Dataset Information

Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing.

ABSTRACT: Comparatively few studies have addressed directly the question of quantifying the benefits to be had from using molecular genetic markers in experimental breeding programmes (e.g. for improved crops and livestock), nor the question of which organisms should be mated with each other to best effect. We argue that this requires in silico modelling, an approach for which there is a large literature in the field of evolutionary computation (EC), but which has not really been applied in this way to experimental breeding programmes. EC seeks to optimise measurable outcomes (phenotypic fitnesses) by optimising in silico the mutation, recombination and selection regimes that are used. We review some of the approaches from EC, and compare experimentally, using a biologically relevant in silico landscape, some algorithms that have knowledge of where they are in the (genotypic) search space (G-algorithms) with some (albeit well-tuned ones) that do not (F-algorithms). For the present kinds of landscapes, F- and G-algorithms were broadly comparable in quality and effectiveness, although we recognise that the G-algorithms were not equipped with any 'prior knowledge' of epistatic pathway interactions. This use of algorithms based on machine learning has important implications for the optimisation of experimental breeding programmes in the post-genomic era when we shall potentially have access to the full genome sequence of every organism in a breeding population. The non-proprietary code that we have used is made freely available (via Supplementary information).

SUBMITTER: O'Hagan S

PROVIDER: S-EPMC3504065 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing.

O'Hagan Steve S Knowles Joshua J Kell Douglas B DB

PloS one 20121121 11

Comparatively few studies have addressed directly the question of quantifying the benefits to be had from using molecular genetic markers in experimental breeding programmes (e.g. for improved crops and livestock), nor the question of which organisms should be mated with each other to best effect. We argue that this requires in silico modelling, an approach for which there is a large literature in the field of evolutionary computation (EC), but which has not really been applied in this way to ex ...[more]

PMID: 23185279

Similar Datasets

Project description:von Neumann architecture based computers isolate computation and storage (i.e. data is shuttled between computation blocks (processor) and memory blocks). The to-and-fro movement of data leads to a fundamental limitation of modern computers, known as the Memory wall. Logic in-Memory (LIM)/In-Memory Computing (IMC) approaches aim to address this bottleneck by directly computing inside memory units thereby eliminating energy-intensive and time-consuming data movement. Several recent works in literature, propose realization of logic function(s) directly using arrays of emerging resistive memory devices (example- memristors, RRAM/ReRAM, PCM, CBRAM, OxRAM, STT-MRAM etc.), rather than using conventional transistors for computing. The logic/embedded-side of digital systems (like processors, micro-controllers) can greatly benefit from such LIM realizations. However, the pure storage-side of digital systems (example SSDs, enterprise storage etc.) will not benefit much from such LIM approaches as when memory arrays are used for logic they lose their core functionality of storage. Thus, there is the need for an approach complementary to existing LIM techniques, that's more beneficial for the storage-side of digital systems; one that gives compute capability to memory arrays not at the cost of their existing stored states. Fundamentally, this would require memory nanodevice arrays that are capable of storing and computing simultaneously. In this paper, we propose a novel 'Simultaneous Logic in-Memory' (SLIM) methodology which is complementary to existing LIM approaches in literature. Through extensive experiments we demonstrate novel SLIM bitcells (1T-1R/2T-1R) comprising non-filamentary bilayer analog OxRAM devices with NMOS transistors. Proposed bitcells are capable of implementing both Memory and Logic operations simultaneously. Detailed programming scheme, array level implementation, and controller architecture are also proposed. Furthermore, to study the impact of proposed SLIM approach for real-world implementations, we performed analysis for two applications: (i) Sobel Edge Detection, and (ii) Binary Neural Network- Multi layer Perceptron (BNN-MLP). By performing all computations in SLIM bitcell array, huge Energy Delay Product (EDP) savings of ≈75× for 1T-1R (≈40× for 2T-1R) SLIM bitcell were observed for edge-detection application while EDP savings of ≈3.5× for 1T-1R (≈1.6× for 2T-1R) SLIM bitcell were observed for BNN-MLP application respectively, in comparison to conventional computing. EDP savings owing to reduction in data transfer between CPU ↔ memory is observed to be ≈780× (for both SLIM bitcells).

Dataset Information

Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing.

Publications

Exploiting genomic knowledge in optimising molecular breeding programmes: algorithms from evolutionary computing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets