56 research outputs found
Regulatory motif discovery using a population clustering evolutionary algorithm
This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences
Evolutionary Algorithms
Evolutionary algorithms (EAs) are population-based metaheuristics, originally
inspired by aspects of natural evolution. Modern varieties incorporate a broad
mixture of search mechanisms, and tend to blend inspiration from nature with
pragmatic engineering concerns; however, all EAs essentially operate by
maintaining a population of potential solutions and in some way artificially
'evolving' that population over time. Particularly well-known categories of EAs
include genetic algorithms (GAs), Genetic Programming (GP), and Evolution
Strategies (ES). EAs have proven very successful in practical applications,
particularly those requiring solutions to combinatorial problems. EAs are
highly flexible and can be configured to address any optimization task, without
the requirements for reformulation and/or simplification that would be needed
for other techniques. However, this flexibility goes hand in hand with a cost:
the tailoring of an EA's configuration and parameters, so as to provide robust
performance for a given class of tasks, is often a complex and time-consuming
process. This tailoring process is one of the many ongoing research areas
associated with EAs.Comment: To appear in R. Marti, P. Pardalos, and M. Resende, eds., Handbook of
Heuristics, Springe
IoTDevID: A Behavior-Based Device Identification Method for the IoT
Device identification is one way to secure a network of IoT devices, whereby
devices identified as suspicious can subsequently be isolated from a network.
In this study, we present a machine learning-based method, IoTDevID, that
recognizes devices through characteristics of their network packets. As a
result of using a rigorous feature analysis and selection process, our study
offers a generalizable and realistic approach to modelling device behavior,
achieving high predictive accuracy across two public datasets. The model's
underlying feature set is shown to be more predictive than existing feature
sets used for device identification, and is shown to generalize to data unseen
during the feature selection process. Unlike most existing approaches to IoT
device identification, IoTDevID is able to detect devices using non-IP and
low-energy protocols
DroidDissector: A Static and Dynamic Analysis Tool for Android Malware Detection
DroidDissector is an extraction tool for both static and dynamic features.
The aim is to provide Android malware researchers and analysts with an
integrated tool that can extract all of the most widely used features in
Android malware detection from one location. The static analysis module
extracts features from both the manifest file and the source code of the
application to obtain a broad array of features that include permissions, API
call graphs and opcodes. The dynamic analysis module runs on the latest version
of Android and analyses the complete behaviour of an application by tracking
the system calls used, network traffic generated, API calls used and log files
produced by the application
Using Epigenetic Networks for the Analysis of Movement Associated with Levodopa Therapy for Parkinson's Disease
© 2016 The Author(s) Levodopa is a drug that is commonly used to treat movement disorders associated with Parkinson's disease. Its dosage requires careful monitoring, since the required amount changes over time, and excess dosage can lead to muscle spasms known as levodopa-induced dyskinesia. In this work, we investigate the potential for using epiNet, a novel artificial gene regulatory network, as a classifier for monitoring accelerometry time series data collected from patients undergoing levodopa therapy. We also consider how dynamical analysis of epiNet classifiers and their transitions between different states can highlight clinically useful information which is not available through more conventional data mining techniques. The results show that epiNet is capable of discriminating between different movement patterns which are indicative of either insufficient or excessive levodopa
Harmonic Versus Chaos Controlled Oscillators in Hexapedal Locomotion
The behavioural diversity of chaotic oscillator can be controlled into periodic dynamics and used to model locomotion using central pattern generators. This paper shows how controlled chaotic oscillators may improve the adaptation of the robot locomotion behaviour to terrain uncertainties when compared to nonlinear harmonic oscillators. This is quantitatively assesses by the stability, changes of direction and steadiness of the robotic movements. Our results show that the controlled Wu oscillator promotes the emergence of adaptive locomotion when deterministic sensory feedback is used. They also suggest that the chaotic nature of chaos controlled oscillators increases the expressiveness of pattern generators to explore new locomotion gaits
Parkinson’s disease diagnosis using convolutional neural networks and figure-copying tasks
Parkinson’s disease (PD) is a progressive neurodegenerative disorder that causes abnormal movements and an array of other symptoms. An accurate PD diagnosis can be a challenging task as the signs and symptoms, particularly at an early stage, can be similar to other medical conditions or the physiological changes of normal ageing. This work aims to contribute to the PD diagnosis process by using a convolutional neural network, a type of deep neural network architecture, to differentiate between healthy controls and PD patients. Our approach focuses on discovering deviations in patient’s movements with the use of drawing tasks. In addition, this work explores which of two drawing tasks, wire cube or spiral pentagon, are more effective in the discrimination process. With accuracy, our convolutional classifier, trained with images of the pentagon drawing task and augmentation techniques, can be used as an objective method to discriminate PD from healthy controls. Our compact model has the potential to be developed into an offline real-time automated single-task diagnostic tool, which can be easily deployed within a clinical setting
A New Evolutionary Algorithm-Based Home Monitoring Device for Parkinson’s Dyskinesia
Parkinson’s disease (PD) is a neurodegenerative movement disorder. Although there is no cure, symptomatic treatments are available and can significantly improve quality of life. The motor, or movement, features of PD are caused by reduced production of the neurotransmitter dopamine. Dopamine deficiency is most often treated using dopamine replacement therapy. However, this therapy can itself lead to further motor abnormalities referred to as dyskinesia. Dyskinesia consists of involuntary jerking movements and muscle spasms, which can often be violent. To minimise dyskinesia, it is necessary to accurately titrate the amount of medication given and monitor a patient’s movements. In this paper, we describe a new home monitoring device that allows dyskinesia to be measured as a patient goes about their daily activities, providing information that can assist clinicians when making changes to medication regimens. The device uses a predictive model of dyskinesia that was trained by an evolutionary algorithm, and achieves AUC>0.9 when discriminating clinically significant dyskinesia
REFORMS: Reporting Standards for Machine Learning Based Science
Machine learning (ML) methods are proliferating in scientific research.
However, the adoption of these methods has been accompanied by failures of
validity, reproducibility, and generalizability. These failures can hinder
scientific progress, lead to false consensus around invalid claims, and
undermine the credibility of ML-based science. ML methods are often applied and
fail in similar ways across disciplines. Motivated by this observation, our
goal is to provide clear reporting standards for ML-based science. Drawing from
an extensive review of past literature, we present the REFORMS checklist
(porting Standards achine Learning
Based cience). It consists of 32 questions and a paired set of
guidelines. REFORMS was developed based on a consensus of 19 researchers across
computer science, data science, mathematics, social sciences, and biomedical
sciences. REFORMS can serve as a resource for researchers when designing and
implementing a study, for referees when reviewing papers, and for journals when
enforcing standards for transparency and reproducibility
Metaheuristics in nature-inspired algorithms
To many people, the terms nature-inspired algorithm and metaheuristic are interchangeable. However, this contem-porary usage is not consistent with the original meaning of the term metaheuristic, which referred to something closer to a design pattern than to an algorithm. In this paper, it is argued that the loss of focus on true metaheuristics is a pri-mary reason behind the explosion of “novel ” nature-inspired algorithms and the issues this has raised. To address this, this paper attempts to explicitly identify the metaheuristics that are used in conventional optimisation algorithms, dis-cuss whether more recent nature-inspired algorithms have delivered any fundamental new knowledge to the field of metaheuristics, and suggest some guidelines for future re-search in this field
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