Related papers: LAPIS is a fast web API for massive open virus seq…
Large Language Models (LLMs) increasingly serve as consumers of API specifications, whether for code generation, autonomous agent interaction, or API-assisted reasoning. The de facto standard for API description, OpenAPI, was designed for…
Crime situations are race against time. An AI-assisted criminal investigation system, providing prompt but precise legal counsel is in need for police officers. We introduce LAPIS (Language Model Augmented Police Investigation System), an…
Portability, performance, and productivity are three critical dimensions for evaluating a programming model or compiler infrastructure. Several modern programming models for computational science focus on performance and portability. On the…
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies,…
Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in…
Researchers across the globe are seeking to rapidly repurpose existing drugs or discover new drugs to counter the the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One promising…
Polycystic Ovary Syndrome (PCOS) constitutes a significant public health issue affecting 10% of reproductive-aged women, highlighting the critical importance of developing effective diagnostic tools. Previous machine learning and deep…
Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A wide range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
Due to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs. We conducted a large-scale virtual screening for small molecules that are potential CoV-2…
SARS-CoV-2 is an upper respiratory system RNA virus that has caused over 3 million deaths and infecting over 150 million worldwide as of May 2021. With thousands of strains sequenced to date, SARS-CoV-2 mutations pose significant challenges…
Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of…
With the rapid global spread of COVID-19, more and more data related to this virus is becoming available, including genomic sequence data. The total number of genomic sequences that are publicly available on platforms such as GISAID is…
Large language models (LLMs) have achieved remarkable progress, demonstrating unprecedented capabilities across various natural language processing tasks. However, the high costs associated with such exceptional performance limit the…
Panoptic segmentation is a key enabler for robotic perception, as it unifies semantic understanding with object-level reasoning. However, the increasing complexity of state-of-the-art models makes them unsuitable for deployment on…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Scientific discoveries must be communicated clearly to realize their full potential. Without effective communication, even the most groundbreaking findings risk being overlooked or misunderstood. The primary way scientists communicate their…