9 research outputs found
Digital control networks for virtual creatures
Robot control systems evolved with genetic algorithms traditionally take the form
of floating-point neural network models. This thesis proposes that digital control systems,
such as quantised neural networks and logical networks, may also be used for
the task of robot control. The inspiration for this is the observation that the dynamics
of discrete networks may contain cyclic attractors which generate rhythmic behaviour,
and that rhythmic behaviour underlies the central pattern generators which drive lowlevel
motor activity in the biological world.
To investigate this a series of experiments were carried out in a simulated physically
realistic 3D world. The performance of evolved controllers was evaluated on two well
known control tasksâpole balancing, and locomotion of evolved morphologies. The
performance of evolved digital controllers was compared to evolved floating-point neural
networks. The results show that the digital implementations are competitive with
floating-point designs on both of the benchmark problems. In addition, the first reported
evolution from scratch of a biped walker is presented, demonstrating that when
all parameters are left open to evolutionary optimisation complex behaviour can result
from simple components
A complex systems approach to education in Switzerland
The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance
Using MapReduce Streaming for Distributed Life Simulation on the Cloud
Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conwayâs life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MRâs applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithmsâ performance on Amazonâs Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp
The population dynamics of a hybrid zone in the alpine grasshopper Podisma pedestris: An ecological and genetic investigation
This thesis describes ecological and genetic investigations of a hybrid zone between incompatible genotypes in the alpine grasshopper Podisma pedestris. The two races are distinguished by a Robertsonian fusion between the X chromosome and an autosome. The dine between them is usually between 400 and 800m wide, and is thought to be maintained by a balance between selection against heterozygotes and dispersal. The Podisma hybrid zone provides an interesting system in which to investigate fitness differences in nature. Measurements of fitness components have been made in the field across the hybrid zone. Counts through the season, in matched vegetation types, show (surprisingly) a substantial difference between the two races in the number of young nymphs: this difference is consistent across years and across transects. Hybrid populations are less dense than the average of the pure populations, but are not significantly different from the sparser of the parental races. Differences in density across the zone decrease through the season, suggesting density-dependent mortality. This is supported by cage and transplant experiments in the field, and by simulation experiments. Less direct ways of measuring fitness components are also explored. Theoretical relations derived by Barton (1983) allow one to infer parameters such as selection pressures from the observed dine shape. Here, computer simulations show that these estimates are robust. Where the cline coincides with a physical barrier, the pattern of chromosome frequencies combine with measures of dispersal to show that selection is acting on many genes, causing an additional barrier to gene flow between the divergent populations. An assessment of the density of Podisma over a wide area allows the expected position of the dine to be estimated. Computer simulations show that the observed position of the dine is consistent with that expected from both direct density estimates, and densities inferred from a vegetation survey
Towards Personalized Medicine: Computational Approaches to Support Drug Design and Clinical Decision Making
The future looks bright for a clinical practice that tailors the
therapy with the best efficacy and highest safety to a patient. Substantial
amounts of funding have resulted in technological advances regarding
patient-centered data acquisition --- particularly genetic data. Yet, the
challenge of translating this data into clinical practice remains open.
To support drug target characterization, we developed a global maximum
entropy-based method that predicts protein-protein complexes including the
three-dimensional structure of their interface from sequence data. To further
speed up the drug development process, we present methods to reposition drugs
with established safety profiles to new indications leveraging paths in
cellular interaction networks. We validated both methods on known data,
demonstrating their ability to recapitulate known protein complexes and
drug-indication pairs, respectively.
After studying the extent and characteristics of genetic variation with a
predicted impact on protein function across 60,607 individuals, we showed that
most patients carry variants in drug-related genes. However, for the majority
of variants, their impact on drug efficacy remains unknown. To inform
personalized treatment decisions, it is thus crucial to first collate knowledge
from open data sources about known variant effects and to then close the
knowledge gaps for variants whose effect on drug binding is still not
characterized. Here, we built an automated annotation pipeline for
patient-specific variants whose value we illustrate for a set of patients with
hepatocellular carcinoma. We further developed a molecular modeling protocol to
predict changes in binding affinity in proteins with genetic variants which we
evaluated for several clinically relevant protein kinases.
Overall, we expect that each presented method has the potential to advance
personalized medicine by closing knowledge gaps about protein interactions and
genetic variation in drug-related genes. To reach clinical applicability,
challenges with data availability need to be overcome and prediction
performance should be validated experimentally.Therapien mit der besten Wirksamkeit und hĂśchsten
Sicherheit werden in Zukunft auf den Patienten zugeschnitten werden. Hier haben
erhebliche finanzielle Mittel zu technologischen Fortschritten bei der
patientenzentrierten Datenerfassung gefĂźhrt, aber diese Daten in die
klinische Praxis zu Ăźbertragen, bleibt aktuell noch eine Herausforderung.
Um die Wirkstoffforschung in der Charakterisierung therapeutischer Zielproteine
zu unterstĂźtzen, haben wir eine Maximum-Entropie-Methode entwickelt,
die Protein-Interaktionen und ihre dreidimensionalen Struktur
aus Sequenzdaten vorhersagt. DarĂźber hinaus, stellen wir Methoden
zur Repositionierung von etablierten Arzneimitteln auf
neue Indikationen vor, die Pfade in zellulären Interaktionsnetze nutzen.
Diese Methoden haben wir anhand bekannter Daten validiert und ihre Fähigkeit
demonstriert, bekannte Proteinkomplexe bzw. Wirkstoff-Indikations-Paare zu
rekapitulieren.
Unsere Analyse genetischer Variation mit einem Einfluss auf die
Proteinfunktion in 60,607 Individuen konnte zeigen, dass nahezu jeder Patient
funktionsverändernde Varianten in Medikamenten-assoziierten Genen
trägt. Der direkte Einfluss der meisten beobachteten Varianten auf die
Medikamenten-Wirksamkeit ist jedoch noch unbekannt. Um dennoch personalisierte
Behandlungsentscheidungen treffen zu kÜnnen, präsentieren wir eine Annotationspipeline fßr genetische
Varianten, deren Wert wir fßr Patienten mit hepatozellulärem
Karzinom illustrieren konnten. DarĂźber hinaus haben wir ein molekulares
Modellierungsprotokoll entwickelt, um die Veränderungen in der
Bindungsaffinität von Proteinen mit genetischen Varianten voraussagen.
Insgesamt sind wir davon Ăźberzeugt, dass jede der vorgestellten Methoden das
Potential hat, WissenslĂźcken Ăźber Proteininteraktionen und
genetische Variationen in medikamentenbezogenen Genen zu schlie{\ss}en und
somit das Feld der personalisierten Medizin voranzubringen. Um klinische
Anwendbarkeit zu erreichen, gilt es in der Zukunft, verbleibende
Herausforderungen bei der Datenverfßgbarkeit zu bewältigen und unsere
Vorhersagen experimentell zu validieren
Macroevolution: Explanation, Interpretation and Evidence
info:eu-repo/semantics/publishedVersio