Related papers: LISA: Towards Learned DNA Sequence Search
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models…
The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck.…
The proposed Laser Interferometer Space Antenna (LISA) mission is tasked with the detection and characterization of gravitational waves from various sources in the universe. This endeavor is challenged by transient displacement and…
We introduce latency-aware network acceleration (LANA) - an approach that builds on neural architecture search techniques and teacher-student distillation to accelerate neural networks. LANA consists of two phases: in the first phase, it…
The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing…
Spatial query and analysis results are often directly applied to decision-making processes such as facility location, proximity resource discovery, accessibility analysis, and risk assessment. Therefore, the efficiency of underlying spatial…
Technological advances in genotyping have given rise to hypothesis-based association studies of increasing scope. As a result, the scientific hypotheses addressed by these studies have become more complex and more difficult to address using…
Automated Short Answer Scoring (ASAS) is a critical component in educational assessment. While traditional ASAS systems relied on rule-based algorithms or complex deep learning methods, recent advancements in Generative Language Models…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
As a key ingredient of the DBMS, index plays an important role in the query optimization and processing. However, it is a non-trivial task to apply existing indexes or design new indexes for new applications, where both data distribution…
Next Generation Sequencing can sample the whole genome (WGS) or the 1-2% of the genome that codes for proteins called the whole exome (WES). Machine learning approaches to variant calling achieve high accuracy in WGS data, but the reduced…
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These…
Training Large Language Models (LLMs) from scratch requires immense computational resources, making it prohibitively expensive. Model scaling-up offers a promising solution by leveraging the parameters of smaller models to create larger…
The space-based gravitational wave detector LISA will observe in the low-frequency gravitational-wave band (0.1 mHz up to 1 Hz). LISA will search for a variety of expected signals, and when it detects a signal it will have to determine a…
The planned Laser Interferometer Space Antenna (LISA) will detect gravitational wave signals from a wide range of sources. However, disentangling individual signals from the source-dominated data stream is a challenging problem and the…
Gene expression profiles obtained through DNA microarray have proven successful in providing critical information for cancer detection classifiers. However, the limited number of samples in these datasets poses a challenge to employ complex…
Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…
By being the first observatory to survey the source rich low frequency region of the gravitational wave spectrum, the Laser Interferometer Space Antenna (LISA) will revolutionize our understanding of the Cosmos. For the first time we will…