Zulal Bingol | Searcharxiv

arXiv2026

FASTR: Reimagining FASTQ via Compact Image-inspired Representation

Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per base and one byte per quality score, leading to inefficient I/O, high storage costs, and redundancy. Existing compression tools can mitigate some issues, but often introduce costly decompression or complex dependency issues. Results: We introduce FASTR, a lossless, computation-native successor to FASTQ that encodes each nucleotide together with its base quality score into a single 8-bit value. FASTR reduces file size by at least 2x while remaining fully reversible and directly usable for downstream analyses. Applying general-purpose compression tools on FASTR consistently yields higher compression ratios, 2.47, 3.64, and 4.8x faster compression, and 2.34, 1.96, 1.75x faster decompression than on FASTQ across Illumina, HiFi, and ONT reads. FASTR is machine-learning-ready, allowing reads to be consumed directly as numerical vectors or image-like representations. We provide a highly parallel software ecosystem for FASTQ-FASTR conversion and show that FASTR integrates with existing tools, such as minimap2, with minimal interface changes and no performance overhead. By eliminating decompression costs and reducing data movement, FASTR lays the foundation for scalable genomics analyses and real-time sequencing workflows. Availability and Implementation: https://github.com/ALSER-Lab/FASTR

q-bio.GN↗

arXiv2025

Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory

We introduce IMPACT, a set of high-throughput main memory-based timing attacks that leverage characteristics of processing-in-memory (PiM) architectures to establish covert and side channels. IMPACT enables high-throughput communication and private information leakage by exploiting the shared DRAM row buffer. To achieve high throughput, IMPACT (i) eliminates expensive cache bypassing steps required by processor-centric memory-based timing attacks and (ii) leverages the intrinsic parallelism of PiM operations. We showcase two applications of IMPACT. First, we build two covert channels that leverage different PiM approaches (i.e., processing-near-memory and processing-using-memory) to establish high-throughput covert communication channels. Our covert channels achieve 8.2 Mb/s and 14.8 Mb/s communication throughput, respectively, which is 3.6x and 6.5x higher than the state-of-the-art main memory-based covert channel. Second, we showcase a side-channel attack that leaks private information of concurrently-running victim applications with a low error rate. Our source-code is openly and freely available at https://github.com/CMU-SAFARI/IMPACT.

cs.CR↗