent

Tsinghua University

Guess where I am?

Februay 2016 - August 2017

Class President

Class Bio47, Tsinghua University

I focused on building a good academic atmosphere during my term. Average GPA of the class increased by 2 percents. We also won the 'Jiatuan' of Tsinghua University, which is a top honor only for the best classes in the university.

And yes - we do have a term limit!

September 2015 - September 2016

Intern

Peking Union Medical College Hospital & Beijing Tsinghua Changgung Hospital

Shadowing program: Dpt. of Neurosurgery and Dpt. of Infectious Disease at Peking Union Medical College Hospital (北京协和医院); Multiple important departments at Beijing Tsinghua Changgung Hospital (北京清华长庚医院).

July 2016

Team Leader

Healper, a 'pre-start-up' company

A Beijing Undergraduate Training Program for Innovation and Entrepreneurship funded by the Government of Beijing. Healper is a chat robot for health management based on questionares. Our project was graded excellence by the committee.

August 2016 - August 2017

Papers & Patents

  1. Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning [bioRxiv] [pdf]
    Haohan Wang, Xiang Liu, Yifeng Tao, Wenting Ye, Qiao Jin, William W. Cohen and Eric P. Xing
    PSB, 2019
  2. AttentionMeSH: Simple, Effective and Interpretable Automatic MeSH Indexer [pdf] [code] [slides]
    Qiao Jin, Bhuwan Dhingra, William W. Cohen and Xinghua Lu
    EMNLP BioASQ, 2018
  3. Neural Models for Reasoning over Multiple Mentions using Coreference [arXiv] [pdf] [code]
    Bhuwan Dhingra, Qiao Jin, Zhilin Yang, William W. Cohen and Ruslan Salakhutdinov
    NAACL, 2018
  4. Visual Servo Control Method of Multi-Task Surgical Robot [Application]
    Shijie Zhu, Yu Chen, Bicong Zhang, Yitong Chen, Qiao Jin, Jiawei Sun, Boyuan Deng, Liyuan Jiang, Gangtie Zheng, Yongwei Pan, Zhe Zhao, Jiuzheng Deng
    Patent filed in China, 2017

Awards & Honors

Scholarships

  • National Scholarship - Ministry of Education of China 2015
  • Scholarship for Academic Excellence - Tsinghua University 2015, 2016, 2017, 2018
  • Scholarship for Science and Technology Innovation - Tsinghua University 2016, 2017
  • Scholarship for Comprehensive Excellence - Tsinghua University 2016, 2017
  • Tsinghua - Wuliangye Technology Jiujiu Scholarship 2016
  • Tsinghua - Dalian Yejian Scholarship 2017, 2018
  • Xuetang Scholarship - Tsinghua University 2016, 2017

Research and Contest Awards

  • Chinese Chemistry Olympiad (CChO) Gold Medal - Chinese Chemical Society (CCS) 2013
  • International Genetically Engineered Machine (iGEM) Competition Gold Medal - iGEM Foundation 2015
  • Second Prize SRT Project (Based on a sequenced pedigree: a novel TTN truncating variant related to dilated cardiomyopathy) - Tsinghua University 2017
  • Second Prize SRT Project (Building of an orthopedics surgical robot with visual servo system) - Tsinghua University 2017

Skills

Programming Languages & Tools
  • R
  • Python
  • PyTorch
  • LaTeX
  • HTML5
Biology Techniques
  • Molecular Biology Techniques (PCR, Electrophoresis ...)
  • Genetics Techiniques (Knock-out mice ...)
  • Cell Biology Techniques (Cell Culture ...)
  • Biochemistry Techniques (ELISA ...)
  • Bioinformatics Techniques (BLAST, RNA-seq data analysis ...)
Basic Medical Sciences
  • Dissection/Biopsy of:
    • Rabbit
    • Toad
    • Mouse
    • Fruit Fly
    • Zebra Fish
    • Human (Body Donation)
  • Culture/Identification of common human-related:
    • Bacteria
    • Viruses
    • Parasites
Clinical Medicine
  • Drawing Blood from Veins
  • Performing Electronic Cardiography (ECG)
Natural Languages
  • Chinese, native
  • English, fluent

Miscellaneous

I have been deeply influenced and inspired by Richard Feynman and Linus Pauling ever since my senior high school.

I enjoy long-distance running, which is inspired by my hero Prof. Yigong Shi.

I love music. Cheer Chen 陳綺貞 is my favorite singer and songwriter.

Travelling is part of me, so I am always on the way. Here are the places I've visited:

  • MAINLAND CHINA 中国大陆 - from 1996 to 2017,
    • Xiangyang City 襄阳市 - Home sweet home - from 1996 to 2014 (when I went to university)
    • Beijing City 北京市 - Not so sweet (especially the air) - from 2014 to 2017
    • Xiamen City 厦门市 - My ideal city to live - 2017 Summer
    • Nanjing City 南京市 - - 2017 Summer
    • Chengdu City 成都市 - Hot weather, hot girls and hot pots - 2017 Summer
    • Chongqing City 重庆市 - Same as Chengdu City - 2014 Summer, 2017 Summer
    • Shenzhen City 深圳市 - - 2017 April
    • Hangzhou City 杭州市 - - 200?, 2015 Summer
    • Suzhou City 苏州市 - Here lied some bad memories - 2015 Summer
    • Zhoushan City 舟山市 - - 2015 Summer
    • Ningbo City 宁波市 - - 2015 Summer
    • Tianjin City 天津市 - With a punk girl - 2015 October
    • Shanghai City 上海市 - - 2010 Summer (Expo)
    • Wuhan City 武汉市 - - Countless times (Wuhan is the capital of the Province I lived in, Hubei)
    • Zhangjiakou City 张家口市 - 2016 October
    • Changde City 常德市 - 200? Summer
    • Zhangjiajie 张家界 - Failed to find a savage. I really tried! - 200? Summer
    • Qingdao City 青岛市 - 200? Summer
    • Guizhou Province 贵州省 - We were literally climbing mountains every day - 2014 Summer
    • Fenghuang Town 凤凰古镇 - - 2014 Summer
    • Chadong Town 茶峒/边城 - - 2014 Summer
    • Jiaxing Town 嘉兴 - - 2015 Summer
  • TAIWAN 台灣 - Planning to visit Taiwan again, any companion? - 2016 Summer
    • Taipei 台北 - Emmm, the city where Cheer Chen lives
    • Hsinchu 新竹
    • Taoyuan 桃園
    • Tainan 台南
    • Kaohsiung 高雄
    • Kenting 墾丁 - Here lied my best memories of 2016
  • HONG KONG 香港 - Where I met Cheer Chen for the first time - 2017 April
  • MACAU 澳門 - I am too young to enter the casinos - 2017 April
  • UNITED STATES
    • Pittsburgh - - from October 2017
    • Washington, D.C. - - 2017 Winter, 2018 September
    • New York - - 2017 Winter
    • Boston - - 2016 November, 2017 Winter
    • Providence - - 2017 Winter
    • Chicago - I physically felt the 'Windy City' before being told the name - 2017 Thanksgiving
    • Raccoon Creek State Park - 2018 Spring
    • New Orleans - 2018 June
    • Yellowstone & Grand Teton National Park - The most beautiful scenery I've seen - 2018 June
    • Philadelphia - 2018 August
    • Erie - 2018 August
    • Great Allegheny Passage (biking Pittsburgh >> Cumberland. 240km for 3 days.) - Great scenery and nice people! - 2018 August
    • Cleveland - 2018 September
  • EUROPE
    • Barcelona - We had a big win against Real Madrid (5:1). Barca, Barca, Barca! - 2018 October
    • Brussels - 2018 November

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