35 research outputs found
SparCL: Sparse Continual Learning on the Edge
Existing work in continual learning (CL) focuses on mitigating catastrophic
forgetting, i.e., model performance deterioration on past tasks when learning a
new task. However, the training efficiency of a CL system is
under-investigated, which limits the real-world application of CL systems under
resource-limited scenarios. In this work, we propose a novel framework called
Sparse Continual Learning(SparCL), which is the first study that leverages
sparsity to enable cost-effective continual learning on edge devices. SparCL
achieves both training acceleration and accuracy preservation through the
synergy of three aspects: weight sparsity, data efficiency, and gradient
sparsity. Specifically, we propose task-aware dynamic masking (TDM) to learn a
sparse network throughout the entire CL process, dynamic data removal (DDR) to
remove less informative training data, and dynamic gradient masking (DGM) to
sparsify the gradient updates. Each of them not only improves efficiency, but
also further mitigates catastrophic forgetting. SparCL consistently improves
the training efficiency of existing state-of-the-art (SOTA) CL methods by at
most 23X less training FLOPs, and, surprisingly, further improves the SOTA
accuracy by at most 1.7%. SparCL also outperforms competitive baselines
obtained from adapting SOTA sparse training methods to the CL setting in both
efficiency and accuracy. We also evaluate the effectiveness of SparCL on a real
mobile phone, further indicating the practical potential of our method.Comment: Published at NeurIPS 2022 as a conference pape
Metagenomic Sequencing Identifies Highly Diverse Assemblages of Dinoflagellate Cysts in Sediments From Ships\u27 Ballast Tanks
Ships\u27 ballast tanks have long been known as vectors for the introduction of organisms. We applied next-generation sequencing to detect dinoflagellates (mainly as cysts) in 32 ballast tank sediments collected during 2001-2003 from ships entering the Great Lakes or Chesapeake Bay and subsequently archived. Seventy-three dinoflagellates were fully identified to species level by this metagenomic approach and single-cell polymerase chain reaction (PCR)-based sequencing, including 19 toxic species, 36 harmful algal bloom (HAB) forming species, 22 previously unreported as producing cysts, and 55 reported from ballast tank sediments for the first time (including 13 freshwater species), plus 545 operational taxonomic units (OTUs) not fully identified due to a lack of reference sequences, indicating tank sediments are repositories of many previously undocumented taxa. Analyses indicated great heterogeneity of species composition among samples from different sources. Light and scanning electron microscopy and single-cell PCR sequencing supported and confirmed results of the metagenomic approach. This study increases the number of fully identified dinoflagellate species from ballast tank sediments to 142 (\u3e 50% increase). From the perspective of ballast water management, the high diversity and spatiotemporal heterogeneity of dinoflagellates in ballast tanks argues for continuing research and stringent adherence to procedures intended to prevent unintended introduction of non-indigenous toxic and HAB-forming species
Alpha-Tubulin and Small Subunit rRNA Phylogenies of Peritrichs Are Congruent and Do Not Support the Clustering of Mobilids and Sessilids (Ciliophora, Oligohymenophorea)
Peritrich ciliates have been traditionally subdivided into two orders, Sessilida and Mobilida within the subclass Peritrichia. However, all the existing small subunit (SSU) rRNA phylogenetic trees showed that the sessilids and mobilids did not branch together. To shed some light on this disagreement, we tested whether or not the classic Peritrichia is a monophyletic group by assessing the reliability of the SSU rRNA phylogeny in terms of congruency with alpha-tubulin phylogeny. For this purpose, we obtained 10 partial alpha-tubulin sequences from peritrichs and built phylogenetic trees based on alpha-tubulin nucleotide and amino acid data. A phylogenetic tree from the alpha-tubulin and SSU rRNA genes in combination was also constructed and compared with that from the SSU rRNA gene using a similar species sampling. Our results show that the mobilids and sessilids are consistently separated in all trees, which reinforces the idea that the peritrichs do not constitute a monophyletic group. However, in all alpha-tubulin gene trees, the urceolariids and trichodiniids do not group together, suggested mobilids may not be a monophyletic group
Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)
Metabarcoding and high-throughput sequencing methods have greatly improved our understanding of protist diversity. Although the V4 region of small subunit ribosomal DNA (SSU-V4 rDNA) is the most widely used marker in DNA metabarcoding of eukaryotic microorganisms, doubts have recently been raised about its suitability. Here, using the widely distributed ciliate genus Pseudokeronopsis as an example, we assessed the potential of SSU-V4 rDNA and four other nuclear and mitochondrial markers for species delimitation and phylogenetic reconstruction. Our studies revealed that SSU-V4 rDNA is too conservative to distinguish species, and a threshold of 97% and 99% sequence similarity detected only one and three OTUs, respectively, from seven species. On the basis of the comparative analysis of the present and previously published data, we proposed the multilocus marker including the nuclear 5.8S rDNA combining the internal transcribed spacer regions (ITS1-5.8S-ITS2) and the hypervariable D2 region of large subunit rDNA (LSU-D2) as an ideal barcode rather than the mitochondrial cytochrome c oxidase subunit 1 gene, and the ITS1-5.8S-ITS2 as a candidate metabarcoding marker for ciliates. Furthermore, the compensating base change and tree-based criteria of ITS2 and LSU-D2 were useful in complementing the DNA barcoding and metabarcoding methods by giving second structure and phylogenetic evidence
Morphology and phylogenetic analysis of five deep-sea golden gorgonians (Cnidaria, Octocorallia, Chrysogorgiidae) in the Western Pacific Ocean, with the description of a new species
Explorations of seamounts in the Western Pacific Ocean and South China Sea resulted in collecting 18 specimens of golden gorgonians. Based on the morphology and the genetic analysis of mtMutS, they are described as one new species, Chrysogorgia carolinensis sp. nov., and four known species, including Chrysogorgia dendritica Xu, Zhan & Xu, 2020, Metallogorgia melanotrichos (Wright & Studer, 1889), Metallogorgia macrospina Kükenthal, 1919, and Pseudochrysogorgia bellona Pante & France, 2010. Chrysogorgia carolinensis belongs to the Chrysogorgia “group A, Spiculosae” with rods or spindles distributed in the polyp-body wall and tentacles, and differs from all of its congeners except C. dendritica by the 1/3L branching sequence and amoeba-shaped sclerites at the basal polyp body. The mtMutS sequence of C. carolinensis sp. nov. has six deletion mutations compared to those of its congeners, supporting the establishment of the new species. Although no genetic variability was observed between the closely related species C. dendritica and C. abludo Pante & Watling, 2012, the former is different from the latter by the apparently irregular sclerites in the polyp body wall. The two specimens of Metallogorgia melanotrichos match well with the original description except for relatively larger polyps, while the M. macrospina specimens have slightly smaller polyps than the holotype. The juvenile of Metallogorgia has an obvious morphological difference with the adults in the colony shape and branches, but they can be unified by the same polyps and sclerites as well as mitochondrial MutS sequences. Thus, the generic diagnosis of Metallogorgia is slightly extended to include the morphology of juveniles. The morphology of Pseudochrysogorgia bellona Pante & France, 2010, as a new record for the South China Sea, matches well with that of the original description. In the phylogenetic trees, the Chrysogorgia species are separated into two clades, and while Metallogorgia and Pseudochrysogorgia formed a sister clade
Morphological and Molecular Characterization of Five Species Including Three New Species of Golden Gorgonians (Cnidaria: Octocorallia) from Seamounts in the Western Pacific
Members of genus Iridogorgia Verrill, 1883 are the typical deep-sea megabenthos with only seven species reported. Based on an integrated morphological-molecular approach, eight sampled specimens of Iridogorgia from seamounts in the tropical Western Pacific are identified as three new species, and two known species I. magnispiralis Watling, 2007 and I. densispicula Xu, Zhan, Li and Xu, 2020. Iridogorgia flexilis sp. nov. is unique in having a very broad polyp body base with stout and thick scales. Iridogorgia densispiralis sp. nov. can be distinguished by rods present in both polyps and coenenchyme, and I. verrucosa sp. nov. is characterized by having numerous verrucae in coenenchyme and irregular spindles and scales in the polyp body wall. Phylogenetic analysis based on the nuclear 28S rDNA indicated that I. densispiralis sp. nov. showed close relationships with I. splendens Watling, 2007 and I. verrucosa sp. nov., and I. flexilis sp. nov. formed a sister clade with I. magnispiralis. In addition, due to Rhodaniridogorgia fragilis Watling, 2007 nested into the Iridogorgia clade in mtMutS-COI trees and shared highly similar morphology to the latter, we propose to eliminate the genus Rhodaniridogorgia by establishing a new combination Iridogorgia fragilis (Watling, 2007) comb. nov. and resurrecting I. superba Nutting, 1908
Studies on western Pacific gorgonians (Anthozoa: Octocorallia, Chrysogorgiidae). Part 1: a review of the genus Chrysogorgia, with description of a new genus and three new species
Xu, Yu, Zhan, Zifeng, Xu, Kuidong (2023): Studies on western Pacific gorgonians (Anthozoa: Octocorallia, Chrysogorgiidae). Part 1: a review of the genus Chrysogorgia, with description of a new genus and three new species. Zootaxa 5321 (1): 1-107, DOI: https://doi.org/10.11646/zootaxa.5321.1.1, URL: http://dx.doi.org/10.11646/zootaxa.5321.1.
Morphology and phylogenetic analysis of two new species of deep-sea golden gorgonians (Cnidaria: Octocorallia: Chrysogorgiidae) from seamounts in the Western Pacific Ocean
Xu, Yu, Zhan, Zifeng, Li, Yang, Xu, Kuidong (2020): Morphology and phylogenetic analysis of two new species of deep-sea golden gorgonians (Cnidaria: Octocorallia: Chrysogorgiidae) from seamounts in the Western Pacific Ocean. Zootaxa 4731 (2): 249-262, DOI: https://doi.org/10.11646/zootaxa.4731.2.
Morphology and phylogenetic analysis of two new deep-sea species of Chrysogorgia (Cnidaria, Octocorallia, Chrysogorgiidae) from Kocebu Guyot (Magellan seamounts) in the Pacific Ocean
Two new species of Chrysogorgia Duchassaing & Michelotti, 1864 collected from Kocebu Guyot in the Magellan seamounts of the Pacific Ocean are described and illustrated: Chrysogorgia ramificans sp. nov. collected from a depth of 1831 m and Chrysogorgia binata sp. nov. collected from a depth of 1669 m. Chrysogorgia ramificans sp. nov. belongs to the Chrysogorgia “group A, Spiculosae” with rods distributed in body wall and tentacles, and C. binata sp. nov. belongs to the “group C, Squamosae typicae” with rods and/or spindles not present but only scales. Chrysogorgia ramificans sp. nov. differs from congeners by its main stem with 2/5R branching sequence at the bottom forming two large bottlebrush-shaped branches with 1/3R branching sequence at the top. Chrysogorgia binata sp. nov. is similar to C. scintillans Bayer & Stefani, 1988, but differs by its larger polyps, larger sclerites in the body wall, and different scales in the upper part of polyps. The mtMutS genetic distances between C. ramificans sp. nov. and C. binata sp. nov. and congeners are in the range of 0.33%–2.28% and 0.33%–2.94%, respectively, while the intraspecific distances are in the range of 0–0.16%. Molecular phylogenetic analysis indicates that C. ramificans sp. nov. is clustered with C. monticola Cairns, 2007 and C. binata sp. nov. is clustered with C. chryseis Bayer & Stefani, 1988, both with high support indicating close relationships