Devin Kwok
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View article: The Butterfly Effect: Neural Network Training Trajectories Are Highly Sensitive to Initial Conditions
The Butterfly Effect: Neural Network Training Trajectories Are Highly Sensitive to Initial Conditions Open
Neural network training is inherently sensitive to initialization and the randomness induced by stochastic gradient descent. However, it is unclear to what extent such effects lead to meaningfully different networks, either in terms of the…
View article: Simultaneous linear connectivity of neural networks modulo permutation
Simultaneous linear connectivity of neural networks modulo permutation Open
Neural networks typically exhibit permutation symmetries which contribute to the non-convexity of the networks' loss landscapes, since linearly interpolating between two permuted versions of a trained network tends to encounter a high loss…
View article: Dataset Difficulty and the Role of Inductive Bias
Dataset Difficulty and the Role of Inductive Bias Open
Motivated by the goals of dataset pruning and defect identification, a growing body of methods have been developed to score individual examples within a dataset. These methods, which we call "example difficulty scores", are typically used …
View article: RAVAR: a curated repository for rare variant–trait associations
RAVAR: a curated repository for rare variant–trait associations Open
Rare variants contribute significantly to the genetic causes of complex traits, as they can have much larger effects than common variants and account for much of the missing heritability in genome-wide association studies. The emergence of…
View article: Neural Networks as Paths through the Space of Representations
Neural Networks as Paths through the Space of Representations Open
Deep neural networks implement a sequence of layer-by-layer operations that are each relatively easy to understand, but the resulting overall computation is generally difficult to understand. We consider a simple hypothesis for interpretin…
View article: Disentangling genetic feature selection and aggregation in transcriptome-wide association studies
Disentangling genetic feature selection and aggregation in transcriptome-wide association studies Open
The success of transcriptome-wide association studies (TWAS) has led to substantial research toward improving the predictive accuracy of its core component of genetically regulated expression (GReX). GReX links expression information with …
View article: webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study Open
The development of transcriptome-wide association studies (TWAS) has enabled researchers to better identify and interpret causal genes in many diseases. However, there are currently no resources providing a comprehensive listing of gene-di…
View article: Power analysis of transcriptome-wide association study: Implications for practical protocol choice
Power analysis of transcriptome-wide association study: Implications for practical protocol choice Open
The transcriptome-wide association study (TWAS) has emerged as one of several promising techniques for integrating multi-scale ‘omics’ data into traditional genome-wide association studies (GWAS). Unlike GWAS, which associates phenotypic v…
View article: Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding
Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding Open
DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple ind…
View article: Disentangling genetic feature selection and aggregation in transcriptome-wide association studies
Disentangling genetic feature selection and aggregation in transcriptome-wide association studies Open
The success of transcriptome-wide association studies (TWAS) has led to substantial research towards improving its core component of genetically regulated expression (GReX). GReX links expression information with phenotype by serving as bo…
View article: kTWAS: Integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes
kTWAS: Integrating kernel-machine with transcriptome-wide association studies improves statistical power and reveals novel genes Open
The power of genotype-phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation metho…