LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences

Background The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases

Review of open neuromorphic architectures and a first integration in the RISC-V PULP platform

Although initially conceived as a tool to empower neuroscientific research by emulating and simulating the human brain, Spiking Neural Networks (SNNs), also known as third generation neural networks, are gaining popularity for their low-power and sparse data processing capabilities. These attributes are valuable for power-constrained edge and Internet of Things (IoT) applications. Several open-source FPGA and ASIC neuromorphic processors have been developed to explore thisfield, although they often require additional computing elements to manage data and communications. In this work, we review recent open-source neuromorphic architectures and the PULP ecosystem. We then present an integration of the ReckOn digitalneuromorphic processor with the PULPissimo RISC-V single core microcontroller to enable edge IoT applications. Our integrated design is validated through QuestaSim hardware simulation. Through this integration of low-power neuromorphic and RISC-V processors, we focus on the promising potential of SNNs for optimizing edge IoT systems constrained by power budgets and data sparsity

Protein alignment HW/SW optimizations

Biosequence alignment recently received an amazing support from both commodity and dedicated hardware platforms. The limitless requirements of this application motivate the search for improved implementations to boost processing time and capabilities. We propose an unprecedented hardware improvement to the classic Smith-Waterman (S-W) algorithm based on a twofold approach: i) an on-the-fly gap-open/gap-extension selection that reduces the hardware implementation complexity; ii) a pre-selection filter that uses reduced amino-acid alphabets to screen out not-significant sequences and to shorten the S-Witerations on huge reference databases.We demonstrated the improvements w.r.t. a classic approach both from the point of view of algorithm efficiency and of HW performance (FPGA and ASIC post-synthesis analysis)

LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences

Background The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases

isomiR-SEA: An RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation

>Background: Massive parallel sequencing of transcriptomes, revealed the presence of many miRNAs and miRNAs variants named isomiRs with a potential role in several cellular processes through their interaction with a target mRNA. Many methods and tools have been recently devised to detect and quantify miRNAs from sequencing data. However, all of them are implemented on top of general purpose alignment methods, thus providing poorly accurate results and no information concerning isomiRs and conserved miRNA-mRNA interaction sites. >Results: To overcome these limitations we present a novel algorithm named isomiR-SEA, that is able to provide users with very accurate miRNAs expression levels and both isomiRs and miRNA-mRNA interaction sites precise classifications. Tags are mapped on the known miRNAs sequences thanks to a specialized alignment algorithm developed on top of biological evidence concerning miRNAs structure. Specifically, isomiR-SEA checks for miRNA seed presence in the input tags and evaluates, during all the alignment phases, the positions of the encountered mismatches, thus allowing to distinguish among the different isomiRs and conserved miRNA-mRNA interaction sites. >Conclusions: isomiR-SEA performances have been assessed on two public RNA-Seq datasets proving that the implemented algorithm is able to account for more reliable and accurate miRNAs expression levels with respect to those provided by two compared state of the art tools. Moreover, differently from the few methods currently available to perform isomiRs detection, the proposed algorithm implements the evaluation of isomiRs and conserved miRNA-mRNA interaction sites already in the first alignment phases, thus avoiding any additional filtering stages potentially responsible for the loss of useful information

Top-down profiling methodology and new Partition and Placement tool to improve Spiking Neural Network simulations on a massively many-core neuromorphic platform

none4nomixedURGESE, GIANVITO; BARCHI, FRANCESCO; MACII, Enrico; ACQUAVIVA, ANDREAURGESE, GIANVITO; BARCHI, FRANCESCO; MACII, Enrico; ACQUAVIVA, ANDRE

Protein Alignment Systolic Array Throughput Optimization

Protein comparison is gaining importance year after year since it has been demonstrated that biologists can find cor- relation between different species, or genetic mutations that can lead to cancer and genetic diseases. Protein sequence alignment is the most computational intensive task when performing protein comparison. In order to speed-up alignment, dedicated processors that can perform different computations in parallel have been designed. Among them, the best performance have been achieved using Systolic Arrays. However, when the Processing Elements of the Systolic Array have an internal loop, performance could be highly reduced. In this work we present an architectural strategy to address this problem applying pipeline interleaving; this strategy is applied to a Systolic Array for Smith Waterman algorithm that we designed. Results encourage the adoption of pipeline interleaving for parallel circuits with loop based Processing Elements. We demonstrate that important benefits in terms of higher operating frequency can be derived without so relevant costs as increased complexity, area and power required

A Parallel Hardware Architecture For Quantum Annealing Algorithm Acceleration

Quantum Annealing (QA) is an emerging technique, derived from Simulated Annealing, providing metaheuristics for multivariable optimisation problems. Studies have shown that it can be applied to solve NP-hard problems with faster convergence and better quality of result than other traditional heuristics, with potential applications in a variety of fields, from transport logistics to circuit synthesis and optimisation. In this paper, we present a hardware architecture implementing a QA-based solver for the Multidimensional Knapsack Problem, designed to improve the performance of the algorithm by exploiting parallelised computation. We synthesised the architecture using as a target an Altera FPGA board and simulated the execution for solving a set of benchmarks available in the literature. Simulation results show that the proposed implementation is about 100 times faster than a single-thread general-purpose CPU without impact on the accuracy of the solution

Techniques for improving localization applications running on low-cost IoT devices

Nowadays, localization features are widespread in low-cost and low-power IoT applications such as bike-sharing,off-road vehicle fleet management, and theft prevention of smart devices. For such use cases, since the item to be tracked is inexpensive, older or power-constrained (e.g. battery-powered vehicles), localization features are realized by the installation of low-cost and low-power devices. In this paper, we describe a set of low-computational power techniques, targeting low-cost IoT devices, to process GPS and INS data for accomplishing specific and accurate localization and tracking tasks. The methods here proposed address the calibration of low-cost INS comprised of accelerometer and gyroscope without the aid of external sensors, correction of GPS drift when the target position is static,and the minimization of localization error at device boot. The performances of the proposed methods are then evaluated on several datasets acquired on the field and representing real use-case scenarios

Spike encoding techniques for IoT time-varying signals benchmarked on a neuromorphic classification task

Spiking Neural Networks (SNNs), known for their potential to enable low energy consumption and computational cost, can bring significant advantages to the realm of embedded machine learning for edge applications. However, input coming from standard digital sensors must be encoded into spike trains before it can be elaborated with neuromorphic computing technologies. We present here a detailed comparison of available spike encoding techniques for the translation of time-varying signals into the event-based signal domain, tested on two different datasets both acquired through commercially available digital devices: the Free Spoken Digit dataset (FSD), consisting of 8-kHz audio files, and the WISDM dataset, composed of 20-Hz recordings of human activity through mobile and wearable inertial sensors. We propose a complete pipeline to benchmark these encoding techniques by performing time-dependent signal classification through a Spiking Convolutional Neural Network (sCNN), including a signal preprocessing step consisting of a bank of filters inspired by the human cochlea, feature extraction by production of a sonogram, transfer learning via an equivalent ANN, and model compression schemes aimed at resource optimization. The resulting performance comparison and analysis provides a powerful practical tool, empowering developers to select the most suitable coding method based on the type of data and the desired processing algorithms, and further expands the applicability of neuromorphic computational paradigms to embedded sensor systems widely employed in the IoT and industrial domains