cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Hoya caudata Hook.
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya caudata

description: Hoya caudata Hook. f.
The Flora of British India 4: 60 (Hooker 1883).
Type material
Lectotype (designated by Rintz (1978), first step, and then by Rodda (2017), second step) MALAYSIA • Malacca, A.C. Maingay 1956 leg.; Kew distritribution no. 1128; K000895134.
Isolectotypes MALAYSIA • Same data as for the lectotype; K000895133, L0004315.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 3, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Hoya coronaria Blume 1824
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya coronaria

description: Hoya coronaria Blume
Bijdragen tot de flora van Nederlandsch Indië: 1063 (Blume 1826). — Eriostemma coronaria (Blume) Kloppenb. & Gilding, Fraterna 14 (2): 1 (Anonymous 2001).
Type material
Lectotype (designated by Kleijn & van Donkelaar 2001: 469) INDONESIA • Java; sine coll. “124/6” leg.; L (sheet no. 898.168–121).
Isolectotype INDONESIA • Same data as for the lectotype; L (sheet no. 898.168–128).
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 3, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Assessing Silica-related Disease in Stone Benchtop Workers
Creators: name: Hore-Lacy, Fiona Elizabeth
Publisher: name: Monash University
Year: 2025
Subjects: classificationCode: 350505
subject: Occupational and workplace health and safety

description: This thesis examines perceived stress and psychometric properties of the PSS-10 in stone benchtop workers in Victoria who are at risk of silicosis. It also describes a significant change in workplace safety practices, and the development of an electronic tool for occupational screening.
Myrmica granulinodis
Creators: name: Smith, F.
Publisher: name: British Museum
Year: 1858
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica granulinodis

description: 7. Myrmica granulinodis.
Myrmica granulinodis, Nyl. Addit. Adno. Mon. Form. Bor. Eur. 1060.
Hab. Siberia.
description: Published as part of Smith, F., 1858, Catalogue of the hymenopterous insects in the collection of the British Museum. Part VI. Formicidae., London :British Museum on page 116
Driving Safety Prediction and Safe Route Mapping Using In-vehicle and Roadside Data
Creators: name: Huang, Yufei
name: Jafari, Mohsen
name: Jin, Peter
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Risk assessment of roadways is commonly practiced based on historical crash data. Information on driver behaviors and real-time traffic situations is sometimes missing. In this paper, the Safe Route Mapping (SRM) model, a methodology for developing dynamic risk heat maps of roadways, is extended to consider driver behaviors when making predictions. An Android App is designed to gather drivers' information and upload it to a server. On the server, facial recognition extracts drivers' data, such as facial landmarks, gaze directions, and emotions. The driver's drowsiness and distraction are detected, and driving performance is evaluated. Meanwhile, dynamic traffic information is captured by a roadside camera and uploaded to the same server. A longitudinal-scanline-based arterial traffic video analytics is applied to recognize vehicles from the video to build speed and trajectory profiles. Based on these data, a LightGBM model is introduced to predict conflict indices for drivers in the next one or two seconds. Then, multiple data sources, including historical crash counts and predicted traffic conflict indicators, are combined using a Fuzzy logic model to calculate risk scores for road segments. The proposed SRM model is illustrated using data collected from an actual traffic intersection and a driving simulation platform. The prediction results show that the model is accurate, and the added driver behavior features will improve the model's performance. Finally, risk heat maps are generated for visualization purposes. The authorities can use the dynamic heat map to designate safe corridors and dispatch law enforcement and drivers for early warning and trip planning.
description: 12 pages, 19 figures, 9 tables
Hoya fauziana subsp. angulata Rodda, A. L. Lamb, Gokusing & S. Rahayu
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya fauziana
Hoya fauziana subsp. angulata rodda, a.l.lamb, gokusing & s.rahayu

description: Hoya fauziana subsp. angulata Rodda, A.L.Lamb, Gokusing & S.Rahayu
Blumea 63: 144 (Rodda et al. 2018).
Type material
Holotype MALAYSIA • Sabah, Tawau, Kalabakan area; 16 May 2017; L. Gokusing LG56/2017 leg.; mixed hill Dipterocarp forest; SAN.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 7, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Ovaticoccus mackenziei Miller and Miller 1992
Creators: name: Miller, Douglass R.
name: Stocks, Ian C.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Eriococcidae
Ovaticoccus
Ovaticoccus mackenziei

description: Ovaticoccus mackenziei Miller
Ovaticoccus mackenziei Miller in Miller and McKenzie 1967: 515–517.
Material examined: not previously reported: California: Imperial Co.: Holtville, II-11-1972, on Ephedra sp., R.A. Flock (1 ad. ♀ on 1 slide) CDFA. San Bernardino Co.: Morongo Valley, V-11-1971, on Ephedra sp., Dixon and Hunter (4 ad. ♀♀ on 4 slides) CDFA.
Etymology: This species was named in honor of the late Howard L. McKenzie, the first author’s major professor and well-known coccidologist.
The adult female and second-instar female (as “first or second instar”) were described by Miller and McKenzie (1967) and information from that paper is not repeated here.
description: Published as part of Miller, Douglass R. & Stocks, Ian C., 2022, New genera and species of felt scales (Hemiptera: Coccomorpha: Eriococcidae), with descriptions of new species and immature instars of described species, pp. 1-213 in Zootaxa 5221 (1) on page 139, DOI: 10.11646/zootaxa.5221.1.1, http://zenodo.org/record/7441371
Myrmica lobicornis
Creators: name: Smith, F.
Publisher: name: British Museum
Year: 1858
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica lobicornis

description: 8. Myrmica lobicornis. Pl. XII. fig. 12. B.M.
Myrmica lobicornis, Nyl. Adno. Mon. Form. Bor. Eur. 932. 4; Addit. Adno. Mon. Form. Bor. Eur. 1052. 21; Addit. ait. 31;
Form. Fr. et d'Alger. 82. 7-
Foerst. Hym. Stud. Form. 69.
Schenck, Beschr. Nass. Ameis. 82.
Mayr. Form. Austr. 140. 7.
Myrmica denticornis, Curtis, Trans. Linn. Soc. xxi. 215. 7. t. 23. f. 18, 19.
Smith, Brit. Form. 120. 5.
Hab. Britain; France; Germany; Hungary; Italy; Finland.
We have compared specimens of this species from Dr, Nylander with others from Mr. Curtis, and they are certainly identical.
description: Published as part of Smith, F., 1858, Catalogue of the hymenopterous insects in the collection of the British Museum. Part VI. Formicidae., London :British Museum on page 116
Correlations of the Thue--Morse sequence
Creators: name: Baake, Michael
name: Coons, Michael
Publisher: name: arXiv
Year: 2022
Subjects: subject: Dynamical Systems (math.DS)
subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 37B10, 52C23

description: The pair correlations of the Thue--Morse sequence and system are revisited, with focus on asymptotic results on various means. First, it is shown that all higher-order correlations of the Thue--Morse sequence with general real weights are effectively determined by a single value of the balanced $2$-point correlation. As a consequence, we show that all odd-order correlations of the balanced Thue--Morse sequence vanish, and that, for any even $n$, the $n$-point correlations of the balanced Thue--Morse sequence have mean value zero, as do their absolute values, raised to an arbitrary positive power. All these results also apply to the entire Thue--Morse system. We finish by showing how the correlations of the Thue--Morse system with general real weights can be derived from the balanced $2$-point correlations.
description: 18 pages, revised version, with minor additions and improvements
Hoya kastbergii Kloppenb.
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya kastbergii

description: Hoya kastbergii Kloppenb.
Fraterna 16 (4): 1 (Anonymous 2003).
Type material
Holotype MALAYSIA • Sarawak, Bau; I.S.A. Kastberg s.n. leg.; UC, missing.
Neotype (designated by Rodda 2017) MALAYSIA • Sarawak, Bau, near Mulu National Park H.Q.; 23 Mar. 1981; I.S. Collenette 2357 leg.; L2726571.
Isoneotype MALAYSIA • Same data as for the neotype; K.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on pages 8-9, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Software Prefetching for Indirect Memory Accesses
Creators: name: Ainsworth, Sam
name: Jones, Timothy M
Publisher: name: IEEE
Year: 2017
Subjects: Software Prefetching
Compiler Analysis

description: Many modern data processing and HPC workloads are heavily memory-latency bound. A tempting proposition to solve this is software prefetching, where special non-blocking loads are used to bring data into the cache hierarchy just before being required. However, these are difficult to insert to effectively improve performance, and techniques for automatic insertion are currently limited. This paper develops a novel compiler pass to automatically generate software prefetches for indirect memory accesses, a special class of irregular memory accesses often seen in high-performance workloads. We evaluate this across a wide set of systems, all of which gain benefit from the technique. We then evaluate the extent to which good prefetch instructions are architecture dependent. Across a set of memory-bound benchmarks, our automated pass achieves average speedups of 1.3$\times$ and 1.1$\times$ for an Intel Haswell processor and an ARM Cortex-A57, both out-of-order cores, and performance improvements of 2.1$\times$ and 3.7$\times$ for the in-order ARM Cortex-A53 and Intel Xeon Phi.
Hoya forbesii King & Gamble
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya forbesii

description: Hoya forbesii King & Gamble
Journal of the Asiatic Society of Bengal 74 (2): 574 (King & Gamble 1908).
Type material
Lectotype (designated by Rodda 2017) INDONESIA • Sumatra, Kaba Volcano; 1881; H.O. Forbes 2896a leg.; K000894730.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 8, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Myrmica caespitum
Creators: name: Smith, F.
Publisher: name: British Museum
Year: 1858
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica caespitum

description: 9. Myrmica caespitum. Pl. VIII. figs. 15,16. B.M.
Formica caespitum, Linn. Faun. Suec. no. 1726; Syst. Nat. i. 963. 11 [[worker]].
Latr. Hist. Nat. Fourm. 251. t. 10. f. 63.
Formica binodis, Linn. Am oe n. Acad. vi. 413. 94; type in Cab. Mus. Linn. Soc.
Myrmica fuscula, Nyl. Adno. Mon. Form. Bor. Eur. 935. 6; "Addit. Mon. Form. 1053. 23; Form. Pr. et d'Alger. 86. 13.
Foerst. Hym. Stud. Form. 56. 29.
Schenck, Beschr. Nass. Ameis. 86.
Myrmica impura, Foerst. Hym. Stud. Form. 48. 22 [[worker]].
Myrmica modesta, Foerst. Hym. Stud. Form. 49. 23 [[worker]].
Myrmica caespitum, Latr. Hist. Nat. Crust, et Ins. xiii. 259.
Losana, Form. Piem. 327.
Curtis, Trans. Linn. Soc. xxi. 215. 8.
Smith, Brit. Form. 122.
Nyl. Form. Fr. et d'Alger. 86. 13.
Tetramorium caespitum, Mayr. Form. Austr. 154. 2; Ungar. Ameis. 19. 1.
Hab. Britain; France; Germany; Hungary; Finland.
description: Published as part of Smith, F., 1858, Catalogue of the hymenopterous insects in the collection of the British Museum. Part VI. Formicidae., London :British Museum on page 117
Causal Fourier Analysis on Directed Acyclic Graphs and Posets
Creators: name: Seifert, Bastian
name: Wendler, Chris
name: Püschel, Markus
Publisher: name: arXiv
Year: 2022
Subjects: subject: Signal Processing (eess.SP)
subject: Discrete Mathematics (cs.DM)
subject: Machine Learning (cs.LG)
subject: Combinatorics (math.CO)
subject: Methodology (stat.ME)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We present a novel form of Fourier analysis, and associated signal processing concepts, for signals (or data) indexed by edge-weighted directed acyclic graphs (DAGs). This means that our Fourier basis yields an eigendecomposition of a suitable notion of shift and convolution operators that we define. DAGs are the common model to capture causal relationships between data values and in this case our proposed Fourier analysis relates data with its causes under a linearity assumption that we define. The definition of the Fourier transform requires the transitive closure of the weighted DAG for which several forms are possible depending on the interpretation of the edge weights. Examples include level of influence, distance, or pollution distribution. Our framework is different from prior GSP: it is specific to DAGs and leverages, and extends, the classical theory of Moebius inversion from combinatorics. For a prototypical application we consider DAGs modeling dynamic networks in which edges change over time. Specifically, we model the spread of an infection on such a DAG obtained from real-world contact tracing data and learn the infection signal from samples assuming sparsity in the Fourier domain.
description: 13 pages, 11 figures
Hoya imperialis Lindl.
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya imperialis

description: Hoya imperialis Lindl.
Edwards’s Botanical Register 32: tab. 68 (Lindley 1846).
Type material
Lectotype (designated by Rodda 2017) MALAYSIA? • Ex herb. J. Lindley [cultivated, from Sarawak via Lowe’s Nursery]; CGE06041.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 8, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Engineering holography with stabilizer graph codes
Creators: name: Munné, Gerard Anglès
name: Kasper, Valentin
name: Huber, Felix
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The discovery of holographic codes established a surprising connection between quantum error correction and the anti-de Sitter-conformal field theory correspondence. Recent technological progress in artificial quantum systems renders the experimental realization of such holographic codes now within reach. Formulating the hyperbolic pentagon code in terms of a stabilizer graph code, we give gate sequences that are tailored to systems with long-range interactions. We show how to obtain encoding and decoding circuits for the hyperbolic pentagon code, before focusing on a small instance of the holographic code on twelve qubits. Our approach allows to verify holographic properties by partial decoding operations, recovering bulk degrees of freedom from their nearby boundary.
description: 23 pages, 11 figures
Hoya glabra Schltr.
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya glabra

description: Hoya glabra Schltr.
Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 40 (92): 14 (Schlechter 1908).
Type material
Lectotype (designated by Rodda 2017) INDONESIA • Borneo, Long Wahau; 2 Aug. 1901; R. Schlechter 13458 leg.; B100277199.
Other material examined
INDONESIA • Sumatra, Monkey reserve; 2°41.589´N, 98°55.656´E; 1215 m a.s.l.; I.M. Liddle 1552 leg.; top of ridge; Singapore Botanic Gardens living collections no. 20123057, vouchered on 11 Feb. 2013 as ‘M. Rodda MR286’; SING.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 8, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
EcoFlow: Efficient Convolutional Dataflows for Low-Power Neural Network Accelerators
Creators: name: Orosa, Lois
name: Koppula, Skanda
name: Umuroglu, Yaman
name: Kanellopoulos, Constantinos
name: Gómez Luna, Juan
name: Blott, Michaela
name: Vissers, Kees
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Machine Learning (cs.LG)
Hardware Architecture (cs.AR)
FOS: Computer and information sciences

description: Dilated and transposed convolutions are widely used in modern convolutional neural networks (CNNs). These kernels are used extensively during CNN training and inference of applications such as image segmentation and high-resolution image generation. Although these kernels have grown in popularity, they stress current compute systems due to their high memory intensity, exascale compute demands, and large energy consumption. We find that commonly-used low-power CNN inference accelerators based on spatial architectures are not optimized for both of these convolutional kernels. Dilated and transposed convolutions introduce significant zero padding when mapped to the underlying spatial architecture, significantly degrading performance and energy efficiency. Existing approaches that address this issue require significant design changes to the otherwise simple, efficient, and well-adopted architectures used to compute direct convolutions. To address this challenge, we propose EcoFlow, a new set of dataflows and mapping algorithms for dilated and transposed convolutions. These algorithms are tailored to execute efficiently on existing low-cost, small-scale spatial architectures and requires minimal changes to the network-on-chip of existing accelerators. EcoFlow eliminates zero padding through careful dataflow orchestration and data mapping tailored to the spatial architecture. EcoFlow enables flexible and high-performance transpose and dilated convolutions on architectures that are otherwise optimized for CNN inference. We evaluate the efficiency of EcoFlow on CNN training workloads and Generative Adversarial Network (GAN) training workloads. Experiments in our new cycle-accurate simulator show that EcoFlow 1) reduces end-to-end CNN training time between 7-85%, and 2) improves end-to-end GAN training performance between 29-42%, compared to state-of-the-art CNN inference accelerators.
description: arXiv
An Experimental Evaluation of Machine Learning Training on a Real Processing-in-Memory System
Creators: name: Gómez Luna, Juan
name: Guo, Yuxin
name: Brocard, Sylvan
name: Legriel, Julien
name: Cimadomo, Remy
name: Oliveira, Geraldo F.
name: Singh, Gagandeep
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
Artificial Intelligence (cs.AI)
Distributed, Parallel, and Cluster Computing (cs.DC)
Machine Learning (cs.LG)
FOS: Computer and information sciences
Machine learning
Processing-in-memory
Regression
Classification
Clustering
Benchmarking

description: Training machine learning (ML) algorithms is a computationally intensive process, which is frequently memory-bound due to repeatedly accessing large training datasets. As a result, processor-centric systems (e.g., CPU, GPU) suffer from costly data movement between memory units and processing units, which consumes large amounts of energy and execution cycles. Memory-centric computing systems, i.e., with processing-in-memory (PIM) capabilities, can alleviate this data movement bottleneck. Our goal is to understand the potential of modern general-purpose PIM architectures to accelerate ML training. To do so, we (1) implement several representative classic ML algorithms (namely, linear regression, logistic regression, decision tree, K-Means clustering) on a real-world general-purpose PIM architecture, (2) rigorously evaluate and characterize them in terms of accuracy, performance and scaling, and (3) compare to their counterpart implementations on CPU and GPU. Our evaluation on a real memory-centric computing system with more than 2500 PIM cores shows that general-purpose PIM architectures can greatly accelerate memory-bound ML workloads, when the necessary operations and datatypes are natively supported by PIM hardware. For example, our PIM implementation of decision tree is $27\times$ faster than a state-of-the-art CPU version on an 8-core Intel Xeon, and $1.34\times$ faster than a state-of-the-art GPU version on an NVIDIA A100. Our K-Means clustering on PIM is $2.8\times$ and $3.2\times$ than state-of-the-art CPU and GPU versions, respectively. To our knowledge, our work is the first one to evaluate ML training on a real-world PIM architecture. We conclude with key observations, takeaways, and recommendations that can inspire users of ML workloads, programmers of PIM architectures, and hardware designers & architects of future memory-centric computing systems.
description: arXiv
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Creators: name: Firtina, Can
name: Pillai, Kamlesh
name: Kalsi, Gurpreet S.
name: Suresh, Bharathwaj
name: Senol Cali, Damla
name: Kim, Jeremie S.
name: Shahroodi, Taha
name: Cavlak, Meryem Banu
name: Lindegger, Joël
name: Alser, Mohammed
name: Gómez Luna, Juan
name: Subramoney, Sreenivas
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
Artificial Intelligence (cs.AI)
Machine Learning (cs.LG)
Genomics (q-bio.GN)
Quantitative Methods (q-bio.QM)
FOS: Computer and information sciences
FOS: Biological sciences

description: Profile hidden Markov models (pHMMs) are widely used in many bioinformatics applications to accurately identify similarities between biological sequences (e.g., DNA or protein sequences). PHMMs use a commonly-adopted and highly-accurate method, called the Baum-Welch algorithm, to calculate these similarities. However, the Baum-Welch algorithm is computationally expensive, and existing works provide either software- or hardware-only solutions for a fixed pHMM design. When we analyze the state-of-the-art works, we find that there is a pressing need for a flexible, high-performant, and energy-efficient hardware-software co-design to efficiently and effectively solve all the major inefficiencies in the Baum-Welch algorithm for pHMMs. We propose ApHMM, the first flexible acceleration framework that can significantly reduce computational and energy overheads of the Baum-Welch algorithm for pHMMs. ApHMM leverages hardware-software co-design to solve the major inefficiencies in the Baum-Welch algorithm by 1) designing a flexible hardware to support different pHMMs designs, 2) exploiting the predictable data dependency pattern in an on-chip memory with memoization techniques, 3) quickly eliminating negligible computations with a hardware-based filter, and 4) minimizing the redundant computations. We implement our 1) hardware-software optimizations on a specialized hardware and 2) software optimizations for GPUs to provide the first flexible Baum-Welch accelerator for pHMMs. ApHMM provides significant speedups of 15.55x-260.03x, 1.83x-5.34x, and 27.97x compared to CPU, GPU, and FPGA implementations of the Baum-Welch algorithm, respectively. ApHMM outperforms the state-of-the-art CPU implementations of three important bioinformatics applications, 1) error correction, 2) protein family search, and 3) multiple sequence alignment, by 1.29x-59.94x, 1.03x-1.75x, and 1.03x-1.95x, respectively.
description: arXiv
Myrmica kollari
Creators: name: Smith, F.
Publisher: name: British Museum
Year: 1858
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica kollari

description: 10. Myrmica Kollari.
Myrmica Kollari, Mayr. Beschr. ein neuer Ameis. 7.
Tetramorium Kollari, Mayr. Form. Austr. 153. 1.
Nyl. Form. Fr. et d'Alger. 87 (note).
Hab. Austria.
description: Published as part of Smith, F., 1858, Catalogue of the hymenopterous insects in the collection of the British Museum. Part VI. Formicidae., London :British Museum on page 117
A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems
Creators: name: Diab, Safaa
name: Nassereldine, Amir
name: Alser, Mohammed
name: Gómez Luna, Juan
name: Mutlu, Onur
name: El Hajj, Izzat
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
Distributed, Parallel, and Cluster Computing (cs.DC)
FOS: Computer and information sciences

description: Sequence alignment is a fundamentally memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using processing-in-memory, and evaluate it on UPMEM, the first publicly-available general-purpose programmable processing-in-memory system. Our evaluation shows that a real processing-in-memory system can substantially outperform server-grade multi-threaded CPU systems running at full-scale when performing sequence alignment for a wide variety of algorithms, read lengths, and edit distance thresholds. We hope that our findings inspire more work on creating and accelerating bioinformatics algorithms for such real processing-in-memory systems.
description: arXiv
Scalable Experimental Bounds for Entangled Quantum State Fidelities
Creators: name: Aktar, Shamminuj
name: Bärtschi, Andreas
name: Badawy, Abdel-Hameed A.
name: Eidenbenz, Stephan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Estimating the state preparation fidelity of highly entangled states on noisy intermediate-scale quantum (NISQ) devices is important for benchmarking and application considerations. Unfortunately, exact fidelity measurements quickly become prohibitively expensive, as they scale exponentially as $O(3^N)$ for $N$-qubit states, using full state tomography with measurements in all Pauli bases combinations. However, Somma and others [PhysRevA.74.052302] established that the complexity could be drastically reduced when looking at fidelity lower bounds for states that exhibit symmetries, such as Dicke States and GHZ States. These bounds must still be tight enough for larger states to provide reasonable estimations on NISQ devices.
 For the first time and more than 15 years after the theoretical introduction, we report meaningful lower bounds for the state preparation fidelity of all Dicke States up to $N=10$ and all GHZ states up to $N=20$ on Quantinuum H1 ion-trap systems using efficient implementations of recently proposed scalable circuits for these states. Our achieved lower bounds match or exceed previously reported exact fidelities on superconducting systems for much smaller states. Furthermore, we provide evidence that for large Dicke States $D^N_{N/2}$, we may resort to a GHZ-based approximate state preparation to achieve better fidelity. This work provides a path forward to benchmarking entanglement as NISQ devices improve in size and quality.
RevaMp3D: Architecting the Processor Core and Cache Hierarchy for Systems with Monolithically-Integrated Logic and Memory
Creators: name: Mansouri Ghiasi, Nika
name: Sadrosadati, Mohammad
name: Oliveira, Geraldo F.
name: Kanellopoulos, Constantinos
name: Ausavarungnirun, Rachata
name: Gómez Luna, Juan
name: Manglik, Aditya
name: Ferreira, João
name: Kim, Jeremie S.
name: Giannoula, Christina
name: Vijaykumar, Nandita
name: Park, Jisung
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
Distributed, Parallel, and Cluster Computing (cs.DC)
FOS: Computer and information sciences

description: Recent nano-technological advances enable the Monolithic 3D (M3D) integration of multiple memory and logic layers in a single chip with fine-grained connections. M3D technology leads to significantly higher main memory bandwidth and shorter latency than existing 3D-stacked systems. We show for a variety of workloads on a state-of-the-art M3D system that the performance and energy bottlenecks shift from the main memory to the core and cache hierarchy. Hence, there is a need to revisit current core and cache designs that have been conventionally tailored to tackle the memory bottleneck. Our goal is to redesign the core and cache hierarchy, given the fundamentally new trade-offs of M3D, to benefit a wide range of workloads. To this end, we take two steps. First, we perform a design space exploration of the cache and core's key components. We highlight that in M3D systems, (i) removing the shared last-level cache leads to similar or larger performance benefits than increasing its size or reducing its latency; (ii) improving L1 latency has a large impact on improving performance; (iii) wider pipelines are increasingly beneficial; (iv) the performance impact of branch speculation and pipeline frontend increases; (v) the current synchronization schemes limit parallel speedup. Second, we propose an optimized M3D system, RevaMp3D, where (i) using the tight connectivity between logic layers, we efficiently increase pipeline width, reduce L1 latency, and enable fine-grained synchronization; (ii) using the high-bandwidth and energy-efficient main memory, we alleviate the amplified energy and speculation bottlenecks by memoizing the repetitive fetched, decoded, and reordered instructions and turning off the relevant parts of the core pipeline when possible. RevaMp3D provides, on average, 81% speedup, 35% energy reduction, and 12.3% smaller area compared to the baseline M3D system.
description: arXiv
Myrmica angustula
Creators: name: Smith, F.
Publisher: name: British Museum
Year: 1858
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica angustula

description: 12. Myrmica angustula.
Myrmica angustula, Nyl. Form. Fr. et d'Alger. 88. 14.
Hab. France.
description: Published as part of Smith, F., 1858, Catalogue of the hymenopterous insects in the collection of the British Museum. Part VI. Formicidae., London :British Museum on page 117
Hoya lasiantha Miq.
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya lasiantha

description: Hoya lasiantha (Korth. ex Blume) Miq.
Flora van Nederlandsch Indie 2: 526 (Miquel 1857). — Plocostemma lasianthum Korth ex Blume, Museum Botanicum Lugduno-Batavum 1: 60 (Blume 1849a).
Original citation
“Ad montem Pamotton insulae Borneo”.
Type material
Lectotype (designated by Rodda 2017) MALAYSIA /INDONESIA? • Borneo; P. Korthals s.n. leg.; U1102625.
Epitype (designated by Rodda 2017) Blume (1849a: fig. 14).
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 9, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Accelerating Time Series Analysis via Processing using Non-Volatile Memories
Creators: name: Fernandez, Ivan
name: Manglik, Aditya
name: Giannoula, Christina
name: Quislant, Ricardo
name: Mansouri Ghiasi, Nika
name: Gómez Luna, Juan
name: Gutierrez, Eladio
name: Plata, Oscar
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
FOS: Computer and information sciences

description: Time Series Analysis (TSA) is a critical workload for consumer-facing devices. Accelerating TSA is vital for many domains as it enables the extraction of valuable information and predict future events. The state-of-the-art algorithm in TSA is the subsequence Dynamic Time Warping (sDTW) algorithm. However, sDTW's computation complexity increases quadratically with the time series' length, resulting in two performance implications. First, the amount of data parallelism available is significantly higher than the small number of processing units enabled by commodity systems (e.g., CPUs). Second, sDTW is bottlenecked by memory because it 1) has low arithmetic intensity and 2) incurs a large memory footprint. To tackle these two challenges, we leverage Processing-using-Memory (PuM) by performing in-situ computation where data resides, using the memory cells. PuM provides a promising solution to alleviate data movement bottlenecks and exposes immense parallelism. In this work, we present MATSA, the first MRAM-based Accelerator for Time Series Analysis. The key idea is to exploit magneto-resistive memory crossbars to enable energy-efficient and fast time series computation in memory. MATSA provides the following key benefits: 1) it leverages high levels of parallelism in the memory substrate by exploiting column-wise arithmetic operations, and 2) it significantly reduces the data movement costs performing computation using the memory cells. We evaluate three versions of MATSA to match the requirements of different environments (e.g., embedded, desktop, or HPC computing) based on MRAM technology trends. We perform a design space exploration and demonstrate that our HPC version of MATSA can improve performance by 7.35x/6.15x/6.31x and energy efficiency by 11.29x/4.21x/2.65x over server CPU, GPU and PNM architectures, respectively.
description: arXiv
Myrmica atratula
Creators: name: Smith, F.
Publisher: name: British Museum
Year: 1858
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Myrmica
Myrmica atratula

description: 11. Myrmica atratula.
Myrmica atratula, Schenck, Beschr. Nass. Ameis. 91. Tetramorium atratulum, Mayr. Form. Austr. 157. 3; Ungar. Ameis. 20. 2.
Nyl. Form. Fr. et d'Alger. 87 (note).
Hab. Austria; Germany; Hungary.
description: Published as part of Smith, F., 1858, Catalogue of the hymenopterous insects in the collection of the British Museum. Part VI. Formicidae., London :British Museum on page 117
Ovaticoccus peninsularis
Creators: name: Miller, Douglass R.
name: Stocks, Ian C.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Eriococcidae
Ovaticoccus
Ovaticoccus peninsularis

description: Ovaticoccus peninsularis (Ferris) rev. comb.
Fonscolombia peninsularis Ferris 1921: 66, 78.
Pseudochermes peninsularis (Ferris); Lindinger 1933b: 31-32, 50 (change of combination).
Gymnococcus peninsularis (Ferris); Ferris 1955: 188 (change of combination).
Ovaticoccus peninsularis (Ferris); Boratynski 1958: 174 (change of combination).
Oregmopyga peninsularis (Ferris); Miller and McKenzie 1967: 501-503 (change of combination).
Etymology: The species epithet “ peninsularis ” is named for the Baja California Peninsula, Mexico, where it was first collected.
The justification for treating Oregmopyga as a junior synonym of Ovaticoccus,leading to this revised combination, is provided in the “Notes” section that follows the generic description above. The adult female was described in detail by Ferris (1921) and Miller and McKenzie (1967) and is not repeated here. No additional specimens have been collected of this species since the original description of Ferris (1921).
description: Published as part of Miller, Douglass R. & Stocks, Ian C., 2022, New genera and species of felt scales (Hemiptera: Coccomorpha: Eriococcidae), with descriptions of new species and immature instars of described species, pp. 1-213 in Zootaxa 5221 (1) on page 149, DOI: 10.11646/zootaxa.5221.1.1, http://zenodo.org/record/7441371
ALP: Alleviating CPU-Memory Data Movement Overheads in Memory-Centric Systems
Creators: name: Mansouri Ghiasi, Nika
name: Vijaykumar, Nandita
name: Oliveira, Geraldo F.
name: Orosa, Lois
name: Fernandez, Ivan
name: Sadrosadati, Mohammad
name: Kanellopoulos, Constantinos
name: Hajinazar, Nastaran
name: Gómez Luna, Juan
name: Mutlu, Onur
Publisher: name: ETH Zurich
Year: 2022
Subjects: Hardware Architecture (cs.AR)
Distributed, Parallel, and Cluster Computing (cs.DC)
FOS: Computer and information sciences
Near-data processing
Inter-segment data movement
Application partitioning

description: Partitioning applications between NDP and host CPU cores causes inter-segment data movement overhead, which is caused by moving data generated from one segment (e.g., instructions, functions) and used in consecutive segments. Prior works take two approaches to this problem. The first class of works maps segments to NDP or host cores based on the properties of each segment, neglecting the inter-segment data movement overhead. The second class of works partitions applications based on the overall memory bandwidth saving of each segment, and does not offload each segment to the best-fitting core if they incur high inter-segment data movement. We show that 1) mapping each segment to its best-fitting core ideally can provide substantial benefits, and 2) the inter-segment data movement reduces this benefit significantly. To this end, we introduce ALP, a new programmer-transparent technique to leverage the performance benefits of NDP by alleviating the inter-segment data movement overhead between host and memory and enabling efficient partitioning of applications. ALP alleviates the inter-segment data movement overhead by proactively and accurately transferring the required data between the segments. This is based on the key observation that the instructions that generate the inter-segment data stay the same across different executions of a program on different inputs. ALP uses a compiler pass to identify these instructions and uses specialized hardware to transfer data between the host and NDP cores at runtime. ALP efficiently maps application segments to either host or NDP considering 1) the properties of each segment, 2) the inter-segment data movement overhead, and 3) whether this overhead can be alleviated in a timely manner. We evaluate ALP across a wide range of workloads and show on average 54.3% and 45.4% speedup compared to only-host CPU or only-NDP executions, respectively.
description: arXiv
Tensor Computations on GPUs: From Dense Contractions to Sparse Decompositions
Creators: name: Szenes, Kalman
Publisher: name: ETH Zurich
Year: 2023
Subjects: Tensor decompositions
GPU
Sparse data
HPC

description: Tensor algorithms are a rapidly growing field of research with applications in many scientific domains ranging from machine learning to quantum physics. Their prevalence in modern scientific computing tasks highlights the need for efficient implementations and motivates the use of Graphics Processing Units (GPUs), given the exceptional performance that they have in linear algebra tasks.
This work evaluates the performance of current state-of-the-art GPU tensor algebra routines for dense and sparse data. We propose a set of guidelines for achieving optimal performance with cuTensor, NVIDIA’s proprietary dense tensor library. Additionally, we demonstrate that our Tensor Times Matrix implementation matches and also, in some cases, exceeds the performance of cuTensor while also utilizing 33% less memory. Furthermore, we show that our approach delivers an up to 2.5-fold increase in throughput for memory-bound tensor operations, such as the Khatri-Rao product. We also implement a GPU-accelerated sparse Tucker decomposition based on the Compressed Sparse Fiber tensor format. Compared to other GPU implementations, our approach achieves a 59-fold speedup in executing the Higher Order Orthogonal Iteration algorithm used to compute the Tucker decomposition.
Hoya latifolia G. Don 1838
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya latifolia

description: Hoya latifolia G.Don
A General History of the Dichlamydeous Plants 4: 127 (Don 1837). — H. macrophylla Wight, Contributions to the Botany of India: 38 (Wight 1834), non Blume, Bijdragen tot de flora van Nederlandsch Indië: 1063 (Blume 1826).
Type material
Lectotype (designated by Rodda 2017) MALAYSIA • Penang; Wallich Asclepiad no. 138 (A = Wallich Catalogue 8161A); K000895124.
Isolectotype MALAYSIA • Same data as for the lectotype; CGE (two sheets, one of which also containing leaves of H. mitrata), E00179576, K000895125.
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 9, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
On the Internal Stability of Diffusively Coupled Multi-Agent Systems and the Dangers of Cancel Culture
Creators: name: Barkai, Gal
name: Mirkin, Leonid
name: Zelazo, Daniel
Publisher: name: arXiv
Year: 2022
Subjects: subject: Systems and Control (eess.SY)
subject: Optimization and Control (math.OC)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Mathematics

description: We study internal stability in the context of diffusively-coupled control architectures, common in multi-agent systems (i.e. the celebrated consensus protocol), for linear time-invariant agents. We derive a condition under which the system can not be stabilized by any controller from that class. In the finite-dimensional case the condition states that diffusive controllers cannot stabilize agents that share common unstable dynamics, directions included. This class always contains the group of homogeneous unstable agents, like integrators. We argue that the underlying reason is intrinsic cancellations of unstable agent dynamics by such controllers, even static ones, where directional properties play a key role. The intrinsic lack of internal stability explains the notorious behavior of some distributed control protocols when affected by measurement noise or exogenous disturbances.
description: 9 pages, 3 figure, accepted for publication by Automatica
Hoya lacunosa Blume
Creators: name: Rahayu, Sri
name: Rodda, Michele
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Hoya
Hoya lacunosa

description: Hoya lacunosa Blume
Bijdragen tot de flora van Nederlandsch Indië: 1063 (Blume 1826). — Otostemma lacunosum (Blume) Blume, Rumphia 4: 30 (Blume 1849b).
Original citation
“Circa Buitenzorg at arbores”.
Type material
Lectotype (designated by Rodda 2017) INDONESIA • “ Hoya lacunosa ”; L [sheet no. 898168–188].
description: Published as part of Rahayu, Sri & Rodda, Michele, 2019, Hoya of Sumatra, an updated checklist, three new species, and a new subspecies, pp. 1-23 in European Journal of Taxonomy 508 on page 9, DOI: 10.5852/ejt.2019.508, http://zenodo.org/record/2612875
Eupolybothrus grossipes C.L. Koch 1847
Creators: name: Pavel Stoev
Publisher: name: Zenodo
Year: 2001
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Chilopoda
Lithobiomorpha
Lithobiidae
Eupolybothrus
Eupolybothrus grossipes

description: Eupolybothrus grossipes (C.L. Koch, 1847) group
Material examined: Shar planina Mts. 1 fm., near Leshnitza Chalet and Krivoshijska River, 1,480-2,200 m a.s.l., 20.07.1995, V. Sakalian, G. Blagoev & A. Lapeva leg.
Remarks. This single female very much resembles E. grossipes, but without enough specimens at disposal, it could not be reliably determined.
description: Published as part of Pavel Stoev, 2001, On the centipedes (Chilopoda) of the Republic of Macedonia, pp. 93-107 in Historia naturalis bulgarica 13 on page 98
Reconstructing random pictures
Creators: name: Narayanan, Bhargav
name: Yap, Corrine
Publisher: name: arXiv
Year: 2022
Subjects: subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60C05 (Primary), 60K35, 68R15 (Secondary)

description: Given a random binary picture $P_n$ of size $n$, i.e., an $n\times n$ grid filled with zeros and ones uniformly at random, when is it possible to reconstruct $P_n$ from its $k$-deck, i.e., the multiset of all its $k\times k$ subgrids? We demonstrate ``two-point concentration'' for the reconstruction threshold by showing that there is an integer $k_c(n) \sim (2 \log n)^{1/2}$ such that if $k > k_c$, then $P_n$ is reconstructible from its $k$-deck with high probability, and if $k < k_c$, then with high probability, it is impossible to reconstruct $P_n$ from its $k$-deck. The proof of this result uses a combination of interface-exploration arguments and entropic arguments.
description: v3: 9 figures, 23 pages, substantial additions made to the presentation of main proofs; final version appearing in RSA
Photocurrent as a multi-physics diagnostic of quantum materials
Creators: name: Ma, Qiong
name: Kumar, Roshan Krishna
name: Xu, Su-Yang
name: Koppens, Frank H. L.
name: Song, Justin C. W.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The photoexcitation life-cycle from incident photon (and creation of photoexcited electron hole pair) to ultimate extraction of electrical current is a complex multi-physics process spanning across a range of spatio-temporal scales of quantum materials. While often viewed through a device-technology lens, photocurrent is a key observable of the life-cycle that is sensitive to a myriad of physical processes across these scales. As a result, photocurrent is emerging as a versatile probe of electronic states, Bloch band quantum geometry, quantum kinetic processes, and device characteristics of quantum materials. This review outlines the key multi-physics principles of photocurrent diagnostics. In particular, we describe how the fundamental link between light-matter interaction and quantum geometry renders photocurrent a wavefunction-sensitive probe capable of resolving bandstructure and characterizing topological materials. We further highlight the sensitivity of the photoexcitation life-cycle to relaxational processes which in turn enables photocurrent to disentangle distinct types of carrier scattering that can range from femtosecond to nanosecond timescales. We survey the intrinsically nonlocal character of photocurrent collection that allows new types remote sensing protocols and photocurrent nanoscopy. These distinctive features underscore photocurrent diagnostics as a novel multi-physics probe for a growing class of quantum materials with properties governed by physics spanning multiple spatio-temporal scales.
description: original submitted version