arXiv subjects

Miguel Graça

Publications and source records attributed to Miguel Graça.

5 recordsLinked to original sources

arXiv2026

Endeavor: Efficient PairHMM for Detection of DNA Variants in Genome-Scale Datasets

DNA variant calling represents a key operation in bioinformatics pipelines that aims at identifying genetic variants. Given an evidenced explosion in genomic data availability, there is an urgent need for a high-performant, portable and efficient solution for variant calling, which can further improve our understanding of genomic structure and genetic basis for complex diseases. In its most common formulation, the Pair Hidden Markov Model (PairHMM) algorithm for variant calling stands as the main bottleneck in the pipeline, accounting for up to 70% of the execution time in large-scale genomic datasets. The state-of-the-art approaches for accelerating PairHMM in CPUs and GPUs do not scale to long DNA sequences and only explore very limited anti-diagonal data parallelism, which yields poor performance. In this work, Endeavor is proposed as a new parallelization strategy for PairHMM that redefines its traditional formulation to explore row-level fine-grained parallelism without loss in solution accuracy. Based on this, a novel and portable SIMD-based approach is derived for efficient and high-performance processing of short and long sequences in CPUs and GPUs, leveraging novel levels of parallelism and synchronization to achieve high throughput in sequences up to 100k basepairs for the first time. Evaluation on Intel and AMD CPUs shows that Endeavor outperforms GKL up to 2.14x in peak throughput and GATK HaplotypeCaller by at least 2x in real-world datasets, while NVIDIA and AMD GPUs achieve up to 2.05x speedups in genome-scale datasets when compared to state-of-the-art GPU-based methods.

cs.DC↗

arXiv2026

TrioSeq: A Novel Approach to Accelerate Triplet Sequence Alignment on GPUs

State-of-the-art multiple sequence alignment (MSA) algorithms are based on progressive approaches that rely on pairwise sequence alignment (PSA) to generate guide trees to align all sequences. Given an evidenced explosion in genomic data availability, research efforts have focused on accelerating PSA on massively-parallel architectures (e.g., GPUs) and specialized hardware (e.g., FPGAs). However, there is increasing evidence that starting from exact 3-way alignments could provide more robust, accurate MSAs, and improve genomic analysis. While the current literature has shown that PSA algorithms can be extended to align sequence triplets, the existent state-of-the-art on hardware acceleration of exact 3-way alignments is still scarce. In particular, current GPU methods are still inefficient due to lacking support for novel hardware features (e.g., cross-thread intrinsics), while being closed-source and vendor-specific. In this paper, TrioSeq is proposed as a fine-grained strategy to efficiently implement 3-way alignments on GPUs, leveraging novel levels of GPU parallelism and synchronization to achieve high throughput in aligning sequence triplets. Evaluation on NVIDIA and AMD GPUs shows that TrioSeq outperforms state-of-the-art GPU progressive methods on 3-way alignment by at least 20% on simulated genomic datasets.

cs.DC↗

arXiv2024

LumberChunker: Long-Form Narrative Document Segmentation

Modern NLP tasks increasingly rely on dense retrieval methods to access up-to-date and relevant contextual information. We are motivated by the premise that retrieval benefits from segments that can vary in size such that a content's semantic independence is better captured. We propose LumberChunker, a method leveraging an LLM to dynamically segment documents, which iteratively prompts the LLM to identify the point within a group of sequential passages where the content begins to shift. To evaluate our method, we introduce GutenQA, a benchmark with 3000 "needle in a haystack" type of question-answer pairs derived from 100 public domain narrative books available on Project Gutenberg. Our experiments show that LumberChunker not only outperforms the most competitive baseline by 7.37% in retrieval performance (DCG@20) but also that, when integrated into a RAG pipeline, LumberChunker proves to be more effective than other chunking methods and competitive baselines, such as the Gemini 1.5M Pro. Our Code and Data are available at https://github.com/joaodsmarques/LumberChunker

cs.CL↗

arXiv2020

When and Why is Unsupervised Neural Machine Translation Useless?

This paper studies the practicality of the current state-of-the-art unsupervised methods in neural machine translation (NMT). In ten translation tasks with various data settings, we analyze the conditions under which the unsupervised methods fail to produce reasonable translations. We show that their performance is severely affected by linguistic dissimilarity and domain mismatch between source and target monolingual data. Such conditions are common for low-resource language pairs, where unsupervised learning works poorly. In all of our experiments, supervised and semi-supervised baselines with 50k-sentence bilingual data outperform the best unsupervised results. Our analyses pinpoint the limits of the current unsupervised NMT and also suggest immediate research directions.

cs.CL↗

arXiv2019

Generalizing Back-Translation in Neural Machine Translation

Back-translation - data augmentation by translating target monolingual data - is a crucial component in modern neural machine translation (NMT). In this work, we reformulate back-translation in the scope of cross-entropy optimization of an NMT model, clarifying its underlying mathematical assumptions and approximations beyond its heuristic usage. Our formulation covers broader synthetic data generation schemes, including sampling from a target-to-source NMT model. With this formulation, we point out fundamental problems of the sampling-based approaches and propose to remedy them by (i) disabling label smoothing for the target-to-source model and (ii) sampling from a restricted search space. Our statements are investigated on the WMT 2018 German - English news translation task.

cs.CL↗