Alice Yue

PhDC in computing science

Hi! I am a PhD candidate in the department of computing science at SFU (CGPA: 4.33/4.33) under the supervision of Cedric Chauve, Maxwell Libbrecht, and Ryan Brinkman. Previously, I recieved my MSc at SFU and my BSc with distinction at UVic (CGPA:8.7/9.0) in the beautiful city of Victoria.

Research interests: I develop machine learning, data mining, and statistical analysis methods for high-dimensional and graph structured data. In bioinformatics, I have applied my methods on flow cytometry, scRNAseq, and DNA sequence data.

Publications

  1. Yue, Alice, et al. “Automated Identification of Maximal Differential Cell Populations in Flow Cytometry Data.” BioRxiv [Accepted to Cytometry Part A], Cold Spring Harbor Laboratory, 2020, p. 837765, doi:10.1101/837765.
  2. Abeler-Dörner, Lucie, et al. “High-Throughput Phenotyping Reveals Expansive Genetic and Structural Underpinnings of Immune Variation.” Nature Immunology, vol. 21, no. 1, Nature Publishing Group, 2020, pp. 86–100, doi:10.1038/s41590-019-0549-0.
  3. Yue, Alice, et al. “Identifying Differential Cell Populations in Flow Cytometry Data Accounting for Marker Frequency.” Poster and Spotlight Presentation at the 14th Machine Learning in Computational Biology (MLCB) Conference, Previously a Workshop of NeurIPS, 2019.
  4. Rajasekaran, Ashwini, et al. “Cholinergic Synapse Pathway Gene Polymorphisms Associated with Allergen-Induced Late Asthmatic Responses.” ERJ Open Research, vol. 5, no. 4, Eur Respiratory Soc, November 2019, doi:10.1183/23120541.00107-2019.
  5. Cossarizza, Andrea, et al. “Guidelines for the Use of Flow Cytometry and Cell Sorting in Immunological Studies.” European Journal of Immunology, vol. 49, no. 10, Wiley Online Library, 2019, pp. 1457–973, doi:10.1002/eji.201970107.
  6. Rahim, Albina, et al. “High Throughput Automated Analysis of Big Flow Cytometry Data.” Methods, vol. 134, Elsevier, 2018, pp. 164–76, doi:10.1016/j.ymeth.2017.12.015.
  7. Yue, Alice. Feature-Based Comparison of Flow Cytometry Data. Applied Sciences: School of Computing Science, 2017.
  8. Cossarizza, Andrea, et al. “Guidelines for the Use of Flow Cytometry and Cell Sorting in Immunological Studies.” European Journal of Immunology, vol. 47, no. 10, Wiley Online Library, 2017, pp. 1584–797.

Paper review

Reviewed papers for: ACM (2018), ISMB (2019, 2020), Neurips (2020), Oxford Bioinformatics (2016, 2020), and RECOMB (2020)

Committe member for: MLCB (2019)

Github repositories

This repository contains the files for the summer 2021 CMPT 127 course at SFU.
Accurately selects cell populations features that differentiate between flow cytometry sample classes by removing top-down dependency between features modelled on a lattice.
Analysis of blood-based omics data to identify biomarkers related to early and dual asthmatic response.
An R script that uses igraph layouts to plot pretty graphs with ggplot2.
A pipeline for extracting features from and biclustering flow cytometry data
Uses RNAseq data and various feature extraction & machine learning algorithms to predict human gestational age.
Compares several different machine learning models and statistical features to predict the liveness of the fingerprint biometric.
Infers the infection pathway of the influenza virus using various sequence and tree statistics: created for the bioinformatics project @ 2018 invent the future, SFU
Uses Bayesian phylogenetic inference and graph-based tree shape algorithms to build separate and consolidated ancestral trees of salmonoid fish
Uses feature engineering to compare and cluster hierarchical FCS data
Implements an interface between relational databases and XML framework built on a common gateway model to convert pharmaceutical data between medical facilities
learns and predicts in an unsupervised manner, missing words given a list of anonymized and corrupted text articles
Implements a PL/SQL-based database and medical information management system; also contains the HCI and relational database EML model designs

Teaching

Summer 2021: Sessional instructor for CMPT 127 (computing laboratory C/C++; see course website [here]).

Summer 2021: Developed introductory programming material for the faculty of applied science START program for entering undergraduate students (see the programming information sheet [here]).

Fall 2018: Guest lecturer for CMPT 884 (data mining seminar).

Teaching assistant for: CMPT 105 (technical writing; Fall 2019), 120 (introduction to computing science; Spring 2018, Fall 2020), and 225 (data structures; Fall 2018).

Part of the pilot program for the first ISG (instructional support group) model for online post-secondary education at SFU.

Scholarships and awards

  • 2021 Wilson Clark Graduate Scholarship, SFU
  • 2015 - 2021 Compting Sience Graduate Fellowship, SFU
  • 2017 - 2020 Canada Graduate Scholarships PGS-D, NSERC
  • 2019 DBMiner Award, SFU
  • 2016 Canada Graduate Scholarships MSc Program, NSERC
  • 2015 MADD-Gen MSc fellowship, SFU, NSERC
  • 2014 Audrey May McCormick Scholarship, UVic
  • 2013, 2014 Mrs Annie Greskiw Scholarship, UVic
  • 2012 - 2015 UVic Excellence Scholarship, UVic
  • 2012, 2013 Dr Ken and Barbara Thornton Memorial Award, UVic
  • 2012 Steven A Huesing Memorial Entrance Scholarship, UVic
  • 2012 Governor General Academic Medal, Chancellery of Honours, Canada
  • 2012 Coast Capital Standing Tall Award
  • 2012 Johnson Inc Sky's the Limit Scholarship
  • 2010-2012 Service Award with Distinction, Byrne Creek
  • 2011 National AP Scholar (Canada)

Service

  • 2017 - 2021 President (past: VP of Finance, GSS councillor, TSSU steward), Computing science graduate student association, SFU

    Sucessfully re-initiated and created administrative structure to an inactive caucus. Provided oversight, and organized social and academic events for the student body;

    e.g. general meetings, lunch social, facuty candidate seminar lunch, game night, logo contest, amenity cleaning socials, buddy program for new students.

    Acted as the liason between the school, GSS (graduate student society), TSSU (union for TA & RA), and the student body.

  • 2017 - 2021 Treasurer, computing science steward, TSSU, SFU

    In charge of bookkeeping (payroll, stipends, remittences, bill payments, etc.), budget creation, financial reporting, and process improvements.

    Acted as liason between students and the TSSU (teachin support staff union).

  • 2018, 2019 Mentor, AI4All Invent the Future Scholars Program SFU

    Mentored and created projects for the bioinformatics group during the first and second annual summer enrichment program for high school girls in Canada.

    Github repositories: [2018], [2019].