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Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

Our understanding of the structure of the brain and its relationships with human traits is largely determined by how we represent the structural connectome. Standard practice divides the brain into regions of interest (ROIs) and represents the connectome as an adjacency matrix having cells measuring connectivity between pairs of ROIs. Statistical analyses are then heavily driven by the (largely arbitrary) choice of ROIs. In this article, we propose a novel tractography-based representation of brain connectomes, which clusters fiber endpoints to define a data adaptive parcellation targeted to explain variation among individuals and predict human traits. This representation leads to Principal Parcellation Analysis (PPA), representing individual brain connectomes by compositional vectors building on a basis system of fiber bundles that captures the connectivity at the population level. PPA reduces subjectivity and facilitates statistical analyses. We illustrate the proposed approach through applications to data from the Human Connectome Project (HCP) and show that PPA connectomes improve power in predicting human traits over state-of-the-art methods based on classical connectomes, while dramatically improving parsimony and maintaining interpretability. Our PPA package is publicly available on GitHub, and can be implemented routinely for diffusion image data.

Fast and effective image compression for multi-dimensional images has become increasingly important for efficient storage and transfer of massive amounts of high-resolution images and videos. Desirable properties in compression methods include (1) high reconstruction quality at a wide range of compression rates while preserving key local details, (2) computational scalability, (3) applicability to a variety of different image/video types and of different dimensions, (4) progressive transmission, and (5) ease of tuning. We present such a method for multi-dimensional image compression called Compression via Adaptive Recursive Partitioning (CARP). CARP uses an optimal permutation of the image pixels inferred from a Bayesian probabilistic model on recursive partitions of the image to reduce its effective dimensionality, achieving a parsimonious representation that preserves information. CARP uses a multi-layer Bayesian hierarchical model to achieve in-situ compression along with self-tuning and regularization, with just one single parameter to be specified by the user to achieve the desired compression rate. Extensive numerical experiments using a variety of datasets including 2D still images, real-life YouTube videos, and surveillance videos show that CARP dominates the state-of-the-art image/video compression approaches---including JPEG, JPEG2000, BPG, MPEG4, HEVC and a neural network-based method---for all of these different image types and on nearly all of the individual images and videos over some methods., Comment: 20 pages, 11 figures