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Despite the success of large language models (LLMs) on general-purpose tasks, their performance in highly specialized domains such as biomedicine remains unsatisfactory. A key limitation is the inability of LLMs to effectively leverage…
Gut microbiota plays a crucial role in modulating pig development and health, and gut microbiota characteristics are associated with differences in feed efficiency. To answer open questions in feed efficiency analysis, biologists seek to…
In this paper, I introduce a Sequence-based Multiscale Model (SeqMM) for the biomolecular data analysis. With the combination of spectral graph method, I reveal the essential difference between the global scale models and local scale ones…
Computationally efficient, accurate, and privacy-preserving data storage and retrieval are among the key challenges faced by practical deployments of biometric identification systems worldwide. In this work, a method of protected indexing…
The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear,…
There are no two identical leaves in the world, so how to find effective markers or features to distinguish them is an important issue. Function transformation, such as f(x,y) and f(x,y,z), can transform two, three, or multiple…
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
In this systems paper, we present MillenniumDB: a novel graph database engine that is modular, persistent, and open source. MillenniumDB is based on a graph data model, which we call domain graphs, that provides a simple abstraction upon…
Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We…
How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…
Biomedical knowledge graphs (BKGs) have emerged as powerful tools for organizing and leveraging the vast and complex data found across the biomedical field. Yet, current reviews of BKGs often limit their scope to specific domains or…
Knowledge Graphs have been one of the fundamental methods for integrating heterogeneous data sources. Integrating heterogeneous data sources is crucial, especially in the biomedical domain, where central data-driven tasks such as drug…
All-atom molecular simulation serves as a quintessential ``computational microscope'' for understanding the machinery of life, yet it remains fundamentally limited by the trade-off between quantum-mechanical (QM) accuracy and biological…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…
Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…
The growing scope, scale, and number of biometric deployments around the world emphasise the need for research into technologies facilitating efficient and reliable biometric identification queries. This work presents a method of indexing…
Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased…