Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination.

BACKGROUND: Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis of normal and abnormal behaviour. In this study, we considered an existing neurobiological model of fast eye movements (saccades), capable of generating realistic simulations of: (i) normal horizontal saccades; and (ii) infantile nystagmus - pathological ocular oscillations that can be subdivided into different waveform classes. By developing appropriate fitness functions, we optimised the model to existing experimental saccade and nystagmus data, using a well-established multi-objective genetic algorithm. This algorithm required the model to be numerically integrated for very large numbers of parameter combinations. To address this computational bottleneck, we implemented a master-slave parallelisation, in which the model integrations were distributed across the compute units of a GPU, under the control of a CPU. RESULTS: While previous nystagmus fitting has been based on reproducing qualitative waveform characteristics, our optimisation protocol enabled us to perform the first direct fits of a model to experimental recordings. The fits to normal eye movements showed that although saccades of different amplitudes can be accurately simulated by individual parameter sets, a single set capable of fitting all amplitudes simultaneously cannot be determined. The fits to nystagmus oscillations systematically identified the parameter regimes in which the model can reproduce a number of canonical nystagmus waveforms to a high accuracy, whilst also identifying some waveforms that the model cannot simulate. Using a GPU to perform the model integrations yielded a speedup of around 20 compared to a high-end CPU. CONCLUSIONS: The results of both optimisation problems enabled us to quantify the predictive capacity of the model, suggesting specific modifications that could expand its repertoire of simulated behaviours. In addition, the optimal parameter distributions we obtained were consistent with previous computational studies that had proposed the saccadic braking signal to be the origin of the instability preceding the development of infantile nystagmus oscillations. Finally, the master-slave parallelisation method we developed to accelerate the optimisation process can be readily adapted to fit other highly parametrised computational biology models to experimental data

Optimisation and Computational Methods to Model the Oculomotor System with Focus on Nystagmus

Open access. Use it freely but cite it.Infantile nystagmus is a condition that causes involuntary, bilateral and conjugate oscillations of the eyes, which are predominately restricted to the horizontal plane. In order to investigate the cause of nystagmus, computational models and nonlinear dynamics techniques have been used to model and analyse the oculomotor system. Computational models are important in making predictions and creating a quantitative framework for the analysis of the oculomotor system. Parameter estimation is a critical step in the construction and analysis of these models. A preliminary parameter estimation of a nonlinear dynamics model proposed by Broomhead et al. [1] has been shown to be able to simulate both normal rapid eye movements (i.e. saccades) and nystagmus oscillations. The application of nonlinear analysis to experimental jerk nystagmus recordings, has shown that the local dimensions number of the oscillation varies across the phase angle of the nystagmus cycle. It has been hypothesised that this is due to the impact of signal dependent noise (SDN) on the neural commands in the oculomotor system. The main aims of this study were: (i) to develop parameter estimation methods for the Broomhead et al. [1] model in order to explore its predictive capacity by fitting it to experimental recordings of nystagmus waveforms and saccades; (ii) to develop a stochastic oculomotor model and examine the hypothesis that noise on the neural commands could be the cause of the behavioural characteristics measured from experimental nystagmus time series using nonlinear analysis techniques. In this work, two parameter estimation methods were developed, one for fitting the model to the experimental nystagmus waveforms and one to saccades. By using the former method, we successfully fitted the model to experimental nystagmus waveforms. This fit allowed to find the specific parameter values that set the model to generate these waveforms. The types of the waveforms that we successfully fitted were asymmetric pseudo-cycloid, jerk and jerk with extended foveation. The fit of other types of nystagmus waveforms were not examined in this work. Moreover, the results showed which waveforms the model can generate almost perfectly and the waveform characteristics of a number of jerk waveforms which it cannot exactly generate. These characteristics were on a specific type of jerk nystagmus waveforms with a very extreme fast phase. The latter parameter estimation method allowed us to explore whether the model can generate horizontal saccades of different amplitudes with the same behaviour as observed experimentally. The results suggest that the model can generate the experimental saccadic velocity profiles of different saccadic amplitudes. However, the results show that best fittings of the model to the experimental data are when different model parameter values were used for different saccadic amplitude. Our parameter estimation methods are based on multi-objective genetic algorithms (MOGA), which have the advantage of optimising biological models with a multi-objective, high-dimensional and complex search space. However, the integration of these models, for a wide range of parameter combinations, is very computationally intensive for a single central processing unit (CPU). To overcome this obstacle, we accelerated the parameter estimation method by utilising the parallel capabilities of a graphics processing unit (GPU). Depending of the GPU model, this could provide a speedup of 30 compared to a midrange CPU. The stochastic model that we developed is based on the Broomhead et al. [1] model, with signal dependent noise (SDN) and constant noise (CN) added to the neural commands. We fitted the stochastic model to saccades and jerk nystagmus waveforms. It was found that SDN and CN can cause similar variability to the local dimensions number of the oscillation as found in the experimental jerk nystagmus waveforms and in the case of saccade generation the saccadic variability recorded experimentally. However, there are small differences in the simulated behaviour compared to the nystagmus experimental data. We hypothesise that these could be caused by the inability of the model to simulate exactly key jerk waveform characteristics. Moreover, the differences between the simulations and the experimental nystagmus waveforms indicate that the proposed model requires further expansion, and this could include other oculomotor subsystem(s).Engineering and Physical Sciences Research Council (EPSRC

Parallel Counting Sort: A Modified of Counting Sort Algorithm

Sorting is one of a classic problem in computer engineer. One well-known sorting algorithm is a Counting Sort algorithm. Counting Sort had one problem, it can’t sort a positive and negative number in the same input list. Then, Modified Counting Sort created to solve that’s problem. The algorithm will split the numbers before the sorting process begin. This paper will tell another modification of this algorithm. The algorithm called Parallel Counting Sort. Parallel Counting Sort able to increase the execution time about 70% from Modified Counting Sort, especially in a big dataset (around 1000 and 10.000 numbers)

Efficient fault tolerance for selected scientific computing algorithms on heterogeneous and approximate computer architectures

Scientific computing and simulation technology play an essential role to solve central challenges in science and engineering. The high computational power of heterogeneous computer architectures allows to accelerate applications in these domains, which are often dominated by compute-intensive mathematical tasks. Scientific, economic and political decision processes increasingly rely on such applications and therefore induce a strong demand to compute correct and trustworthy results. However, the continued semiconductor technology scaling increasingly imposes serious threats to the reliability and efficiency of upcoming devices. Different reliability threats can cause crashes or erroneous results without indication. Software-based fault tolerance techniques can protect algorithmic tasks by adding appropriate operations to detect and correct errors at runtime. Major challenges are induced by the runtime overhead of such operations and by rounding errors in floating-point arithmetic that can cause false positives. The end of Dennard scaling induces central challenges to further increase the compute efficiency between semiconductor technology generations. Approximate computing exploits the inherent error resilience of different applications to achieve efficiency gains with respect to, for instance, power, energy, and execution times. However, scientific applications often induce strict accuracy requirements which require careful utilization of approximation techniques. This thesis provides fault tolerance and approximate computing methods that enable the reliable and efficient execution of linear algebra operations and Conjugate Gradient solvers using heterogeneous and approximate computer architectures. The presented fault tolerance techniques detect and correct errors at runtime with low runtime overhead and high error coverage. At the same time, these fault tolerance techniques are exploited to enable the execution of the Conjugate Gradient solvers on approximate hardware by monitoring the underlying error resilience while adjusting the approximation error accordingly. Besides, parameter evaluation and estimation methods are presented that determine the computational efficiency of application executions on approximate hardware. An extensive experimental evaluation shows the efficiency and efficacy of the presented methods with respect to the runtime overhead to detect and correct errors, the error coverage as well as the achieved energy reduction in executing the Conjugate Gradient solvers on approximate hardware

Colour videos with depth : acquisition, processing and evaluation

The human visual system lets us perceive the world around us in three dimensions by integrating evidence from depth cues into a coherent visual model of the world. The equivalent in computer vision and computer graphics are geometric models, which provide a wealth of information about represented objects, such as depth and surface normals. Videos do not contain this information, but only provide per-pixel colour information. In this dissertation, I hence investigate a combination of videos and geometric models: videos with per-pixel depth (also known as RGBZ videos). I consider the full life cycle of these videos: from their acquisition, via filtering and processing, to stereoscopic display. I propose two approaches to capture videos with depth. The first is a spatiotemporal stereo matching approach based on the dual-cross-bilateral grid – a novel real-time technique derived by accelerating a reformulation of an existing stereo matching approach. This is the basis for an extension which incorporates temporal evidence in real time, resulting in increased temporal coherence of disparity maps – particularly in the presence of image noise. The second acquisition approach is a sensor fusion system which combines data from a noisy, low-resolution time-of-flight camera and a high-resolution colour video camera into a coherent, noise-free video with depth. The system consists of a three-step pipeline that aligns the video streams, efficiently removes and fills invalid and noisy geometry, and finally uses a spatiotemporal filter to increase the spatial resolution of the depth data and strongly reduce depth measurement noise. I show that these videos with depth empower a range of video processing effects that are not achievable using colour video alone. These effects critically rely on the geometric information, like a proposed video relighting technique which requires high-quality surface normals to produce plausible results. In addition, I demonstrate enhanced non-photorealistic rendering techniques and the ability to synthesise stereoscopic videos, which allows these effects to be applied stereoscopically. These stereoscopic renderings inspired me to study stereoscopic viewing discomfort. The result of this is a surprisingly simple computational model that predicts the visual comfort of stereoscopic images. I validated this model using a perceptual study, which showed that it correlates strongly with human comfort ratings. This makes it ideal for automatic comfort assessment, without the need for costly and lengthy perceptual studies

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 Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s 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 algorithms’ performance on Amazon’s 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

Additional file 1 of Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination

Contains Supplementary Figures S1-S27 and Supplementary Tables S1-S11. (PDF 5998 kb