Biology subjects

Dunne, R.

Publications and source records attributed to Dunne, R..

3 recordsLinked to original sources

bioRxiv2024

Got meat? The mechanical signature of plant-based and animal meat

Eating less meat is associated with a healthier body and planet. Yet, we remain reluctant to switch to a plant-based diet, largely due to the sensory experience of plant-based meat. Food scientists characterize meat using a double compression test, which only probes one-dimensional behavior. Here we use tension, compression, and shear tests-combined with constitutive neural networks-to automatically discover the behavior of eight plant-based and animal meats across the entire three-dimensional spectrum. We find that plant-based sausage and hotdog, with stiffnesses of 95.9{+/-}14.1kPa and 38.7{+/-}3.0kPa, successfully mimic their animal counterparts, with 63.5{+/-}45.7kPa and 44.3{+/-}13.2 kPa, while tofurky is twice as stiff, and tofu is twice as soft. Strikingly, a complementary food tasting survey produces in nearly identical stiffness rankings for all eight products ({rho} =0.833, p=0.015). Probing the fully three-dimensional signature of meats is critical to understand subtle differences in texture that may result in a different perception of taste. Our data and code are freely available at https://github.com/LivingMatterLab/CANN

bioengineering↗

bioRxiv2022

Detecting epistatic interactions in genomic data using Random Forests

Epistatic interactions can play an important role in the genetic mechanisms that control phenotypic variation. However, identifying these interactions in high dimensional genomic data can be very challenging due to the large computational burden induced by the high volume of combinatorial tests that have to be performed to explore the entire search space. Random Forests Decision Trees are widely used in a variety of disciplines and are often said to detect interactions. However, Random Forests models do not explicitly detect variable interactions. Most Random Forests based methods that claim to detect interactions rely on different forms of variable importance measures that suffer when the interacting variables have very small or no marginal effects. The proposed Random Forests based method detects interactions using a two-stage approach and is computationally efficient. The approach is demonstrated and validated through its application on several simulated datasets representing different data structures with respect to genomic data and trait heritabilities. The method is also applied to two high dimensional genomics data sets to validate the approach. In both cases, the method results were used to identify several genes closely positioned to the interacting markers that showed strong biological potential for contributing to the genetic control for the respective traits tested. Contacthawlader.almamun@csiro.au

bioinformatics↗

bioRxiv2019

VariantSpark, A Random Forest Machine Learning Implementation for Ultra High Dimensional Data

The demands on machine learning methods to cater for ultra high dimensional datasets, datasets with millions of features, have been increasing in domains like life sciences and the Internet of Things (IoT). While Random Forests are suitable for \"wide\" datasets, current implementations such as Googles PLANET lack the ability to scale to such dimensions. Recent improvements by Yggdrasil begin to address these limitations but do not extend to Random Forest. This paper introduces CursedForest, a novel Random Forest implementation on top of Apache Spark and part of the VariantSpark platform, which parallelises processing of all nodes over the entire forest. CursedForest is 9 and up to 89 times faster than Googles PLANET and Yggdrasil, respectively, and is the first method capable of scaling to millions of features.

bioinformatics↗