A control algorithm for autonomous optimization of extracellular recordings

This paper develops a control algorithm that can autonomously position an electrode so as to find and then maintain an optimal extracellular recording position. The algorithm was developed and tested in a two-neuron computational model representative of the cells found in cerebral cortex. The algorithm is based on a stochastic optimization of a suitably defined signal quality metric and is shown capable of finding the optimal recording position along representative sampling directions, as well as maintaining the optimal signal quality in the face of modeled tissue movements. The application of the algorithm to acute neurophysiological recording experiments and its potential implications to chronic recording electrode arrays are discussed

Event-Based Motion Segmentation by Motion Compensation

In contrast to traditional cameras, whose pixels have a common exposure time, event-based cameras are novel bio-inspired sensors whose pixels work independently and asynchronously output intensity changes (called "events"), with microsecond resolution. Since events are caused by the apparent motion of objects, event-based cameras sample visual information based on the scene dynamics and are, therefore, a more natural fit than traditional cameras to acquire motion, especially at high speeds, where traditional cameras suffer from motion blur. However, distinguishing between events caused by different moving objects and by the camera's ego-motion is a challenging task. We present the first per-event segmentation method for splitting a scene into independently moving objects. Our method jointly estimates the event-object associations (i.e., segmentation) and the motion parameters of the objects (or the background) by maximization of an objective function, which builds upon recent results on event-based motion-compensation. We provide a thorough evaluation of our method on a public dataset, outperforming the state-of-the-art by as much as 10%. We also show the first quantitative evaluation of a segmentation algorithm for event cameras, yielding around 90% accuracy at 4 pixels relative displacement.Comment: When viewed in Acrobat Reader, several of the figures animate. Video: https://youtu.be/0q6ap_OSBA

The application of ANFIS prediction models for thermal error compensation on CNC machine tools

Thermal errors can have significant effects on CNC machine tool accuracy. The errors come from thermal deformations of the machine elements caused by heat sources within the machine structure or from ambient temperature change. The effect of temperature can be reduced by error avoidance or numerical compensation. The performance of a thermal error compensation system essentially depends upon the accuracy and robustness of the thermal error model and its input measurements. This paper first reviews different methods of designing thermal error models, before concentrating on employing an adaptive neuro fuzzy inference system (ANFIS) to design two thermal prediction models: ANFIS by dividing the data space into rectangular sub-spaces (ANFIS-Grid model) and ANFIS by using the fuzzy c-means clustering method (ANFIS-FCM model). Grey system theory is used to obtain the influence ranking of all possible temperature sensors on the thermal response of the machine structure. All the influence weightings of the thermal sensors are clustered into groups using the fuzzy c-means (FCM) clustering method, the groups then being further reduced by correlation analysis. A study of a small CNC milling machine is used to provide training data for the proposed models and then to provide independent testing data sets. The results of the study show that the ANFIS-FCM model is superior in terms of the accuracy of its predictive ability with the benefit of fewer rules. The residual value of the proposed model is smaller than ±4 μm. This combined methodology can provide improved accuracy and robustness of a thermal error compensation system

Linear, Deterministic, and Order-Invariant Initialization Methods for the K-Means Clustering Algorithm

Over the past five decades, k-means has become the clustering algorithm of choice in many application domains primarily due to its simplicity, time/space efficiency, and invariance to the ordering of the data points. Unfortunately, the algorithm's sensitivity to the initial selection of the cluster centers remains to be its most serious drawback. Numerous initialization methods have been proposed to address this drawback. Many of these methods, however, have time complexity superlinear in the number of data points, which makes them impractical for large data sets. On the other hand, linear methods are often random and/or sensitive to the ordering of the data points. These methods are generally unreliable in that the quality of their results is unpredictable. Therefore, it is common practice to perform multiple runs of such methods and take the output of the run that produces the best results. Such a practice, however, greatly increases the computational requirements of the otherwise highly efficient k-means algorithm. In this chapter, we investigate the empirical performance of six linear, deterministic (non-random), and order-invariant k-means initialization methods on a large and diverse collection of data sets from the UCI Machine Learning Repository. The results demonstrate that two relatively unknown hierarchical initialization methods due to Su and Dy outperform the remaining four methods with respect to two objective effectiveness criteria. In addition, a recent method due to Erisoglu et al. performs surprisingly poorly.Comment: 21 pages, 2 figures, 5 tables, Partitional Clustering Algorithms (Springer, 2014). arXiv admin note: substantial text overlap with arXiv:1304.7465, arXiv:1209.196

Sparse optical flow regularisation for real-time visual tracking

Optical flow can greatly improve the robustness of visual tracking algorithms. While dense optical flow algorithms have various applications, they can not be used for real-time solutions without resorting to GPU calculations. Furthermore, most optical flow algorithms fail in challenging lighting environments due to the violation of the brightness constraint. We propose a simple but effective iterative regularisation scheme for real-time, sparse optical flow algorithms, that is shown to be robust to sudden illumination changes and can handle large displacements. The algorithm proves to outperform well known techniques in real life video sequences, while being much faster to calculate. Our solution increases the robustness of a real-time particle filter based tracking application, consuming only a fraction of the available CPU power. Furthermore, a new and realistic optical flow dataset with annotated ground truth is created and made freely available for research purposes

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site