Fast Mapping Approach Research Articles

An approximate fast-mapping approach to the surface NMR forward problem

SUMMARY A surface nuclear magnetic resonance (NMR) forward model based on the full-Bloch equation improves the accuracy of the forward response given an arbitrary excitation pulse and a wider range of relaxation conditions. However, the full-Bloch solution imposes a significant slowdown in inversion times compared to the traditional forward model. We present a fast-mapping approach capable of dramatic increases in inversion speeds with minimal sacrifices in forward response accuracy. We show that the look-up tables used to calculate the transverse magnetization and the full surface NMR forward response are smoothly varying functions of the underlying T2* and T2 values. We exploit this smoothness to form a polynomial representation of the look-up tables and surface NMR forward responses, where a fast-mapping approximation of each are reduced to a simple matrix multiplication. Accurate approximations with less than 1 per cent error can be produced using 21 coefficient representations of the look-up tables for each B1 value and for the signal expected from a particular depth layer for a particular pulse moment. In essence, the proposed fast-mapping approach front-loads all expensive calculations and stores the results in a compressed form as a coefficient matrix containing less than a half a million elements. This allows all subsequent inversions to be performed at greatly improved speeds.

Detection and localization of weak impulses and continuous sources within the urban acoustic environment

Signal detection and localization with large aperture acoustic arrays in urban environments can be inherently difficult. This poster presents some preliminary approaches under investigation for; determining the direction of arrival of continuous sources that are changing in frequency, detecting and localizing low signal to noise ratio impulses in the presence of coherent background noise, and a fast mapping approach for converting array element delays to direction of arrival using a neural network fitting function. For uniform circular array geometries with a central reference array element, the direction of arrival of sources with changing frequency can be visualized by applying the Hilbert transform and analyzing the relative phase angle rate of change of the outer array elements. Next, various computational approaches for low level impulse detection in the presence of coherent acoustical noise are presented. Last, a neural network fitting function is discussed that performs array specific delay mapping to direction of arrival with high computational efficiency and trained noise immunity.

SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation

Mapping reads to a reference genome is a routine yet computationally intensive task in research based on high-throughput sequencing. In recent years, the sequencing reads of the Illumina platform have become longer and their quality scores higher. According to our calculation, this allows perfect k-mer seed match for almost all reads when a close reference genome is available subject to reasonable specificity. Our other observation is that the majority reads contain at most one short INDEL polymorphism. Based on these observations, we propose a fast-mapping approach, referred to as "SEME," which has two core steps: First it scans a read sequentially in a specific order for a k-mer exact match seed; next it extends the alignment on both sides allowing, at most, one short INDEL each using a novel method called "auto-match function." We decompose the evaluation of the sensitivity and specificity into two parts corresponding to the seed and extension step, and the composite result provides an approximate overall reliability estimate of each mapping. We compare SEME with some existing mapping methods on several datasets, and SEME shows better performance in terms of both running time and mapping rates.

Microphytobenthos biomass mapping using the optical model of diatom biofilms: Application to hyperspectral images of Bourgneuf Bay

A new fast mapping approach based on an optical model was developed and applied to hyperspectral airborne HySpex images of Bourgneuf Bay (French Atlantic coast). The aims were (1) to discriminate diatom biofilms (from the Bacillariophyceae class) constituting microphytobenthos on any mudflat and (2) to estimate their biomass expressed in mgChla·m−2 by remote sensing of poorly accessible mudflats.Due to the distinct absorption peaks of certain pigments of different microalgae classes constituting microphytobenthos, the high spectral resolution of hyperspectral images was employed in order to detect the pigment assemblage characterizing diatom biofilms. Thus, the HySpex 1600 VNIR camera was used both in the laboratory for estimating biomass under controlled conditions and in an airborne setting. 1) The mapping approach used known spectral indices (NDVI and MPBI) and new ones (IDiatom and IEuglenid) to characterize quickly the key pigments of two main microphytobenthos classes, for a fast selection of diatom and euglenid biofilms by two different masks. 2) The inherent spectral properties of biofilms in the 700–900nm range were also used to calculate an original estimate of the substrate/environmental effects in each mask. 3) Biomass quantification of the diatom biofilms was finally performed by application of the microphytobenthos optical model (MPBOM).This approach was first tested on laboratory HySpex images of synthetic biofilms for which the in vitro biomass measurements by chromatography (HPLC) were available. The comparison between estimated and measured biomass values showed the reliability of the mapping approach for biomass estimation. Finally, a map of diatom biomass was obtained at the scale of the entire Bourgneuf Bay. The range of biomass variation (0–35mgChla·m−2) was in close agreement with the biomass maps presented in previous studies.