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Column type annotation is the task of annotating the columns of a relational table with the semantic type of the values contained in each column. Column type annotation is an important pre-processing step for data search and data…
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…
Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states…
Large pre-trained language models have exhibited unprecedented capabilities in producing high-quality text via prompting techniques. This fact introduces new possibilities for data collection and annotation, particularly in situations where…
Annotated data plays a critical role in Natural Language Processing (NLP) in training models and evaluating their performance. Given recent developments in Large Language Models (LLMs), models such as ChatGPT demonstrate zero-shot…
The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a…
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks…
Single-cell foundation models such as scGPT represent a significant advancement in single-cell omics, with an ability to achieve state-of-the-art performance on various downstream biological tasks. However, these models are inherently…
Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes…
A knowledge gap persists between machine learning (ML) developers (e.g., data scientists) and practitioners (e.g., clinicians), hampering the full utilization of ML for clinical data analysis. We investigated the potential of the ChatGPT…
Large Language Models (LLMs) have revo lutionized natural language processing Natural Language Processing (NLP), with Chat Generative Pre-trained Transformer (ChatGPT) standing out as a notable exampledue to its advanced capabilities and…
Automated single-cell annotation is difficult when the most abundant genes are not the most discriminative ones, or when a target state is poorly covered by a fixed reference atlas. GPTCelltype-style one-shot prompting allows large language…
In recent times, the grandeur of Large Language Models (LLMs) has not only shone in the realm of natural language processing but has also cast its brilliance across a vast array of applications. This remarkable display of LLM capabilities…
ChatGPT, as a recently launched large language model (LLM), has shown superior performance in various natural language processing (NLP) tasks. However, two major limitations hinder its potential applications: (1) the inflexibility of…
Interest in Large Language Models (LLMs) has increased drastically since the emergence of ChatGPT and the outstanding positive societal response to the ease with which it performs tasks in Natural Language Processing (NLP). The triumph of…
We introduce HiCat (Hybrid Cell Annotation using Transformative embeddings), a novel semi-supervised pipeline for annotating cell types from single-cell RNA sequencing data. HiCat fuses the strengths of supervised learning for known cell…
Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding…
Large language models such as ChatGPT have increased scholarly output, but whether this productivity boost produces genuine intellectual advancement remains untested. I address this gap by measuring the semantic novelty of 13,847 articles…
This paper examines the application of ChatGPT, a large language model (LLM), for question-and-answer (Q&A) tasks in the highly specialized field of nuclear data. The primary focus is on evaluating ChatGPT's performance on a curated test…
Generative Language Models gained significant attention in late 2022 / early 2023, notably with the introduction of models refined to act consistently with users' expectations of interactions with AI (conversational models). Arguably the…