Emil Vatai

Ritvik Prabhu, Emil Vatai, Bernard Moussad et al.

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.

João Eduardo Batista, Emil Vatai, Mohamed Wahib

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.