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1. The K-mer File Format: a standardized and compact disk representation of sets of k -mers

   https://doi.org/10.1093/bioinformatics/btac528  

   Dufresne, Yoann; Lemane, Teo; Marijon, Pierre; Peterlongo, Pierre; Rahman, Amatur; Kokot, Marek; Medvedev, Paul; Deorowicz, Sebastian; Chikhi, Rayan; Birol, ed., Inanc (July 2022, Bioinformatics)

   Abstract SummaryBioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3–5× compared to other formats, and bringing interoperability across tools. Availability and implementationFormat specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. Supplementary informationSupplementary data are available at Bioinformatics online. 

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2. Practical selection of representative sets of RNA-seq samples using a hierarchical approach

   https://doi.org/10.1093/bioinformatics/btab315  

   Tung, Laura H; Kingsford, Carl (July 2021, Bioinformatics)

   Abstract Motivation Despite numerous RNA-seq samples available at large databases, most RNA-seq analysis tools are evaluated on a limited number of RNA-seq samples. This drives a need for methods to select a representative subset from all available RNA-seq samples to facilitate comprehensive, unbiased evaluation of bioinformatics tools. In sequence-based approaches for representative set selection (e.g. a k-mer counting approach that selects a subset based on k-mer similarities between RNA-seq samples), because of the large numbers of available RNA-seq samples and of k-mers/sequences in each sample, computing the full similarity matrix using k-mers/sequences for the entire set of RNA-seq samples in a large database (e.g. the SRA) has memory and runtime challenges; this makes direct representative set selection infeasible with limited computing resources. Results We developed a novel computational method called ‘hierarchical representative set selection’ to handle this challenge. Hierarchical representative set selection is a divide-and-conquer-like algorithm that breaks representative set selection into sub-selections and hierarchically selects representative samples through multiple levels. We demonstrate that hierarchical representative set selection can achieve summarization quality close to that of direct representative set selection, while largely reducing runtime and memory requirements of computing the full similarity matrix (up to 8.4× runtime reduction and 5.35× memory reduction for 10 000 and 12 000 samples respectively that could be practically run with direct subset selection). We show that hierarchical representative set selection substantially outperforms random sampling on the entire SRA set of RNA-seq samples, making it a practical solution to representative set selection on large databases like the SRA. Availability and implementation The code is available at https://github.com/Kingsford-Group/hierrepsetselection and https://github.com/Kingsford-Group/jellyfishsim. Supplementary information Supplementary data are available at Bioinformatics online. 

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3. Feature Compression for Rate Constrained Object Detection on the Edge

   Yuan, Zhongzheng; Samyak Rawlekar; Siddharth Garg; Elza Erkip; Yao Wang (August 2022, In MLSys 2023 Workshop on Resource-Constrained Learning in Wireless Networks)

   Recent advances in computer vision has led to a growth of interest in deploying visual analytics model on mobile devices. However, most mobile devices have limited computing power, which prohibits them from running large scale visual analytics neural networks. An emerging approach to solve this problem is to offload the computation of these neural networks to computing resources at an edge server. Efficient computation offloading requires optimizing the trade-off between multiple objectives including compressed data rate, analytics performance, and computation speed. In this work, we consider a “split computation” system to offload a part of the computation of the YOLO object detection model. We propose a learnable feature compression approach to compress the intermediate YOLO features with lightweight computation. We train the feature compression and decompression module together with the YOLO model to optimize the object detection accuracy under a rate constraint. Compared to baseline methods that apply either standard image compression or learned image compression at the mobile and perform image de-compression and YOLO at the edge, the proposed system achieves higher detection accuracy at the low to medium rate range. Furthermore, the proposed system requires substantially lower computation time on the mobile device with CPU only. 

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4. eCAMI: simultaneous classification and motif identification for enzyme annotation

   https://doi.org/10.1093/bioinformatics/btz908  

   Xu, Jing; Zhang, Han; Zheng, Jinfang; Dovoedo, Philippe; Yin, Yanbin; Xu, ed., Jinbo (December 2019, Bioinformatics)

   Abstract MotivationCarbohydrate-active enzymes (CAZymes) are extremely important to bioenergy, human gut microbiome, and plant pathogen researches and industries. Here we developed a new amino acid k-mer-based CAZyme classification, motif identification and genome annotation tool using a bipartite network algorithm. Using this tool, we classified 390 CAZyme families into thousands of subfamilies each with distinguishing k-mer peptides. These k-mers represented the characteristic motifs (in the form of a collection of conserved short peptides) of each subfamily, and thus were further used to annotate new genomes for CAZymes. This idea was also generalized to extract characteristic k-mer peptides for all the Swiss-Prot enzymes classified by the EC (enzyme commission) numbers and applied to enzyme EC prediction. ResultsThis new tool was implemented as a Python package named eCAMI. Benchmark analysis of eCAMI against the state-of-the-art tools on CAZyme and enzyme EC datasets found that: (i) eCAMI has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction. Lastly, we confirmed that the k-mer-based tools have the unique ability to identify the characteristic k-mer peptides in the predicted enzymes. Availability and implementationhttps://github.com/yinlabniu/eCAMI and https://github.com/zhanglabNKU/eCAMI. Supplementary informationSupplementary data are available at Bioinformatics online. 

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5. E2M: an energy-efficient middleware for computer vision applications on autonomous mobile robots

   https://doi.org/10.1145/3318216.3363302  

   Liu, Liangkai; Chen, Jiamin; Brocanelli, Marco; Shi, Weisong (November 2019, SEC '19: Proceedings of the 4th ACM/IEEE Symposium on Edge Computing)

   Autonomous mobile robots (AMRs) have been widely utilized in industry to execute various on-board computer-vision applications including autonomous guidance, security patrol, object detection, and face recognition. Most of the applications executed by an AMR involve the analysis of camera images through trained machine learning models. Many research studies on machine learning focus either on performance without considering energy efficiency or on techniques such as pruning and compression to make the model more energy-efficient. However, most previous work do not study the root causes of energy inefficiency for the execution of those applications on AMRs. The computing stack on an AMR accounts for 33% of the total energy consumption and can thus highly impact the battery life of the robot. Because recharging an AMR may disrupt the application execution, it is important to efficiently utilize the available energy for maximized battery life. In this paper, we first analyze the breakdown of power dissipation for the execution of computer-vision applications on AMRs and discover three main root causes of energy inefficiency: uncoordinated access to sensor data, performance-oriented model inference execution, and uncoordinated execution of concurrent jobs. In order to fix these three inefficiencies, we propose E2M, an energy-efficient middleware software stack for autonomous mobile robots. First, E2M regulates the access of different processes to sensor data, e.g., camera frames, so that the amount of data actually captured by concurrently executing jobs can be minimized. Second, based on a predefined per-process performance metric (e.g., safety, accuracy) and desired target, E2M manipulates the process execution period to find the best energy-performance trade off. Third, E2M coordinates the execution of the concurrent processes to maximize the total contiguous sleep time of the computing hardware for maximized energy savings. We have implemented a prototype of E2M on a real-world AMR. Our experimental results show that, compared to several baselines, E2M leads to 24% energy savings for the computing platform, which translates into an extra 11.5% of battery time and 14 extra minutes of robot runtime, with a performance degradation lower than 7.9% for safety and 1.84% for accuracy. 

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