Peptide mass fingerprinting using field-programmable gate arrays

The reconfigurable computing paradigm, which exploits the flexibility and versatility of field-programmable gate arrays (FPGAs), has emerged as a powerful solution for speeding up time-critical algorithms. This paper describes a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-TOF instruments. The hardware-implemented algorithms for denoising, baseline correction, peak identification, and deisotoping, running on a Xilinx Virtex-2 FPGA at 180 MHz, generate a mass fingerprint that is over 100 times faster than an equivalent algorithm written in C, running on a Dual 3-GHz Xeon server. The results obtained using the FPGA implementation are virtually identical to those generated by a commercial software package MassLynx

Complexity-reduced hardware-based track-trigger for CMS upgrade

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonThe Compact Muon Solenoid (CMS) detector at the Large Hadron Collider (LHC) is designed to study the results of proton-proton collisions. The Tracker sub-detector is designed to detect and reconstruct the trajectories of charged particles produced by the collisions. During the lifetime of the CMS detector, there have been several upgrades aimed at increasing the chance of discovering new physics through increased luminosity levels and instrumentation of advanced technology. The High-Luminosity upgrade optimises the LHC to accelerate high-energy particles with an average of 200 proton-proton interactions per bunch crossing. The Level-1 Trigger system promptly analyses and filters collisions using hardware to reduce the data volume in real-time. For the upgrade, the trigger mechanism will use a particle trajectory estimator that discriminates between particles based on their transverse momentum (pT ). Particles with pT ≥ 2 GeV/c will be transmitted to the Level-1 Track-Trigger system for trajectory reconstruction within a fixed 3 μs latency. This thesis presents a novel Hardware-based Multivariate Linear Fitter (MVLF) system focusing on robustness in tracking efficiency and reduction in logic resource usage within the specified latency. The system components are implemented in Field Programmable Gate Arrays (FPGA), targeting 16 nm FinFET UltraScale+ silicon technology. The development was performed using the High-Level Synthesis (HLS) automation tools and the Hardware acceleration platform for Application-Specific Integrated Circuits (ASIC). A firmware demonstrator has been assembled to verify the feasibility and compatibility of the scaled system with the CMS Level-1 Track-Trigger infrastructure. The system’s performance is compared to past and current system developments, and the results are presented accordingly

A Novel Systolic Parallel Hardware Architecture for the FPGA Acceleration of Feedforward Neural Networks

New chips for machine learning applications appear, they are tuned for a specific topology, being efficient by using highly parallel designs at the cost of high power or large complex devices. However, the computational demands of deep neural networks require flexible and efficient hardware architectures able to fit different applications, neural network types, number of inputs, outputs, layers, and units in each layer, making the migration from software to hardware easy. This paper describes novel hardware implementing any feedforward neural network (FFNN): multilayer perceptron, autoencoder, and logistic regression. The architecture admits an arbitrary input and output number, units in layers, and a number of layers. The hardware combines matrix algebra concepts with serial-parallel computation. It is based on a systolic ring of neural processing elements (NPE), only requiring as many NPEs as neuron units in the largest layer, no matter the number of layers. The use of resources grows linearly with the number of NPEs. This versatile architecture serves as an accelerator in real-time applications and its size does not affect the system clock frequency. Unlike most approaches, a single activation function block (AFB) for the whole FFNN is required. Performance, resource usage, and accuracy for several network topologies and activation functions are evaluated. The architecture reaches 550 MHz clock speed in a Virtex7 FPGA. The proposed implementation uses 18-bit fixed point achieving similar classification performance to a floating point approach. A reduced weight bit size does not affect the accuracy, allowing more weights in the same memory. Different FFNN for Iris and MNIST datasets were evaluated and, for a real-time application of abnormal cardiac detection, a x256 acceleration was achieved. The proposed architecture can perform up to 1980 Giga operations per second (GOPS), implementing the multilayer FFNN of up to 3600 neurons per layer in a single chip. The architecture can be extended to bigger capacity devices or multi-chip by the simple NPE ring extension

A Binaural Neuromorphic Auditory Sensor for FPGA: A Spike Signal Processing Approach

This paper presents a new architecture, design flow, and field-programmable gate array (FPGA) implementation analysis of a neuromorphic binaural auditory sensor, designed completely in the spike domain. Unlike digital cochleae that decompose audio signals using classical digital signal processing techniques, the model presented in this paper processes information directly encoded as spikes using pulse frequency modulation and provides a set of frequency-decomposed audio information using an address-event representation interface. In this case, a systematic approach to design led to a generic process for building, tuning, and implementing audio frequency decomposers with different features, facilitating synthesis with custom features. This allows researchers to implement their own parameterized neuromorphic auditory systems in a low-cost FPGA in order to study the audio processing and learning activity that takes place in the brain. In this paper, we present a 64-channel binaural neuromorphic auditory system implemented in a Virtex-5 FPGA using a commercial development board. The system was excited with a diverse set of audio signals in order to analyze its response and characterize its features. The neuromorphic auditory system response times and frequencies are reported. The experimental results of the proposed system implementation with 64-channel stereo are: a frequency range between 9.6 Hz and 14.6 kHz (adjustable), a maximum output event rate of 2.19 Mevents/s, a power consumption of 29.7 mW, the slices requirements of 11 141, and a system clock frequency of 27 MHz.Ministerio de Economía y Competitividad TEC2012-37868-C04-02Junta de Andalucía P12-TIC-130