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Metagenomic disease prediction commonly relies on species abundance tables derived from large, incomplete reference catalogs, constraining resolution and discarding valuable information contained in DNA reads. To overcome these limitations,…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be…
In the context of large-angle cone-beam tomography (CBCT), we present a practical iterative reconstruction (IR) scheme designed for rapid convergence as required for large datasets. The robustness of the reconstruction is provided by the…
Inspired by the importance of diversity in biological system, we built an heterogeneous system that could achieve this goal. Our architecture could be summarized in two basic steps. First, we generate a diverse set of classification…
Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data.…
Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…
We present a self-certifying compiler for the COGENT systems language. COGENT is a restricted, polymorphic, higher-order, and purely functional language with linear types and without the need for a trusted runtime or garbage collector. It…
With the rise of generative paradigms, generative recommendation has garnered increasing attention. The core component is the item code, generally derived by quantizing collaborative or semantic representations to serve as candidate items…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg.…
Pretrained multi-modal large language models (MLLMs) demonstrate strong performance on diverse multimodal tasks, but remain limited in reasoning capabilities for domains where annotations are difficult to collect. In this work, we focus on…
Humans possess an innate ability to group objects by similarity, a cognitive mechanism that clustering algorithms aim to emulate. Recent advances in community detection have enabled the discovery of configurations -- valid hierarchical…
Language models can be sampled multiple times to access the distribution underlying their responses, but existing methods cannot efficiently synthesize rich epistemic signals across different long-form responses. We introduce Consensus…
We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an inverted index and Bloom filters. Our target application is to index $k$-mers of DNA samples or $q$-grams from text documents and process approximate…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…