Understanding the Language of Life

The Vision

Cancer. Every year millions of people have their lives prematurely cut short. Bird Flu. Over half a billion chickens have died due to bird flu since 2023. This disease is slowly becoming a threat to a variety of ecosystems, whose services human lives and livelihoods depend on. AMR. Drug resistant strains of bacteria and fungus may very well bring us back to a time where a simple paper cut leads to an amputation. All of these diseases & problems are connected by changes in the DNA and we at DeOxy Tech, aim to build a world where the complexities of biology are understood and controlled.

Projects

Life as a Function: Why Transformer Architectures Struggle to Gain Genome-Level Foundational Capabilities

Recent years have seen a flurry of generative nucleotide models, mostly of limited utility. In this paper, we use the functional representation of DNA as a complex, composite function on the plane of evolution to extend the theoretical unification of ecological and evolutionary change to the problem of synthetic DNA models. Through experiments on synthetic and real DNA sequences we show that next-token prediction decoder transformer architectures are limited in their capacity to learn such functions.

Preprint: bioRxiv

DVQ: DNA Visualisations and Quick comparisons

We introduce DVQ (DNA Visualisations and Quick comparisons), an open-source Python library for exploring nucleotide sequences using a variety of methods. Understanding DNA sequences intuitively isimportant for a variety of tasks in biology. DVQ aims to be a one-stop comprehensive library that makes explainable DNA easy for geneticists, researchers, and practitioners who need explanations. For practitioners, the library provides an easy-to-use interface to generate visualisations for their sequencesby only writing a few lines of code. In this report, we demonstrate several example use cases across different types of sequences as well as visualisations.

Package repo: DVQ

If you have any questions, feel free to reach out to us!