Neuromorphic computing is rising as a promising paradigm for efficient AI, leveraging event-driven computation to achieve low-power and high-performance computing. Due to the real-time processing required by edge devices with minimal power consumption, optimizing neuromorphic models for on-edge applications can be crucial to address the issue of power efficiency and resource-constraint devices. This work explores the definition of a neuromorphic state space model and its deployment on non-dedicated hardware. Structured sparsity and quantization techniques are leveraged to enhance the model’s efficiency. By compressing synaptic operations and memory footprint, we demonstrate how neuromorphic models can be adapted for on-edge deployment, ensuring low-latency and memory efficient inference. This study highlights the potential of neuromorphic models as a scalable solution for real-world embedded systems with limited resources.

Neuromorphic computing promises significant improvements in latency and energy efficiency for machine intelligence at the edge. However, its adoption in the IoT domain is still limited by the heterogeneity of the HW, the immaturity of the toolchains, and the poor reproducibility of experiments. The present paper sets out the inNuCE RI, a two-pillar facility composed of a physical inNuCE Lab and a cloud-based inNuCE HPP. The purpose of the inNuCE RI is to enable developers to prototype, evaluate and compare neuromorphic and conventional end-to-end digital solutions. From a methodological perspective, we formalize the adaptation of MLOps to event-driven sensing and brain-inspired computation as NMLOps. We illustrate how inNuCE RI instantiates NMLOps through containerized toolchains orchestrated with Kubernetes and Slurm-managed heterogeneous resources (neuromorphic chips, FPGAs, GPUs, MCUs). The approach is analyzed on representative AIoT use cases, including HAR, Braille reading, event-based gesture recognition, Hi-Co semantization of memories, navigation tracking, and constraint satisfaction problems. The development of inNuCE RI has been driven by the need to facilitate the transition from prototype (in nuce) to engineered AIoT systems for lower entry barriers and enforce reproducibility. This paves the way for future system-of-systems engineering.

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.

BACKGROUND: Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using Copy Number Aberrations (CNAs). Nowadays ITH can be assessed at the highest possible resolution using single-cell DNA (scDNA) sequencing technology. Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass. However, since the technology required to generate large scDNA sequencing datasets is relatively recent, dedicated analytical approaches are still lacking. RESULTS: We present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated. Starting from the CNA data produced with third party instruments, it computes a score, the Spatial Heterogeneity score, aimed at distinguishing spatially intermixed cell populations from spatially segregated ones. Additionally, it provides functionalities to facilitate scDNA analysis, such as feature selection and dimensionality reduction methods, visualization tools and a flexible clustering module. CONCLUSIONS: PhyliCS represents a valuable instrument to explore the extent of spatial heterogeneity in multi-regional tumour sampling, exploiting the potential of scCNA data.

One of the key targets of Industry 4.0 and digital production, in general, is the support of faster, cleaner, and increasingly customizable manufacturing processes. Additive manufacturing (AM) is a natural fit in this context, as it offers the possibility to produce complex parts without the design constraints of traditional manufacturing routes, typically reducing both material waste and time to market. Nonetheless, the lack of repeatability of the manufacturing process, which typically translates into a lack of reproducibility and reliability of the quality of the final products compared to traditional subtractive technologies, is currently one of the major barriers to the widespread adoption of AM in mass production. To overcome this limitation, there are growing efforts in recent years toward better integration of advanced information technologies into AM, exploiting the layer-by-layer nature of the build. The consequence of these efforts is twofold: 1) the integration of advanced sensing technologies into the AM systems, making possible the in situ monitoring of huge amounts of data at multiple time scales and resolutions and 2) the ever-increasing role of data-driven approaches [especially machine learning (ML)] in the analysis of such data to provide real-time quality monitoring and process optimization. This article introduces and reviews the key technological developments of this phenomenon, with a special focus on metal powder bed fusion (PBF) technologies that are attracting the highest attention by the industrial AM community. After introducing the main manufacturing quality issues and needs that have to be developed and optimized, we provide a wide overview of the latest progress of in situ monitoring and control in metal PBF, with special regards to sensing technologies and ML approaches. Finally, we identify the open challenges and future research directions in this field.

The Internet of Things (IoT), and more specifically the industrial IoT, is revolutionising industry. This technology has catalyzed the fourth industrial revolution and inspired movements such as Industry 4.0, the Industrial Internet Consortium and Society 5.0. Morphing an industrial process or assembly line to aggregate Internet-connected devices and systems does not complete the picture. The concept penetrates all aspects of the engineering process (EP) which encompasses the full life-cycle of the product/solution. Phases of the EP traditionally tended to be sequential but, with the IoT, can now evolve and influence other phases throughout the product/solution life-cycle. The EU-funded Arrowhead Tools project aims to promote a service-oriented architecture (SOA) to allow tools within each phase of the engineering process to interact with each other. This paper, applies the proposed EP model to a real value chain composed of multiple stakeholders adopting different EPs for the life-cycle management of a Smart Boiler System.

MOTIVATION: MicroRNAs (miRNAs) are small RNA molecules (∼22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. RESULTS: To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification. AVAILABILITY AND IMPLEMENTATION: https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user. AVAILABILITY AND IMPLEMENTATION: Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially for machines with limited hardware capabilities. As the redundancy of the sequences typically increases with coverage, collapsing such files into compact sets of non-redundant reads has the 2-fold advantage of reducing file size and speeding-up the alignment, avoiding to map the same sequence multiple times. METHOD: BioSeqZip generates compact and sorted lists of alignment-ready non-redundant sequences, keeping track of their occurrences in the raw files as well as of their quality score information. By exploiting a memory-constrained external sorting algorithm, it can be executed on either single- or multi-sample datasets even on computers with medium computational capabilities. On request, it can even re-expand the compacted files to their original state. RESULTS: Our extensive experiments on RNA-Seq data show that BioSeqZip considerably brings down the computational costs of a standard sequence analysis pipeline, with particular benefits for the alignment procedures that typically have the highest requirements in terms of memory and execution time. In our tests, BioSeqZip was able to compact 2.7 billion of reads into 963 million of unique tags reducing the size of sequence files up to 70% and speeding-up the alignment by 50% at least. AVAILABILITY AND IMPLEMENTATION: BioSeqZip is available at https://github.com/bioinformatics-polito/BioSeqZip. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Modern heterogeneous platforms require compilers capable of choosing the appropriate device for the execution of program portions. This paper presents a machine learning method designed for supporting mapping decisions through the analysis of the program source code represented in LLVM assembly language (IR) for exploiting the advantages offered by this generalised and optimised representation. To evaluate our solution, we trained an LSTM neural network on OpenCL kernels compiled in LLVM-IR and processed with our tokenizer capable of filtering less-informative tokens. We tested the network that reaches an accuracy of 85% in distinguishing the best computational unit.

In this paper, we present a methodology for effi-ciently mapping neural networks over a neuromorphic computing architecture. The target architecture is a globally asynchronous locally synchronous (GALS) multi-core designed for simulating spiking neural networks (SNN) in real-time, that is spike timings should be the same as in the human brain. The SNN is implemented as a set of concurrent tasks modelling the behaviour of biological neurons, which are executed on the processing cores and communicate through spikes travelling on a network-on-chip. The problem of neuron-to-core mapping is relevant as a non-efficient allocation may impact real-time and reliability of the neural network execution. We designed a task placement pipeline capable of analysing the network of neurons and producing a placement configuration that enables a reduction of communication between computational nodes. The neuron-to-core mapping problem has been formalised as a problem of minimisation of synaptic elongation. Intuitively, this metric represents the cumulative distance that spikes generated by neurons running on a specific core have to travel to reach their destination core. The proposed placement methodology allows using different techniques to solve the problem. In this work Spectral Analysis, Multilevel Static Mapping, and Simulated Annealing were compared evaluating the overall post-placement synaptic elongation. Results point out that mapping solutions taking into account the directionality of the SNN provide a better placement and quantify this impact. Between all techniques considered only the Simulated Annealing was able to overcome an improvement of 25% compared to a random placement.

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.

The impact of process variations and wear-out mechanisms in current and next generation technology nodes is becoming relevant and cannot be compensated at the device or architectural level. Intra-die process variations raising at the core level and platform level makes parallel multicore platforms intrinsically heterogeneous, because the various cores are clocked at different operational frequencies. Power consumption becomes heterogeneous too, both considering dynamic and leakage consumption. Wear-out processes add further uncertainty over time. In this context, to fully exploit the computational capability of the platform parallelism, variability and wear-out aware task allocation strategies must be developed. In this work, we discuss techniques to perform task allocation and we show how they can be integrated in a software toolchain. We report results of the implementation of variability and wear-out awareness in state-of-art multicore platforms.

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.

Protein comparison is gaining importance year after year since it has been demonstrated that biologists can find correlation 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. To speed-up alignment, dedicated processors that can perform different computations in parallel have been designed. Among them, the best performance has been achieved using systolic arrays (SAs). However, when the processing elements of the SA have an internal loop, performance could be highly reduced. In this paper, we present an architectural strategy to address this problem applying pipeline interleaving; this strategy is applied to an SA 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.