Aaron Ge

Aaron Ge, Monjoy Saha, Maire A. Duggan et al.

Background: Tissue Microarrays (TMAs) significantly increase analytical efficiency in histopathology and large-scale epidemiologic studies by allowing multiple tissue cores to be scanned on a single slide. The individual cores can be digitally extracted and then linked to metadata for analysis in a process known as de-arraying. However, TMAs often contain core misalignments and artifacts due to assembly errors, which can adversely affect the reliability of the extracted cores during the de-arraying process. Moreover, conventional approaches for TMA de-arraying rely on desktop solutions.Therefore, a robust yet flexible de-arraying method is crucial to account for these inaccuracies and ensure effective downstream analyses. Results: We developed TMA-Grid, an in-browser, zero-footprint, interactive web application for TMA de-arraying. This web application integrates a convolutional neural network for precise tissue segmentation and a grid estimation algorithm to match each identified core to its expected location. The application emphasizes interactivity, allowing users to easily adjust segmentation and gridding results. Operating entirely in the web-browser, TMA-Grid eliminates the need for downloads or installations and ensures data privacy. Adhering to FAIR principles (Findable, Accessible, Interoperable, and Reusable), the application and its components are designed for seamless integration into TMA research workflows. Conclusions: TMA-Grid provides a robust, user-friendly solution for TMA dearraying on the web. As an open, freely accessible platform, it lays the foundation for collaborative analyses of TMAs and similar histopathology imaging data. Availability: Web application: https://episphere.github.io/tma-grid Code: https://github.com/episphere/tma-grid Tutorial: https://youtu.be/miajqyw4BVk

Aaron Ge, Jeya Balasubramanian, Xueyao Wu et al.

Genotype imputation enhances genetic data by predicting missing SNPs using reference haplotype information. Traditional methods leverage linkage disequilibrium (LD) to infer untyped SNP genotypes, relying on the similarity of LD structures between genotyped target sets and fully sequenced reference panels. Recently, reference-free deep learning-based methods have emerged, offering a promising alternative by predicting missing genotypes without external databases, thereby enhancing privacy and accessibility. However, these methods often produce models with tens of millions of parameters, leading to challenges such as the need for substantial computational resources to train and inefficiency for client-sided deployment. Our study addresses these limitations by introducing a baseline for a novel genotype imputation pipeline that supports client-sided imputation models generalizable across any genotyping chip and genomic region. This approach enhances patient privacy by performing imputation directly on edge devices. As a case study, we focus on PRS313, a polygenic risk score comprising 313 SNPs used for breast cancer risk prediction. Utilizing consumer genetic panels such as 23andMe, our model democratizes access to personalized genetic insights by allowing 23andMe users to obtain their PRS313 score. We demonstrate that simple linear regression can significantly improve the accuracy of PRS313 scores when calculated using SNPs imputed from consumer gene panels, such as 23andMe. Our linear regression model achieved an R^2 of 0.86, compared to 0.33 without imputation and 0.28 with simple imputation (substituting missing SNPs with the minor allele frequency). These findings suggest that popular SNP analysis libraries could benefit from integrating linear regression models for genotype imputation, providing a viable and light-weight alternative to reference based imputation.

Jonas S Almeida, Daniel E Russ, Susana Vinga et al.

Motivation: With the advent of Language Models using Transformers, popularized by ChatGPT, there is a renewed interest in exploring encoding procedures that numerically represent symbolic sequences at multiple scales and embedding dimensions. The challenge that encoding addresses is the need for mechanisms that uniquely retain contextual information about the succession of individual symbols, which can then be modeled by nonlinear formulations such as neural networks. Context: Universal Sequence Maps(USM) are iterated functions that bijectively encode symbolic sequences onto embedded numerical spaces. USM is composed of two Chaos Game Representations (CGR), iterated forwardly and backwardly, that can be projected into the frequency domain (FCGR). The corresponding USM coordinates can be used to compute a Chebyshev distance metric as well as k-mer frequencies, without having to recompute the embedded numeric coordinates, and, paradoxically, allowing for non-integers values of k. Results: This report advances the bijective fractal encoding by Universal Sequence Maps (USM) by resolving seeding biases affecting the iterated process. The resolution had two results, the first expected, the second an intriguing outcome: 1) full reconciliation of numeric positioning with sequence identity; and 2) uncovering the nature of USM as an efficient numeric process converging towards a steady state sequence embedding solution. We illustrate these results for genomic sequences because of the convenience of a planar representation defined by an alphabet with only 4 tokens (the 4 nucleotides). Nevertheless, the application to alphabet of arbitrary cardinality was found to be straightforward.