A Novel and Fast Approach for Population Structure Inference Using Kernel-PCA and Optimization (PSIKO)

Population structure is a confounding factor in Genome Wide Association Studies, increasing the rate of false positive associations. In order to correct for it, several model-based algorithms such as ADMIXTURE and STRUCTURE have been proposed. These tend to suffer from the fact that they have a considerable computational burden, limiting their applicability when used with large datasets, such as those produced by Next Generation Sequencing (NGS) techniques. To address this, non-model based approaches such as SNMF and EIGENSTRAT have been proposed, which scale better with larger data. Here we present a novel non-model based approach, PSIKO, which is based on a unique combination of linear kernel-PCA and least-squares optimization and allows for the inference of admixture coefficients, principal components, and number of founder populations of a dataset. PSIKO has been compared against existing leading methods on a variety of simulation scenarios, as well as on real biological data. We found that in addition to producing results of the same quality as other tested methods, PSIKO scales extremely well with dataset size, being considerably (up to 30 times) faster for longer sequences than even state of the art methods such as SNMF. PSIKO and accompanying manual are freely available at https://www.uea.ac.uk/computing/psiko

A hybrid keyboard-guitar interface using capacitive touch sensing and physical modeling

This paper was presented at the 9th Sound and Music Computing Conference, Copenhagen, Denmark.This paper presents a hybrid interface based on a touch- sensing keyboard which gives detailed expressive control over a physically-modeled guitar. Physical modeling al- lows realistic guitar synthesis incorporating many expres- sive dimensions commonly employed by guitarists, includ- ing pluck strength and location, plectrum type, hand damp- ing and string bending. Often, when a physical model is used in performance, most control dimensions go unused when the interface fails to provide a way to intuitively con- trol them. Techniques as foundational as strumming lack a natural analog on the MIDI keyboard, and few digital controllers provide the independent control of pitch, vol- ume and timbre that even novice guitarists achieve. Our interface combines gestural aspects of keyboard and guitar playing. Most dimensions of guitar technique are control- lable polyphonically, some of them continuously within each note. Mappings are evaluated in a user study of key- boardists and guitarists, and the results demonstrate its playa- bility by performers of both instruments

The Mode of Computing

The Turing Machine is the paradigmatic case of computing machines, but there are others, such as Artificial Neural Networks, Table Computing, Relational-Indeterminate Computing and diverse forms of analogical computing, each of which based on a particular underlying intuition of the phenomenon of computing. This variety can be captured in terms of system levels, re-interpreting and generalizing Newell's hierarchy, which includes the knowledge level at the top and the symbol level immediately below it. In this re-interpretation the knowledge level consists of human knowledge and the symbol level is generalized into a new level that here is called The Mode of Computing. Natural computing performed by the brains of humans and non-human animals with a developed enough neural system should be understood in terms of a hierarchy of system levels too. By analogy from standard computing machinery there must be a system level above the neural circuitry levels and directly below the knowledge level that is named here The mode of Natural Computing. A central question for Cognition is the characterization of this mode. The Mode of Computing provides a novel perspective on the phenomena of computing, interpreting, the representational and non-representational views of cognition, and consciousness.Comment: 35 pages, 8 figure

Fault-tolerant distributed computing scheme based on erasure codes

Some emerging classes of distributed computing systems, such peer-to-peer or grid computing computing systems, are composed of heterogeneous computing resources potentially unreliable. This paper proposes to use erasure codes to improve the fault-tolerance of parallel distributed computing applications in this context. A general method to generate redundant processes from a set of parallel processes is presented. This scheme allows the recovery of the result of the application even if some of the processes crash