Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 1808.05766

The Function Transformation Omics - Funomics

Yongshuai Jiang·Jing Xu·Simeng Hu·Di Liu·Linna Zhao·Xu Zhou
View original source ↗Read source document ↗Export metadata ↓

Abstract

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 input/observation variables (in biology, it generally refers to the observed/measured value of biomarkers, biological characteristics, or other indicators) into a new output variable (new characteristics or indicators). This provided us a chance to re-cognize objective things or relationships beyond the original measurements. For example, Body Mass Index, which transform weight and high into a new indicator BMI=x/y^2 (where x is weight and y is high), is commonly used in to gauge obesity. Here, we proposed a new system, Funomics (Function Transformation Omics), for understanding the world in a different perspective. Funome can be understood as a set of math functions consist of basic elementary functions (such as power functions and exponential functions) and basic mathematical operations (such as addition, subtraction). By scanning the whole Funome, researchers can identify some special functions (called handsome functions) which can generate the novel important output variable (characteristics or indicators). We also start "the Funome project" to develop novel methods, function library and analysis software for Funome studies. The Funome project will accelerate the discovery of new useful indicators or characteristics, will improve the utilization efficiency of directly measured data, and will enhance our ability to understand the world. The analysis tools and data resources about the Funome project can be found gradually at http://www.funome.com.

Explore related subjects

q-bio.OTstat.AP

Keep this discovery

BibTeXRIS

Yongshuai Jiang, Jing Xu, Simeng Hu, Di Liu, Linna Zhao, Xu Zhou. 2018-08-17. The Function Transformation Omics - Funomics. https://arxiv.org/abs/1808.05766

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

MarkerScout: A Disease-Agnostic Machine Learning Framework for Biomarker Prediction from Multi-Scale Mechanistic Models

We demonstrate the framework on three infectious diseases derived from a companion mechanistic immune-simulation platform: SARS-CoV-2, Influenza A Virus, and Plasmodium falciparum. Each disease was evaluated across hospitalization and intensive care unit cohorts, yielding six cohorts in total. Best-pipeline cross-validated macro F1 ranged from 0.82 for IAV-HOSP to 0.99 for COV-ICU, and the framework produced tiered, direction-aware biomarker lists for each disease and phase. Interleukin-18 (IL-18) reached the strongest tier in both SARS-CoV-2 phases with consistent direction. When benchmarked against three separate, independently collected clinical ICU datasets, MarkerScout's top-ranked features outperformed 94.4% of randomly selected feature sets of equivalent size for SARS-CoV-2, with a weaker but directionally consistent advantage for Influenza A Virus (66.7%) and Plasmodium falciparum (60.7%).

q-bio.OT↗
arXiv2026

Enhancing Clinical Decision Support and Differential Diagnosis with Knowledge Graphs, and Retrieval Augmented Generation in Generative AI

Diagnostic error carries a burden, while unconstrained large language models (LLMs) remain vulnerable to hallucination and weak integration of quantitative laboratory dynamics. We developed a decision-support pipeline combining disease-specific biomarker correlation graphs, ordinary differential equations (ODEs), deep sequence classification, and retrieval-augmented generation (RAG). For 103 disease classes from a full blood count (FBC) repository, biomarker networks were used as coupling matrices to generate 30 trajectories per disease (3,090 total). A one-dimensional convolutional neural network (CNN) and long short-term memory (LSTM) network classified disease trajectories and six dynamical clusters. A constrained GPT-4o-mini RAG layer used a 19-pattern BMJ Best Practice/NICE corpus to generate differential diagnoses evaluated for diagnostic suitability, evidential grounding, and clinical plausibility. Across five random-seed runs, disease-level accuracy was $0.940 \pm 0.006$ for the CNN (95\% CI 0.933--0.948) and $0.852 \pm 0.019$ for the LSTM (95\% CI 0.828--0.875); the CNN advantage was 8.87 percentage points (95\% CI 6.47--11.27; $t(4)=10.26$, $p=5.1\times10^{-4}$; Hedges' $g=3.67$). Among 100 sampled RAG cases, 96 parsed successfully; evidence was cited in 97.9\%, the true diagnosis was mentioned in 71.9\%, and the composite score was 3.82/5 with a 47.9\% strict pass rate. The central finding was a decoupling between grounding and diagnostic correctness: classifier-correct versus classifier-wrong outputs differed in diagnostic suitability but not evidential grounding. Post-hoc analysis confirmed a 1.02-point diagnostic-score difference (Mann--Whitney $p=0.0024$; Hedges' $g=0.72$), whereas grounding differed by only $-0.02$ points ($p=0.839$; $g=-0.04$).

q-bio.OT↗
arXiv2026

Expanding the Human Ancestry Ontology to include under-represented populations and ethnicities for broader utility in annotations

Successful discovery, integration and reuse of data relies on the availability of rich, well-structured and machine-readable metadata to describe every aspect of the data, from sample sources to collection processes to experimental protocols. The use of standardised terminologies to express concepts in a harmonised fashion lies at the core of high-quality data annotation, increasing the FAIRness of the data, facilitating data integration and promoting reproducibility. Here, we describe the Human Ancestry Ontology (HANCESTRO), originally developed to improve standardised reporting of genetic ancestry genomic resources such as the NHGRI-EBI GWAS Catalog and the Human Cell Atlas through high-level population descriptors, and more recently expanded to include diverse and previously under-represented populations in genomics and genetics research. HANCESTRO provides a framework for population descriptors that includes both ancestry based on the analysis of genetic information and self-reported ethnicity, which is based on social and cultural factors that don't necessarily align with genetic populations. By enabling the accurate and interoperable representation of population-related data, it promotes inclusive, representative and reproducible science.

q-bio.OT↗