Work Experience
Data Scientist - Omics data - Machine learning application, GSK
• Develop ML pipeline to perform target nomination, causal network inference and in silico perturbation
• Validation, benchmarking and optimization of statistical and machine learning models
Research Associate , Imperial College London
• Annotation of patient disease profile via natural language processing of clinical documents
- Optical character recognition, RegEx pattern matching, Name Entity Recognition,
pre-trained Bert text embedding
• Genome wide association study of neurodegenerative diseases
- Detect potential causal genetic variants in a sample that comprised of 2.6 millions Single Nucleotide Polymorphisms (Linear Mixed Effect Model, LDSC, MAGMA, gene set enrichment)
- Evaluate the causal relationship of hit genes using eQTL data (Bayes Factor colocalization),
single cell RNAseq (MAGMA cell type specificity), and tissue transcriptomics (WGCNA)
- Designed a browser application for users to search for genotypes information (R shiny)
Principal Investigator, The Alan Turing Institute Data Science Hackathon
• Modelling Amyloid Beta Plaque Formation in Alzheimer's Disease using VAE and VGG-16
Project link
- Development of image segmentation methodology to automatically extract amyloid plaque regions from immunohistochemistry stainned brain images
- Leverage Variational Autoencoder (VAE) and pretrained VGG-16 convolutional neural network for the extraction of amyloid plaque morphological features
- Evaluate the relationship between plaque image features and spatial transcriptomics gene expression information
Research Associate, University College London
• Identify the key features in brain oscillation that influence motor-behavioral outcome
- Time frequency spectral analysis, linear mixed effects models, permutation statistics
- Created recurrent neural networks (LSTM, GRU) and Bayesian optimized XGBoost models to
learn the relationship between brain oscillations and motor behavior
- Using SHAP approach to evaluate the key determinants in model decision
• Generated a data processing pipeline for the neurophysiological and behavioral data
- Multi-sources data extraction, alignment, noise detection and removal
- Neuronal spike sorting: filtering, SVD whitening, PCA, superparamagnetic clustering
• Designed and engineered training devices for monkeys
- Programmed an android app and Arduino device for cue delivery and trial counting
• 3D registration of brain recording location using stereotaxic and MRI image coordinates
- MRI brain image processing, 3D rigid transform
• Performed brain implants and electromyography surgeries as the second surgeon
Businees Partner, LebeLohas
