36 research outputs found

    Learning Sparse & Ternary Neural Networks with Entropy-Constrained Trained Ternarization (EC2T)

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    Deep neural networks (DNN) have shown remarkable success in a variety of machine learning applications. The capacity of these models (i.e., number of parameters), endows them with expressive power and allows them to reach the desired performance. In recent years, there is an increasing interest in deploying DNNs to resource-constrained devices (i.e., mobile devices) with limited energy, memory, and computational budget. To address this problem, we propose Entropy-Constrained Trained Ternarization (EC2T), a general framework to create sparse and ternary neural networks which are efficient in terms of storage (e.g., at most two binary-masks and two full-precision values are required to save a weight matrix) and computation (e.g., MAC operations are reduced to a few accumulations plus two multiplications). This approach consists of two steps. First, a super-network is created by scaling the dimensions of a pre-trained model (i.e., its width and depth). Subsequently, this super-network is simultaneously pruned (using an entropy constraint) and quantized (that is, ternary values are assigned layer-wise) in a training process, resulting in a sparse and ternary network representation. We validate the proposed approach in CIFAR-10, CIFAR-100, and ImageNet datasets, showing its effectiveness in image classification tasks.Comment: Proceedings of the CVPR'20 Joint Workshop on Efficient Deep Learning in Computer Vision. Code is available at https://github.com/d-becking/efficientCNN

    Compositional analysis of bacterial communities in seawater, sediment, and sponges in the Misool coral reef system, Indonesia

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    Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges.publishe

    Urban coral reefs: Degradation and resilience of hard coral assemblages in coastal cities of East and Southeast Asia

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    © 2018 The Author(s) Given predicted increases in urbanization in tropical and subtropical regions, understanding the processes shaping urban coral reefs may be essential for anticipating future conservation challenges. We used a case study approach to identify unifying patterns of urban coral reefs and clarify the effects of urbanization on hard coral assemblages. Data were compiled from 11 cities throughout East and Southeast Asia, with particular focus on Singapore, Jakarta, Hong Kong, and Naha (Okinawa). Our review highlights several key characteristics of urban coral reefs, including “reef compression” (a decline in bathymetric range with increasing turbidity and decreasing water clarity over time and relative to shore), dominance by domed coral growth forms and low reef complexity, variable city-specific inshore-offshore gradients, early declines in coral cover with recent fluctuating periods of acute impacts and rapid recovery, and colonization of urban infrastructure by hard corals. We present hypotheses for urban reef community dynamics and discuss potential of ecological engineering for corals in urban areas

    Neoproterozoic iron formation: An evaluation of its temporal, environmental and tectonic significance

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    Sponge species composition, abundance, and cover in marine lakes and coastal mangroves in Berau, Indonesia

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    We compared the species composition, abundance, and cover of sponges in 2 marine lakes (Kakaban Lake and Haji Buang Lake) and adjacent coastal mangroves on the islands of Kakaban and Maratua in the Berau region of Indonesia. We recorded a total of 115 sponge spe- cies, 33 of which were restricted to Kakaban Lake, 18 to Haji Buang Lake, and 30 to coastal man- groves on Maratua Island. Only 13 species were shared among all habitats. The 2 marine lakes are located 10 km apart, but their assemblages were more similar to each other than to the bay man- grove systems just 200 to 500 m away. Our results show that marine lakes represent a distinct habitat with significantly higher sponge cover and abundance as well as a markedly different spe- cies composition when compared with coastal mangroves. In both lake and coastal mangrove habitats there was a pronounced gradient in composition away from the shore with the primary difference between solid (root or rock) and soft substrate (mud or sand). Each substrate type har- bored different sets of species in both lake and coastal mangrove habitats. There was no signifi- cant difference in sponge species composition, abundance, or cover between semi-permanent transects sampled in 2008 and 2009. We show for the first time that mangroves in the Indo-Pacific harbor a diverse array of sponge species and, further, that marine lakes harbor numerous unique species hitherto unknown to science.Bahruddin, Estradivari, N. Santo domingo, E. Dondorp, and W. Renema were invaluable sources of information and help in the field. We also thank the following people for their help in various ways: B. Hoeksema, Suharsono, Y. Tuti, E. Oberhauser, R. Suhr, and the staff of TNC/World Wildlife Foundation (WWF) Berau Office, Nabucco Island Dive Resort, and of Derawan Dive Resort. This study is part of a PhD project (L.E.B.) funded by NWO, division Earth and Life Sciences (ALW IPJ-07002; # 817.01.008). Fieldwork in Indonesia was made possible through additional financial support of WWF NetherlandsINNO Fund, the Schure-Beijerinck-Popping Fund of the Royal Dutch Academy of Science (KNAW), the TreubMaatschappij Fund, The Netherlands WWF-INNO Subsidy, the Leiden University Fund (LUF)/Slingelands, Singapore Airlines, the A.M. Buitendijk Fund and the J.J. ter Pelkwijk Fund (NCB Naturalis). D.F.R.C. was supported by the Portuguese Foundation for Science and Technology, FCT, project LESS CORAL, PTDC/AAC-AMB/115304/2009. We are grateful to the Indonesian Institute of Sciences (LIPI) and the Indonesian State Ministry of Research and Technology (RISTEK) for providing re search permits in Indonesia. R. van Soest, B. Hoeksema, and 4 anonymous reviewers provided valuable comments on the original manuscript.publishe

    FantastIC4: A Hardware-Software Co-Design Approach for Efficiently Running 4Bit-Compact Multilayer Perceptrons

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    With the growing demand for deploying Deep Learning models to the “edge”, it is paramount to develop techniques that allow to execute state-of-the-art models within very tight and limited resource constraints. In this work we propose a software-hardware optimization paradigm for obtaining a highly efficient execution engine of deep neural networks (DNNs) that are based on fully-connected layers. The work’s approach is centred around compression as a means for reducing the area as well as power requirements of, concretely, multilayer perceptrons (MLPs) with high predictive performances. Firstly, we design a novel hardware architecture named FantastIC4, which (1) supports the efficient on-chip execution of multiple compact representations of fully-connected layers and (2) minimizes the required number of multipliers for inference down to only 4 (thus the name). Moreover, in order to make the models amenable for efficient execution on FantastIC4, we introduce a novel entropy-constrained training method that renders them to be robust to 4bit quantization and highly compressible in size simultaneously. The experimental results show that we can achieve throughputs of 2.45 TOPS with a total power consumption of 3.6W on a Virtual Ultrascale FPGA XCVU440 device implementation, and achieve a total power efficiency of 20.17 TOPS/W on a 22nm process ASIC version. When compared to other state-of-the-art accelerators designed for the Google Speech Command (GSC) dataset, FantastIC4 is better by 51×51\times in terms of throughput and 145×145\times in terms of area efficiency (GOPS/mm2)

    Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes

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    In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications

    Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters

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    Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific.Research was funded by Project LESS CORAL – FCOMP01-0124-FEDER013994, refª PTDC/AAC-AMB/115304/ 2009, Project PEst-C/MAR/LA0017/2011, cofunded by both the Portuguese Foundation for Science and Technology and COMPETE (POFC) and The Netherlands Organisation for Scientific Research (ALW #817.01.008, Rubicon #825.12.007). The Indonesian Institute of Sciences (PPO-LIPI) and the Indonesian State Ministry of Research and Technology (RISTEK) provided the research permits in Indonesia.publishe
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