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Rare diseases (RDs) are collectively common and affect 300 million people worldwide. Accurate phenotyping is critical for informing diagnosis and treatment, but RD phenotypes are often embedded in unstructured text and time-consuming to…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
Existing large language models have to run K times to generate a sequence of K tokens. In this paper, we present RecycleGPT, a generative language model with fast decoding speed by recycling pre-generated model states without running the…
Bibliographic catalogues store millions of data. The use of computer techniques such as web-scraping allows the extraction of data in an efficient and accurate manner. The recent emergence of ChatGPT is facilitating the development of…
ChatGPT is a powerful large language model (LLM) that covers knowledge resources such as Wikipedia and supports natural language question answering using its own knowledge. Therefore, there is growing interest in exploring whether ChatGPT…
Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative…
We develop a new class of genetic algorithm that computationally determines efficient pulse sequences to implement a quantum gate U in a three-qubit system. The method is shown to be quite general, and the same algorithm can be used to…
The Gradient Boosted Tree (GBT) algorithm is one of the most popular machine learning algorithms used in production, for tasks that include Click-Through Rate (CTR) prediction and learning-to-rank. To deal with the massive datasets…
With the rapid development of big data and artificial intelligence technologies, the demand for effective processing and retrieval of vector data is growing. Against this backdrop, I have developed the Bhakti vector database, aiming to…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
random_tree() is a linear time and space C++ implementation able to create trees of up to a billion nodes for genetic programming and genetic improvement experiments. A 3.60GHz CPU can generate more than 18 million random nodes for GP…
Benchmarking and characterising quantum states and logic gates is essential in the development of devices for quantum computing. We introduce a Bayesian approach to self-consistent process tomography, called fast Bayesian tomography (FBT),…
A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing,…
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…
Recent advances in large language models (LLMs) have stepped forward the development of multilingual speech and machine translation by its reduced representation errors and incorporated external knowledge. However, both translation tasks…
Program synthesis is the process of generating a computer program following a set of specifications, which can be a high-level description of the problem and/or a set of input-output examples. The synthesis can be modeled as a search…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Motivation: Networks underlie the generation and interpretation of many biological datasets: gene networks shed light on the regulatory structure of the genome, and cell networks can capture structure of the tumor micro-environment.…
In addressing the pivotal role of translating natural language queries into SQL commands, we propose a suite of compact, fine-tuned models and self-refine mechanisms to democratize data access and analysis for non-expert users, mitigating…