arXiv subjects

Emil Vatai

Publications and source records attributed to Emil Vatai.

5 recordsLinked to original sources

arXiv2026

Looking for (Genomic) Needles in a Haystack: Sparsity-Driven Search for Identifying Correlated Genetic Mutations in Cancer

Cancer typically arises not from a single genetic mutation (i.e., hit) but from multi-hit combinations that accumulate within cells. However, enumerating multi-hit combinations becomes exponentially more expensive computationally as the number of candidate hit gene combinations grow, i.e. on the order of 20,000 choose h, where 20,000 is the number of genes in the human genome and h is the number of hits. To address this challenge, we present an algorithmic framework, called Pruned Depth-First Search (P-DFS) that leverages the high sparsity in tumor mutation data to prune large portions of the search space. Specifically, P-DFS (the main contribution of this paper) - a pruning technique that exploits sparsity to drastically reduce the otherwise exponential h-hit search space for candidate combinations used by Weighted Set Cover - which is grounded in a depth-first search backtracking technique, prunes infeasible gene subsets early, while a weighted set cover formulation systematically scores and selects the most discriminative combinations. By intertwining these ideas with optimized bitwise operations and a scalable distributed algorithm on high-performance computing clusters, our algorithm can achieve approximately 90 - 98% reduction in visited combinations for 4-hits, and roughly a 183x speedup over the exhaustive set cover approach(which is algorithmically NP-complete) measured on 147,456 ranks. In doing so, our method can feasibly handle four-hit and even higher-order gene hits, achieving both speed and resource efficiency.

cs.DC↗

arXiv2025

SAFE: Improving LLM Systems using Sentence-Level In-generation Attribution

Large Language Models (LLMs) are increasingly applied in various science domains, yet their broader adoption remains constrained by a critical challenge: the lack of trustworthy, verifiable outputs. Current LLMs often generate answers without reliable source attribution, or worse, with incorrect attributions, posing a barrier to their use in scientific and high-stakes settings, where traceability and accountability are paramount. To be reliable, attribution systems require high accuracy for short-length attribution on retrieved data, i.e., attribution to a sentence within a document rather than the entire document. We propose SAFE, a Sentence-level A ttribution FramEwork for Retrieve-Augmented Generation (RAG) systems that attributes generated sentences during generation. This allows users to verify sentences as they read them and correct the model when the attribution indicates the generated text is not grounded in the documents, increasing the safety of LLM systems. This framework consists of two steps: predicting the required number of references for a sentence, and attributing the sentence. Our approach achieved 95% accuracy in the first step, which translated to 2.1\~6.0% improvements in the accuracy (normalized for maximum possible accuracy) of all attribution algorithms in our clean dataset, when compared to their top-1 accuracy. We also applied SAFE in real-world scenarios with documents containing hundreds to thousands of sentences. In these settings, SAFE reliably attributed sentences to their source documents, demonstrating that the method generalizes beyond controlled benchmarks. The SAFE framework and the training dataset are publicly available on GitHub.

cs.CL↗

arXiv2024

Tadashi: Enabling AI-Based Automated Code Generation With Guaranteed Correctness

Frameworks and domain-specific languages for auto-generating code have traditionally depended on human experts to implement rigorous methods ensuring the legality of code transformations. Recently, machine learning (ML) has gained traction for generating code optimized for specific hardware targets. However, ML approaches-particularly black-box neural networks-offer no guarantees on the correctness or legality of the transformations they produce. To address this gap, we introduce Tadashi, an end-to-end system that leverages the polyhedral model to support researchers in curating datasets critical for ML-based code generation. Tadashi provides an end-to-end system capable of applying, verifying, and evaluating candidate transformations on polyhedral schedules with both reliability and practicality. We formally prove that Tadashi guarantees the legality of generated transformations, demonstrate its low runtime overhead, and showcase its broad applicability. Tadashi available at https://github.com/vatai/tadashi/.

cs.LG↗

arXiv2023

At the Locus of Performance: Quantifying the Effects of Copious 3D-Stacked Cache on HPC Workloads

Over the last three decades, innovations in the memory subsystem were primarily targeted at overcoming the data movement bottleneck. In this paper, we focus on a specific market trend in memory technology: 3D-stacked memory and caches. We investigate the impact of extending the on-chip memory capabilities in future HPC-focused processors, particularly by 3D-stacked SRAM. First, we propose a method oblivious to the memory subsystem to gauge the upper-bound in performance improvements when data movement costs are eliminated. Then, using the gem5 simulator, we model two variants of a hypothetical LARge Cache processor (LARC), fabricated in 1.5 nm and enriched with high-capacity 3D-stacked cache. With a volume of experiments involving a broad set of proxy-applications and benchmarks, we aim to reveal how HPC CPU performance will evolve, and conclude an average boost of 9.56x for cache-sensitive HPC applications, on a per-chip basis. Additionally, we exhaustively document our methodological exploration to motivate HPC centers to drive their own technological agenda through enhanced co-design.

cs.DC↗

arXiv2021

Matrix Engines for High Performance Computing:A Paragon of Performance or Grasping at Straws?

Matrix engines or units, in different forms and affinities, are becoming a reality in modern processors; CPUs and otherwise. The current and dominant algorithmic approach to Deep Learning merits the commercial investments in these units, and deduced from the No.1 benchmark in supercomputing, namely High Performance Linpack, one would expect an awakened enthusiasm by the HPC community, too. Hence, our goal is to identify the practical added benefits for HPC and machine learning applications by having access to matrix engines. For this purpose, we perform an in-depth survey of software stacks, proxy applications and benchmarks, and historical batch job records. We provide a cost-benefit analysis of matrix engines, both asymptotically and in conjunction with state-of-the-art processors. While our empirical data will temper the enthusiasm, we also outline opportunities to misuse these dense matrix-multiplication engines if they come for free.

cs.DC↗