Phase space reconstruction using input-output time series data.

Parallel implementations of the False Nearest Neighbors method to study the behavior of dynamical models

The analysis of observed time series from nonlinear systems is usually done by making a time-delay reconstruction to unfold the dynamics on a multi-dimensional state space. An important aspect of the analysis is the choice of the correct embedding dimension. The conventional procedure used for this is either the method of false nearest neighbors or the saturation of some invariant measure, such as, correlation dimension. Here we examine this issue from a complex network perspective and propose a recurrence network based measure to determine the acceptable minimum embedding dimension to be used for such analysis. The measure proposed here is based on the well known Kullback-Leibler divergence commonly used in information theory. We show that the measure is simple and direct to compute and give accurate result for short time series. To show the significance of the measure in the analysis of practical data, we present the analysis of two EEG signals as examples.

Analysis of the global warming dynamics from temperature time series

Thread-based implementations of the false nearest neighbors method

The False Nearest Neighbors (FNN) method is particularly relevant in several fields of science and engineering (medicine, economics, oceanography, biological systems, etc.). In some of these applications, it is important to give results within a reasonable time scale, so the execution time of the FNN method has to be reduced. This paper describes two parallel implementations of the FNN method based on the distribution of embedding dimensions for distributed memory architectures. A "Single-Program, Multiple Data" (SPMD) paradigm is employed using a simple data decomposition approach where each processor runs the same program but acts on a different subset of the data. The computationally intensive part of the method lies mainly in the neighbor search and this task is therefore parallelized and executed using 4 to 64 processors. The accuracy and performance of the two parallel approaches are then assessed and compared to the best sequential implementation of the FNN method which appears in the TISEAN project. The results indicate that the two parallel approaches, when the method is run using 64 processors on the MareNostrum supercomputer, are between 17 and 37 times faster than the sequential one. Efficiency is between 26% and 59%.

The paper presents the analysis of the Heart Rate Variability (HRV) signal in 19 subjects who recently had a Myocardial Infarction episode (MI). The study follows a nonlinear approach based on the multiparametric analysis of some invariant properties of the dynamical system generating the time series. First the authors reconstruct the system embedding space from the HRV time series. The False Nearest Neighbors (FNN) criterion provides the real embedding dimension value. Results show that through the FNN method it is possible to identify the correct number of LE in the system. Parameter values significantly separate subjects who after MI keep a good performance of the cardiac pump (normal ventricular ejection function, NEF) vs. the group which after MI shows a reduced ventricular ejection fraction (REF).

The great advances in deep learning enable human beings to extract the semantic information in ubiquitous unstructured data into high-dimensional vectors, leading to an urgent priority of managing vector data. Nearest neighbor (NN) query is a pivotal question in vector data management. Unfortunately, the NN query has been proved to be intrinsically hard. Researchers, thus, turn to approximate nearest neighbor (ANN) query which targets better efficiency by slightly compromising accuracy. Despite this, existing ANN methods still incur high time and space costs, which are mainly due to the high dimensionality. Specifically, in most in-memory ANN algorithms, the time cost is dominated by the time for comparing the distances among vectors. Each distance comparison operation (DCO) involves hundreds of arithmetic operations as each vector has hundreds of dimensions. Similarly, the space cost is dominated by the space for storing the vectors. Towards the goal of reducing the time and space costs, we present three methods in this thesis. First, we observe that, for a DCO, if an approximate distance can confirm that a vector is not a NN, then it can be discarded without computing exact distances. Based on this observation, we propose a method named ADSampling. For a DCO, it iteratively and incrementally samples a few dimensions and computes an approximate distance. When this distance is accurate enough to decide the result of the DCO, it terminates sampling. Second, to further improve the efficiency of DCOs, we design an efficient distance estimator. We propose a new quantization method named RaBitQ, which maps $D$-dimensional vectors into $D$-bit strings. RaBitQ provides an unbiased and asymptotically optimal estimator with good empirical accuracy. In addition, we introduce efficient implementations of RaBitQ based on bitwise operations or SIMD-based operations. Third, by extending the RaBitQ method, we develop an algorithm which compresses a floating-point vector into a $B$-bit unsigned integer vector. We prove that our algorithm is asymptotically optimal in terms of the space-accuracy trade-off.

Case Based Reasoning (CBR) is a method that aims to resolve a new case by adapting the solutions contained in previous cases that are similar to the new case. The system built in this study is the CBR system to make recommendations on the topic of student thesis concentration. This study used data from undergraduate students of Informatics Engineering IST AKPRIND Yogyakarta with a total of 115 data consisting of 80 training data and 35 test data. This study aims to design and build a Case Based Reasoning system using the Nearest Neighbor and Manhattan Distance Similarity Methods, and to compare the results of the accuracy value using the Nearest Neighbor Similarity and Manhattan Distance Similarity methods. The recommendation process is carried out by calculating the value of closeness or similarity between new cases and old cases stored on a case basis using the Nearest Neighbor Method and Manhattan Distance. The features used in this study consisted of GPA and course grades. The case taken is the case with the highest similarity value. If a case doesnt get a topic recommendation or is less than the trashold value of 0.8, a case revision will be carried out by an expert. Successfully revised cases are stored in the system to be made new knowledge. The test results using the Nearest Neighbor Method get an accuracy value of 97.14% and Manhattan Distance Method 94.29%.

In this paper, we study the problem of continuous monitoring of reverse k nearest neighbors queries in Euclidean space as well as in spatial networks. Existing techniques are sensitive toward objects and queries movement. For example, the results of a query are to be recomputed whenever the query changes its location. We present a framework for continuous reverse k nearest neighbor (RkNN) queries by assigning each object and query with a safe region such that the expensive recomputation is not required as long as the query and objects remain in their respective safe regions. This significantly improves the computation cost. As a byproduct, our framework also reduces the communication cost in client---server architectures because an object does not report its location to the server unless it leaves its safe region or the server sends a location update request. We also conduct a rigid cost analysis for our Euclidean space RkNN algorithm. We show that our techniques can also be applied to answer bichromatic RkNN queries in Euclidean space as well as in spatial networks. Furthermore, we show that our techniques can be extended for the spatial networks that are represented by directed graphs. The extensive experiments demonstrate that our techniques outperform the existing techniques by an order of magnitude in terms of computation cost and communication cost.

Nearest neighbor search is a fundamental problem in computer vision and machine learning. The straightforward solution, linear scan, is both computationally and memory intensive in large scale high-dimensional cases, hence is not preferable in practice. Therefore, there have been a lot of interests in algorithms that perform approximate nearest neighbor (ANN) search. In this paper, we propose a novel addition-based vector quantization algorithm, Asymmetric Mapping Quantization (AMQ), to efficiently conduct ANN search. Unlike existing addition-based quantization methods that suffer from handling the problem caused by the norm of database vector, we map the query vector and database vector using different mapping functions to transform the computation of L-2 distance to inner product similarity, thus do not need to evaluate the norm of database vector. Moreover, we further propose Distributed Asymmetric Mapping Quantization (DAMQ) to enable AMQ to work on very large dataset by distributed learning. Extensive experiments on approximate nearest neighbor search and image retrieval validate the merits of the proposed AMQ and DAMQ.

Broadcasting data with an index is an effective way to disseminate public information to a large clients. For a server, using multiple channels to provide services (e.g., location-based services) makes the broadcast cycle shorter than using one channel. Among location-based services, the k nearest neighbors (k-NN) search is an important one and finds the fc closest objects to a query point in a multi-dimensional space. This paper considers k nearest neighbors search on a broadcast R-tree in a multi-channel environment. We assume that a mobile client can only tune into a specified channel at one time instance. We study how a server generates the broadcast schedules on multiple channels and explore how a client executes the k-NN search on the broadcast. Different broadcast schedules with the client k-NN search processing makes different k-NN search protocols. The objectives of the protocols is to minimize the latency (i.e., the time elapsed between issuing and termination of the query), tuning time (i.e., the amount of time spent on listening to the channel), and the memory usage for k-NN search processing. Last, we present our experiments and the experiment results validate that our mechanisms achieve the objectives.

Developed from Nearest Neighbor (NN) queries, Aggregate Nearest Neighbor (ANN) queries return the object that minimizes an aggregate distance function with respect to a set of query points. Because of the multiple query points, ANN queries are much more complex than NN queries. For optimizing the query processing and improving the query efficiency, many ANN queries algorithms utilizes pruning strategies, with or without an index structure. Obviously, the pruning effect highly depends on the tightness of the bound estimation. In this paper, we figure out a property in vector space and develop some efficient bound estimations for two most popular types of ANN queries. Based on these bounds, we design the indexed and non-index ANN algorithms, and conduct experimental studies. Our algorithms show good performance, especially for high dimensional queries, for both real dataset and synthetic datasets.

Spatial interpolations are commonly used in geometric modeling for life science applications. In large-scale spatial interpolations, it is always needed to find a local set of data points for each interpolated point using the k Nearest Neighbor (kNN) search procedure. To improve the computational efficiency of kNN search, spatial decomposition structures such as grids and trees are employed to fastly locate the nearest neighbors. Among those spatial decomposition structures, the uniform grid is the simplest one, and the size of the grid cell could strongly affect the efficiency of kNN search. In this paper, we evaluate the effect of the size of uniform grid cell on the efficiency of kNN search. Our objective is to find the relatively optimal size of grid cell by considering the distribution of scattered points (i.e., the data points and the interpolated points). We employ the Standard Deviation of points’ coordinates to measure the spatial distribution of scattered points. For the irregularly distributed scattered points, we perform several series of kNN search procedures in two dimensions. Benchmark results indicate that: in two dimensions, with the increase of the Standard Deviation of points’ coordinates, the relatively optimal size of the grid cell decreases and eventually converges. The relationships between the Standard Deviation of scattered points’ coordinates and the relatively optimal size of grid cell are also fitted. The fitted relationships could be applied to determine the relatively optimal grid cell in kNN search, and further, improve the computational efficiency of spatial interpolations.

Here we report PPB2 as a target prediction tool assigning targets to a query molecule based on ChEMBL data. PPB2 computes ligand similarities using molecular fingerprints encoding composition (MQN), molecular shape and pharmacophores (Xfp), and substructures (ECfp4) and features an unprecedented combination of nearest neighbor (NN) searches and Naı̈ve Bayes (NB) machine learning, together with simple NN searches, NB and Deep Neural Network (DNN) machine learning models as further options. Although NN(ECfp4) gives the best results in terms of recall in a 10-fold cross-validation study, combining NN searches with NB machine learning provides superior precision statistics, as well as better results in a case study predicting off-targets of a recently reported TRPV6 calcium channel inhibitor, illustrating the value of this combined approach. PPB2 is available to assess possible off-targets of small molecule drug-like compounds by public access at http://gdb.unibe.ch .

During this period in which the IEEE Control Systems Society and the American Automatic Control Council (AACC) celebrates more than 50 years of successful service to the control community, one of the names best known to members of these organizations is that of Donald P. Eckman. The Eckman Award recognizes outstanding young contributors to the control field and is the oldest AACC award. Probably less well known are the contributions of Donald Eckman himself and the nature of the man for whom the award is named.