matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the COVID-19 pandemic. One transformative approach, online phylogenetics, aims to incrementally add samples to an ever-growing phylogeny, but there are no previously-existing approaches that can efficiently optimize this vast phylogeny under the time constraints of the pandemic. Here, we present matOptimize, a fast and memory-efficient phylogenetic tree optimization tool based on parsimony that can be parallelized across multiple CPU threads and nodes, and provides orders of magnitude improvement in runtime and peak memory usage compared to existing state-of-the-art methods. We have developed this method particularly to address the pressing need during the COVID-19 pandemic for daily maintenance and optimization of a comprehensive SARS-CoV-2 phylogeny. Thus, our approach addresses an important need for daily maintenance and refinement of a comprehensive SARS-CoV-2 phylogeny.

Semantic segmentation of large-scale point clouds based on dilated nearest neighbors graph

Three-dimensional (3D) semantic segmentation of point clouds is important in many scenarios, such as automatic driving, robotic navigation, while edge computing is indispensable in the devices. Deep learning methods based on point sampling prove to be computation and memory efficient to tackle large-scale point clouds (e.g. millions of points). However, some local features may be abandoned while sampling. In this paper, We present one end-to-end 3D semantic segmentation framework based on dilated nearest neighbor encoding. Instead of down-sampling point cloud directly, we propose a dilated nearest neighbor encoding module to broaden the network’s receptive field to learn more 3D geometric information. Without increase of network parameters, our method is computation and memory efficient for large-scale point clouds. We have evaluated the dilated nearest neighbor encoding in two different networks. The first is the random sampling with local feature aggregation. The second is the Point Transformer. We have evaluated the quality of the semantic segmentation on the benchmark 3D dataset S3DIS, and demonstrate that the proposed dilated nearest neighbor encoding exhibited stable advantages over baseline and competing methods.

Improved N-Best Extraction with an Evaluation on Language Data

We show that a previously proposed algorithm for the N-best trees problem can be made more efficient by changing how it arranges and explores the search space. Given an integer N and a weighted tree automaton (wta) M over the tropical semiring, the algorithm computes N trees of minimal weight with respect to M. Compared to the original algorithm, the modifications increase the laziness of the evaluation strategy, which makes the new algorithm asymptotically more efficient than its predecessor. The algorithm is implemented in the software Betty, and compared to the state-of-the-art algorithm for extracting the N best runs, implemented in the software toolkit Tiburon. The data sets used in the experiments are wtas resulting from real-world natural language processing tasks, as well as artificially created wtas with varying degrees of nondeterminism. We find that Betty outperforms Tiburon on all tested data sets with respect to running time, while Tiburon seems to be the more memory-efficient choice.

Efficient ancestry and mutation simulation with msprime 1.0

Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

Memory-Efficient AI Algorithm for Infant Sleeping Death Syndrome Detection in Smart Buildings

Artificial intelligence (AI) is fundamentally transforming smart buildings by increasing energy efficiency and operational productivity, improving life experience, and providing better healthcare services. Sudden Infant Death Syndrome (SIDS) is an unexpected and unexplained death of infants under one year old. Previous research reports that sleeping on the back can significantly reduce the risk of SIDS. Existing sensor-based wearable or touchable monitors have serious drawbacks such as inconvenience and false alarm, so they are not attractive in monitoring infant sleeping postures. Several recent studies use a camera, portable electronics, and AI algorithm to monitor the sleep postures of infants. However, there are two major bottlenecks that prevent AI from detecting potential baby sleeping hazards in smart buildings. In order to overcome these bottlenecks, in this work, we create a complete dataset containing 10,240 day and night vision samples, and use post-training weight quantization to solve the huge memory demand problem. Experimental results verify the effectiveness and benefits of our proposed idea. Compared with the state-of-the-art AI algorithms in the literature, the proposed method reduces memory footprint by at least 89%, while achieving a similar high detection accuracy of about 90%. Our proposed AI algorithm only requires 6.4 MB of memory space, while other existing AI algorithms for sleep posture detection require 58.2 MB to 275 MB of memory space. This comparison shows that the memory is reduced by at least 9 times without sacrificing the detection accuracy. Therefore, our proposed memory-efficient AI algorithm has great potential to be deployed and to run on edge devices, such as micro-controllers and Raspberry Pi, which have low memory footprint, limited power budget, and constrained computing resources.

Dataset-adaptive minimizer order reduces memory usage in k-mer counting

The rapid, continuous growth of deep sequencing experiments requires development and improvement of many bioinformatics applications for analysis of large sequencing datasets, including k-mer counting and assembly. Several applications reduce RAM usage by binning sequences. Binning is done by employing minimizer schemes, which rely on a specific order of the minimizers. It has been demonstrated that the choice of the order has a major impact on the performance of the applications. Here we introduce a method for tailoring the order to the dataset. Our method repeatedly samples the dataset and modifies the order so as to flatten the k-mer load distribution across minimizers. We integrated our method into Gerbil, a state-of-the-art memory efficient k-mer counter, and were able to reduce its memory footprint by 50% or more for large k, with only minor increase in runtime. Our tests also showed that the orders produced by our method produced superior results when transferred across datasets from the same species, with little or no order change. This enables memory reduction with essentially no increase in runtime.

Parameter Estimation to Improve Coastal Accuracy in a Global Tide Model

Global tide and surge models play a major role in forecasting coastal flooding due to extreme events or climate change. The model performance is strongly affected by parameters such as bathymetry and bottom friction. In this study, we propose a method that estimates bathymetry globally and the bottom friction coefficient in the shallow waters for a Global Tide and Surge Model (GTSMv4.1). However, the estimation effect is limited by the scarcity of available tide gauges. We propose to complement sparse tide gauges with tide time-series generated using FES2014. The FES2014 dataset outperforms GTSM in most areas and is used as observations for the deep ocean and some coastal areas, such as Hudson Bay/Labrador, where tide gauges are scarce but energy dissipation is large. The experiment is performed with a computation and memory efficient iterative parameter estimation scheme applied to Global Tide and Surge Model (GTSMv4.1). Estimation results show that model performance is significantly improved for deep ocean and shallow waters, especially in the European Shelf directly using the CMEMS tide gauge data in the estimation. GTSM is also validated by comparing to tide gauges from UHSLC, CMEMS, and some Arctic stations in the year 2014.