Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm

The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class–II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming and cost intensive. Therefore, computational methods have been found helpful in classifying these peptides as binders or non-binders. We have applied negative selection algorithm, an artificial immune system approach to predict MHC class–II binders and non-binders. For the evaluation of the NSA algorithm, five fold cross validation has been used and six MHC class–II alleles have been taken. The average area under ROC curve for HLA-DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1501, DRB1*1301 have been found to be 0.75, 0.77, 0.71, 0.72, and 0.69, and 0.84 respectively indicating good predictive performance for the small training set

HBST: A Hamming Distance embedding Binary Search Tree for Visual Place Recognition

Reliable and efficient Visual Place Recognition is a major building block of modern SLAM systems. Leveraging on our prior work, in this paper we present a Hamming Distance embedding Binary Search Tree (HBST) approach for binary Descriptor Matching and Image Retrieval. HBST allows for descriptor Search and Insertion in logarithmic time by exploiting particular properties of binary Feature descriptors. We support the idea behind our search structure with a thorough analysis on the exploited descriptor properties and their effects on completeness and complexity of search and insertion. To validate our claims we conducted comparative experiments for HBST and several state-of-the-art methods on a broad range of publicly available datasets. HBST is available as a compact open-source C++ header-only library.Comment: Submitted to IEEE Robotics and Automation Letters (RA-L) 2018 with International Conference on Intelligent Robots and Systems (IROS) 2018 option, 8 pages, 10 figure

Adiabatic Quantum Optimization for Associative Memory Recall

Hopfield networks are a variant of associative memory that recall information stored in the couplings of an Ising model. Stored memories are fixed points for the network dynamics that correspond to energetic minima of the spin state. We formulate the recall of memories stored in a Hopfield network using energy minimization by adiabatic quantum optimization (AQO). Numerical simulations of the quantum dynamics allow us to quantify the AQO recall accuracy with respect to the number of stored memories and the noise in the input key. We also investigate AQO performance with respect to how memories are stored in the Ising model using different learning rules. Our results indicate that AQO performance varies strongly with learning rule due to the changes in the energy landscape. Consequently, learning rules offer indirect methods for investigating change to the computational complexity of the recall task and the computational efficiency of AQO.Comment: 22 pages, 11 figures. Updated for clarity and figures, to appear in Frontiers of Physic

Pigment Melanin: Pattern for Iris Recognition

Recognition of iris based on Visible Light (VL) imaging is a difficult problem because of the light reflection from the cornea. Nonetheless, pigment melanin provides a rich feature source in VL, unavailable in Near-Infrared (NIR) imaging. This is due to biological spectroscopy of eumelanin, a chemical not stimulated in NIR. In this case, a plausible solution to observe such patterns may be provided by an adaptive procedure using a variational technique on the image histogram. To describe the patterns, a shape analysis method is used to derive feature-code for each subject. An important question is how much the melanin patterns, extracted from VL, are independent of iris texture in NIR. With this question in mind, the present investigation proposes fusion of features extracted from NIR and VL to boost the recognition performance. We have collected our own database (UTIRIS) consisting of both NIR and VL images of 158 eyes of 79 individuals. This investigation demonstrates that the proposed algorithm is highly sensitive to the patterns of cromophores and improves the iris recognition rate.Comment: To be Published on Special Issue on Biometrics, IEEE Transaction on Instruments and Measurements, Volume 59, Issue number 4, April 201

A Cerebellar-model Associative Memory as a Generalized Random-access Memory

A versatile neural-net model is explained in terms familiar to computer scientists and engineers. It is called the sparse distributed memory, and it is a random-access memory for very long words (for patterns with thousands of bits). Its potential utility is the result of several factors: (1) a large pattern representing an object or a scene or a moment can encode a large amount of information about what it represents; (2) this information can serve as an address to the memory, and it can also serve as data; (3) the memory is noise tolerant--the information need not be exact; (4) the memory can be made arbitrarily large and hence an arbitrary amount of information can be stored in it; and (5) the architecture is inherently parallel, allowing large memories to be fast. Such memories can become important components of future computers