Artificial neural networks : A comparative study of implementations for human chromosome classification

Artificial neural networks are a popular field of artificial intelligence and have commonly been applied to solve many prediction, classification and diagnostic tasks. One such task is the analysis of human chromosomes. This thesis investigates the use of artificial neural networks (ANNs) as automated chromosome classifiers. The investigation involves the thorough analysis of seven different implementation techniques. These include three techniques using artificial neural networks, two techniques using ANN s supported by another method and two techniques not using ANNs. These seven implementations are evaluated according to the classification accuracy achieved and according to their support of important system measures, such as robustness and validity. The results collected show that ANNs perform relatively well in terms of classification accuracy, though other implementations achieved higher results. However, ANNs provide excellent support of essential system measures. This leads to a well-rounded implementation, consisting of a good balance between accuracy and system features, and thus an effective technique for automated human chromosome classification

Evolving collective behavior in an artificial ecology

Collective behavior refers to coordinated group motion, common to many animals. The dynamics of a group can be seen as a distributed model, each “animal” applying the same rule set. This study investigates the use of evolved sensory controllers to produce schooling behavior. A set of artificial creatures “live” in an artificial world with hazards and food. Each creature has a simple artificial neural network brain that controls movement in different situations. A chromosome encodes the network structure and weights, which may be combined using artificial evolution with another chromosome, if a creature should choose to mate. Prey and predators coevolve without an explicit fitness function for schooling to produce sophisticated, nondeterministic, behavior. The work highlights the role of species’ physiology in understanding behavior and the role of the environment in encouraging the development of sensory systems

On evolution of relatively large combinational logic circuits

Evolvable hardware (EHW) (Yao and Higuchi, 1999) is a technique introduced to automatically design circuits where the circuit configuration is carried out by evolutionary algorithms. One of the main difficulties in using EHW to solve real-world problems is the scalability. Until now, several strategies have been proposed to avoid this problem, but none of them completely tackle the issue. In this paper three different methods for evolving the most complex circuits have been tested for their scalability. These methods are bi-directional incremental evolution (SO-BIE); generalised disjunction decomposition (GD-BIE) and evolutionary strategies (ES) with dynamic mutation rate. In order to achieve the generalised conclusions the chosen approaches were tested using multipliers, traditionally used in EHW, but also logic circuits taken from MCNC (Yang, 1991) benchmark library and randomly generated circuits. The analysis of the approaches demonstrated that PLA-based ES is capable of evolving logic circuits of up to 12 inputs. The use of SO-BIE allows the generation of fully functional circuits of 14 inputs and GD-BIE is estimated to be able to evolve circuits of 21 inputs

Using Genetic Algorithms for Automatic Recurrent ANN Development: an Application to EEG Signal Classification

[Abstract] ANNs are one of the most successful learning systems. For this reason, many techniques have been published that allow the obtaining of feed-forward networks. However, fe w works describe techniques for developing recurrent networks. This work uses a genetic algorithm for automatic recurrent ANN devel opment. This system has been applied to solve a well-known problem: classi fication of EEG signals from epileptic patients. Results show the high performance of this system, and its ability to develop simple networks, with a low number of neurons and connections.Red Gallega de Investigación sobre Cáncer Colorrectal; ref. 2009/58Programa Ibeoramericano de Ciencia y Tecnología para el Desarrollo; 209RT0366Ministerio de Industria, Turismo y Comercio; TSI-020110-2009-53Xunta de Galicia; 10SIN105004PRInstituto de Salud Carlos III; PIO52048Instituto de Salud Carlos III; RD07/0067/000

Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumors.

Autophagy, particularly with BECN1, has paradoxically been highlighted as tumor promoting in Ras-driven cancers, but potentially tumor suppressing in breast and ovarian cancers. However, studying the specific role of BECN1 at the genetic level is complicated due to its genomic proximity to BRCA1 on both human (chromosome 17) and murine (chromosome 11) genomes. In human breast and ovarian cancers, the monoallelic deletion of these genes is often co-occurring. To investigate the potential tumor suppressor roles of two of the most commonly deleted autophagy genes in ovarian cancer, BECN1 and MAP1LC3B were knocked-down in atypical (BECN1+/+ and MAP1LC3B+/+) ovarian cancer cells. Ultra-performance liquid chromatography mass-spectrometry metabolomics revealed reduced levels of acetyl-CoA which corresponded with elevated levels of glycerophospholipids and sphingolipids. Migration rates of ovarian cancer cells were increased upon autophagy gene knockdown. Genomic instability was increased, resulting in copy-number alteration patterns which mimicked high grade serous ovarian cancer. We further investigated the causal role of Becn1 haploinsufficiency for oncogenesis in a MISIIR SV40 large T antigen driven spontaneous ovarian cancer mouse model. Tumors were evident earlier among the Becn1+/- mice, and this correlated with an increase in copy-number alterations per chromosome in the Becn1+/- tumors. The results support monoallelic loss of BECN1 as permissive for tumor initiation and potentiating for genomic instability in ovarian cancer

Neuroevolution in Deep Neural Networks: Current Trends and Future Challenges

A variety of methods have been applied to the architectural configuration and learning or training of artificial deep neural networks (DNN). These methods play a crucial role in the success or failure of the DNN for most problems and applications. Evolutionary Algorithms (EAs) are gaining momentum as a computationally feasible method for the automated optimisation and training of DNNs. Neuroevolution is a term which describes these processes of automated configuration and training of DNNs using EAs. While many works exist in the literature, no comprehensive surveys currently exist focusing exclusively on the strengths and limitations of using neuroevolution approaches in DNNs. Prolonged absence of such surveys can lead to a disjointed and fragmented field preventing DNNs researchers potentially adopting neuroevolutionary methods in their own research, resulting in lost opportunities for improving performance and wider application within real-world deep learning problems. This paper presents a comprehensive survey, discussion and evaluation of the state-of-the-art works on using EAs for architectural configuration and training of DNNs. Based on this survey, the paper highlights the most pertinent current issues and challenges in neuroevolution and identifies multiple promising future research directions.Comment: 20 pages (double column), 2 figures, 3 tables, 157 reference

"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin