5 papers
Fractal Language Modelling by Universal Sequence Maps (USM)
Jonas S Almeida, Daniel E Russ, Susana Vinga +6
Motivation: With the advent of Language Models using Transformers, popularized by ChatGPT, there is a renewed interest in exploring encoding procedures that numerically represent s…
TMA-Grid: An open-source, zero-footprint web application for FAIR Tissue MicroArray De-arraying
Aaron Ge, Monjoy Saha, Maire A. Duggan +6
Background: Tissue Microarrays (TMAs) significantly increase analytical efficiency in histopathology and large-scale epidemiologic studies by allowing multiple tissue cores to be s…
FastImpute: A Baseline for Open-source, Reference-Free Genotype Imputation Methods -- A Case Study in PRS313
Aaron Ge, Jeya Balasubramanian, Xueyao Wu +2
Genotype imputation enhances genetic data by predicting missing SNPs using reference haplotype information. Traditional methods leverage linkage disequilibrium (LD) to infer untype…
mSigSDK -- private, at scale, computation of mutation signatures
Aaron Ge, Yasmmin Côrtes Martins, Tongwu Zhang +5
In our previous work, we demonstrated that it is feasible to perform analysis on mutation signature data without the need for downloads or installations and analyze individual pati…
A FAIR platform for reproducing mutational signature detection on tumor sequencing data
Aaron Ge, Tongwu Zhang, Clara Bodelon +3
This paper presents a portable, privacy-preserving, in-browser platform for the reproducible assessment of mutational signature detection methods from sparse sequencing data genera…