The Mathematics of Phylogenomics

The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within populations. We are therefore able to ask, for the first time, fundamental questions about the evolution of genomes, the structure of genes and their regulation, and the connections between genotypes and phenotypes of individuals. The answers to these questions are all predicated on progress in a variety of computational, statistical, and mathematical fields. The rapid growth in the characterization of genomes has led to the advancement of a new discipline called Phylogenomics. This discipline results from the combination of two major fields in the life sciences: Genomics, i.e., the study of the function and structure of genes and genomes; and Molecular Phylogenetics, i.e., the study of the hierarchical evolutionary relationships among organisms and their genomes. The objective of this article is to offer mathematicians a first introduction to this emerging field, and to discuss specific mathematical problems and developments arising from phylogenomics.Comment: 41 pages, 4 figure

An application of the MPP to the interactive manipulation of stereo images of digital terrain models

Massively Parallel Processor algorithms were developed for the interactive manipulation of flat shaded digital terrain models defined over grids. The emphasis is on real time manipulation of stereo images. Standard graphics transformations are applied to a 128 x 128 grid of elevations followed by shading and a perspective projection to produce the right eye image. The surface is then rendered using a simple painter's algorithm for hidden surface removal. The left eye image is produced by rotating the surface 6 degs about the viewer's y axis followed by a perspective projection and rendering of the image as described above. The left and right eye images are then presented on a graphics device using standard stereo technology. Performance evaluations and comparisons are presented

Optimal Exploitation of the Sentinel-2 Spectral Capabilities for Crop Leaf Area Index Mapping

The continuously increasing demand of accurate quantitative high quality information on land surface properties will be faced by a new generation of environmental Earth observation (EO) missions. One current example, associated with a high potential to contribute to those demands, is the multi-spectral ESA Sentinel-2 (S2) system. The present study focuses on the evaluation of spectral information content needed for crop leaf area index (LAI) mapping in view of the future sensors. Data from a field campaign were used to determine the optimal spectral sampling from available S2 bands applying inversion of a radiative transfer model (PROSAIL) with look-up table (LUT) and artificial neural network (ANN) approaches. Overall LAI estimation performance of the proposed LUT approach (LUTN₅₀) was comparable in terms of retrieval performances with a tested and approved ANN method. Employing seven- and eight-band combinations, the LUTN₅₀ approach obtained LAI RMSE of 0.53 and normalized LAI RMSE of 0.12, which was comparable to the results of the ANN. However, the LUTN50 method showed a higher robustness and insensitivity to different band settings. Most frequently selected wavebands were located in near infrared and red edge spectral regions. In conclusion, our results emphasize the potential benefits of the Sentinel-2 mission for agricultural applications

Within-socket Myoelectric Prediction of Continuous Ankle Kinematics for Control of a Powered Transtibial Prosthesis

Objective. Powered robotic prostheses create a need for natural-feeling user interfaces and robust control schemes. Here, we examined the ability of a nonlinear autoregressive model to continuously map the kinematics of a transtibial prosthesis and electromyographic (EMG) activity recorded within socket to the future estimates of the prosthetic ankle angle in three transtibial amputees. Approach. Model performance was examined across subjects during level treadmill ambulation as a function of the size of the EMG sampling window and the temporal \u27prediction\u27 interval between the EMG/kinematic input and the model\u27s estimate of future ankle angle to characterize the trade-off between model error, sampling window and prediction interval. Main results. Across subjects, deviations in the estimated ankle angle from the actual movement were robust to variations in the EMG sampling window and increased systematically with prediction interval. For prediction intervals up to 150 ms, the average error in the model estimate of ankle angle across the gait cycle was less than 6°. EMG contributions to the model prediction varied across subjects but were consistently localized to the transitions to/from single to double limb support and captured variations from the typical ankle kinematics during level walking. Significance. The use of an autoregressive modeling approach to continuously predict joint kinematics using natural residual muscle activity provides opportunities for direct (transparent) control of a prosthetic joint by the user. The model\u27s predictive capability could prove particularly useful for overcoming delays in signal processing and actuation of the prosthesis, providing a more biomimetic ankle response

Learning to automatically detect features for mobile robots using second-order Hidden Markov Models

In this paper, we propose a new method based on Hidden Markov Models to interpret temporal sequences of sensor data from mobile robots to automatically detect features. Hidden Markov Models have been used for a long time in pattern recognition, especially in speech recognition. Their main advantages over other methods (such as neural networks) are their ability to model noisy temporal signals of variable length. We show in this paper that this approach is well suited for interpretation of temporal sequences of mobile-robot sensor data. We present two distinct experiments and results: the first one in an indoor environment where a mobile robot learns to detect features like open doors or T-intersections, the second one in an outdoor environment where a different mobile robot has to identify situations like climbing a hill or crossing a rock.Comment: 200

Massive MIMO is a Reality -- What is Next? Five Promising Research Directions for Antenna Arrays

Massive MIMO (multiple-input multiple-output) is no longer a "wild" or "promising" concept for future cellular networks - in 2018 it became a reality. Base stations (BSs) with 64 fully digital transceiver chains were commercially deployed in several countries, the key ingredients of Massive MIMO have made it into the 5G standard, the signal processing methods required to achieve unprecedented spectral efficiency have been developed, and the limitation due to pilot contamination has been resolved. Even the development of fully digital Massive MIMO arrays for mmWave frequencies - once viewed prohibitively complicated and costly - is well underway. In a few years, Massive MIMO with fully digital transceivers will be a mainstream feature at both sub-6 GHz and mmWave frequencies. In this paper, we explain how the first chapter of the Massive MIMO research saga has come to an end, while the story has just begun. The coming wide-scale deployment of BSs with massive antenna arrays opens the door to a brand new world where spatial processing capabilities are omnipresent. In addition to mobile broadband services, the antennas can be used for other communication applications, such as low-power machine-type or ultra-reliable communications, as well as non-communication applications such as radar, sensing and positioning. We outline five new Massive MIMO related research directions: Extremely large aperture arrays, Holographic Massive MIMO, Six-dimensional positioning, Large-scale MIMO radar, and Intelligent Massive MIMO.Comment: 20 pages, 9 figures, submitted to Digital Signal Processin