Peter Kraft

Robert Redmond, Nathan W. Weckwerth, Brian S. Xia et al.

We recently proposed a new cluster operating system stack, DBOS, centered on a DBMS. DBOS enables unique support for ML applications by encapsulating ML code within stored procedures, centralizing ancillary ML data, providing security built into the underlying DBMS, co-locating ML code and data, and tracking data and workflow provenance. Here we demonstrate a subset of these benefits around two ML applications. We first show that image classification and object detection models using GPUs can be served as DBOS stored procedures with performance competitive to existing systems. We then present a 1D CNN trained to detect anomalies in HTTP requests on DBOS-backed web services, achieving SOTA results. We use this model to develop an interactive anomaly detection system and evaluate it through qualitative user feedback, demonstrating its usefulness as a proof of concept for future work to develop learned real-time security services on top of DBOS.

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.

Peter Kraft, Daniel Kang, Deepak Narayanan et al.

Systems for ML inference are widely deployed today, but they typically optimize ML inference workloads using techniques designed for conventional data serving workloads and miss critical opportunities to leverage the statistical nature of ML. In this paper, we present Willump, an optimizer for ML inference that introduces two statistically-motivated optimizations targeting ML applications whose performance bottleneck is feature computation. First, Willump automatically cascades feature computation for classification queries: Willump classifies most data inputs using only high-value, low-cost features selected through empirical observations of ML model performance, improving query performance by up to 5x without statistically significant accuracy loss. Second, Willump accurately approximates ML top-K queries, discarding low-scoring inputs with an automatically constructed approximate model and then ranking the remainder with a more powerful model, improving query performance by up to 10x with minimal accuracy loss. Willump automatically tunes these optimizations' parameters to maximize query performance while meeting an accuracy target. Moreover, Willump complements these statistical optimizations with compiler optimizations to automatically generate fast inference code for ML applications. We show that Willump improves the end-to-end performance of real-world ML inference pipelines curated from major data science competitions by up to 16x without statistically significant loss of accuracy.