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51. Standards for Graph Algorithm Primitives

Author

Mattson, Tim, Bader, David, Berry, Jon, Buluc, Aydin, Dongarra, Jack, Faloutsos, Christos, Feo, John, Gilbert, John, Gonzalez, Joseph, Hendrickson, Bruce, Kepner, Jeremy, Leiserson, Charles, Lumsdaine, Andrew, Padua, David, Poole, Stephen, Reinhardt, Steve, Stonebraker, Mike, Wallach, Steve, and Yoo, Andrew

Subjects
Computer Science - Mathematical Software, Computer Science - Discrete Mathematics, Computer Science - Data Structures and Algorithms
Abstract

It is our view that the state of the art in constructing a large collection of graph algorithms in terms of linear algebraic operations is mature enough to support the emergence of a standard set of primitive building blocks. This paper is a position paper defining the problem and announcing our intention to launch an open effort to define this standard., Comment: 2 pages, IEEE HPEC 2013

Published
2014
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55. Triangle Counting Through Cover-Edges

Author

Bader, David A., primary, Li, Fuhuan, additional, Ganeshan, Anya, additional, Gundogdu, Ahmet, additional, Lew, Jason, additional, Rodriguez, Oliver Alvarado, additional, and Du, Zhihui, additional

Published
2023
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56. Epigenetic loss of AOX1 expression via EZH2 leads to metabolic deregulations and promotes bladder cancer progression

Author

Vantaku, Venkatrao, Putluri, Vasanta, Bader, David A., Maity, Suman, Ma, Jing, Arnold, James M., Rajapakshe, Kimal, Donepudi, Sri Ramya, von Rundstedt, Friedrich-Carl, Devarakonda, Vaishnavi, Dubrulle, Julien, Karanam, Balasubramanyam, McGuire, Sean E., Stossi, Fabio, Jain, Abhinav K., Coarfa, Cristian, Cao, Qi, Sikora, Andrew G., Villanueva, Hugo, Kavuri, Shyam M., Lotan, Yair, Sreekumar, Arun, and Putluri, Nagireddy

Published
2020
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57. Correction: Epigenetic loss of AOX1 expression via EZH2 leads to metabolic deregulations and promotes bladder cancer progression

Author

Vantaku, Venkatrao, Putluri, Vasanta, Bader, David A., Maity, Suman, Ma, Jing, Arnold, James M., Rajapakshe, Kimal, Donepudi, Sri Ramya, von Rundstedt, Friedrich-Carl, Devarakonda, Vaishnavi, Dubrulle, Julien, Karanam, Balasubramanyam, McGuire, Sean E., Stossi, Fabio, Jain, Abhinav K., Coarfa, Cristian, Cao, Qi, Sikora, Andrew G., Villanueva, Hugo, Kavuri, Shyam M., Lotan, Yair, Sreekumar, Arun, and Putluri, Nagireddy

Published
2020
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59. Sustainable Software Development for Next-Gen Sequencing (NGS) Bioinformatics on Emerging Platforms

Author

Swenson, Shel, Simmhan, Yogesh, Prasanna, Viktor, Parashar, Manish, Riedy, Jason, Bader, David, and Vuduc, Richard

Subjects
Computer Science - Computational Engineering, Finance, and Science, Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between the potential of this technology and the development of computational methods to realize this potential. Bridging this gap holds possibilities for broad impacts toward multiple grand challenges and offers unprecedented opportunities for software innovation and research. We argue that NGS-enabled applications need a critical mass of sustainable software to benefit from emerging computing platforms' transformative potential. Accumulating the necessary critical mass will require leaders in computational biology, bioinformatics, computer science, and computer engineering work together to identify core opportunity areas, critical software infrastructure, and software sustainability challenges. Furthermore, due to the quickly changing nature of both bioinformatics software and accelerator technology, we conclude that creating sustainable accelerated bioinformatics software means constructing a sustainable bridge between the two fields. In particular, sustained collaboration between domain developers and technology experts is needed to develop the accelerated kernels, libraries, frameworks and middleware that could provide the needed flexible link from NGS bioinformatics applications to emerging platforms., Comment: 4 pages

Published
2013

60. A Brief Study of Open Source Graph Databases

Author

McColl, Rob, Ediger, David, Poovey, Jason, Campbell, Dan, and Bader, David

Subjects
Computer Science - Databases, Computer Science - Data Structures and Algorithms, Computer Science - Software Engineering
Abstract

With the proliferation of large irregular sparse relational datasets, new storage and analysis platforms have arisen to fill gaps in performance and capability left by conventional approaches built on traditional database technologies and query languages. Many of these platforms apply graph structures and analysis techniques to enable users to ingest, update, query and compute on the topological structure of these relationships represented as set(s) of edges between set(s) of vertices. To store and process Facebook-scale datasets, they must be able to support data sources with billions of edges, update rates of millions of updates per second, and complex analysis kernels. These platforms must provide intuitive interfaces that enable graph experts and novice programmers to write implementations of common graph algorithms. In this paper, we explore a variety of graph analysis and storage platforms. We compare their capabil- ities, interfaces, and performance by implementing and computing a set of real-world graph algorithms on synthetic graphs with up to 256 million edges. In the spirit of full disclosure, several authors are affiliated with the development of STINGER., Comment: WSSSPE13, 4 Pages, 18 Pages with Appendix, 25 figures

Published
2013

63. The kinetochore protein, CENPF, is mutated in human ciliopathy and microcephaly phenotypes

Author

Waters, Aoife M, Asfahani, Rowan, Carroll, Paula, Bicknell, Louise, Lescai, Francesco, Bright, Alison, Chanudet, Estelle, Brooks, Anthony, Christou-Savina, Sonja, Osman, Guled, Walsh, Patrick, Bacchelli, Chiara, Chapgier, Ariane, Vernay, Bertrand, Bader, David M, Deshpande, Charu, O' Sullivan, Mary, Ocaka, Louise, Stanescu, Horia, Stewart, Helen S, Hildebrandt, Friedhelm, Otto, Edgar, Johnson, Colin A, Szymanska, Katarzyna, Katsanis, Nicholas, Davis, Erica, Kleta, Robert, Hubank, Mike, Doxsey, Stephen, Jackson, Andrew, Stupka, Elia, Winey, Mark, and Beales, Philip L

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Pediatric, Human Genome, Congenital Structural Anomalies, Aetiology, 2.1 Biological and endogenous factors, Animals, Centrioles, Chromosomal Proteins, Non-Histone, Cilia, Exome, Female, Fetus, Genetics, Medical, HEK293 Cells, High-Throughput Nucleotide Sequencing, Humans, Male, Mice, Microcephaly, Microfilament Proteins, Mutation, NIH 3T3 Cells, Pedigree, Pregnancy, Zebrafish, CENPF, Ciliopathy, Clinical genetics, Molecular genetics, Medical and Health Sciences, Genetics & Heredity, Clinical sciences
Abstract

BackgroundMutations in microtubule-regulating genes are associated with disorders of neuronal migration and microcephaly. Regulation of centriole length has been shown to underlie the pathogenesis of certain ciliopathy phenotypes. Using a next-generation sequencing approach, we identified mutations in a novel centriolar disease gene in a kindred with an embryonic lethal ciliopathy phenotype and in a patient with primary microcephaly.Methods and resultsWhole exome sequencing data from a non-consanguineous Caucasian kindred exhibiting mid-gestation lethality and ciliopathic malformations revealed two novel non-synonymous variants in CENPF, a microtubule-regulating gene. All four affected fetuses showed segregation for two mutated alleles [IVS5-2A>C, predicted to abolish the consensus splice-acceptor site from exon 6; c.1744G>T, p.E582X]. In a second unrelated patient exhibiting microcephaly, we identified two CENPF mutations [c.1744G>T, p.E582X; c.8692 C>T, p.R2898X] by whole exome sequencing. We found that CENP-F colocalised with Ninein at the subdistal appendages of the mother centriole in mouse inner medullary collecting duct cells. Intraflagellar transport protein-88 (IFT-88) colocalised with CENP-F along the ciliary axonemes of renal epithelial cells in age-matched control human fetuses but did not in truncated cilia of mutant CENPF kidneys. Pairwise co-immunoprecipitation assays of mitotic and serum-starved HEKT293 cells confirmed that IFT88 precipitates with endogenous CENP-F.ConclusionsOur data identify CENPF as a new centriolar disease gene implicated in severe human ciliopathy and microcephaly related phenotypes. CENP-F has a novel putative function in ciliogenesis and cortical neurogenesis.

Published
2015

66. Approximating Personalized Katz Centrality in Dynamic Graphs

Author

Nathan, Eisha, Bader, David A., Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Wyrzykowski, Roman, editor, Dongarra, Jack, editor, Deelman, Ewa, editor, and Karczewski, Konrad, editor

Published
2018
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70. On the random access performance of Cell Broadband Engine with graph analysis application

Author

Chen, Mingyu and Bader, David A.

Subjects
Computer Science - Computational Engineering, Finance, and Science, Computer Science - Performance, D.1.3, C.4
Abstract

The Cell Broad Engine (BE) Processor has unique memory access architecture besides its powerful computing engines. Many computing-intensive applications have been ported to Cell/BE successfully. But memory-intensive applications are rarely investigated except for several micro benchmarks. Since Cell/BE has powerful software visible DMA engine, this paper studies on whether Cell/BE is suit for applica- tions with large amount of random memory accesses. Two benchmarks, GUPS and SSCA#2, are used. The latter is a rather complex one that in representative of real world graph analysis applications. We find both benchmarks have good performance on Cell/BE based IBM QS20/22. Com- pared with 2 conventional multi-processor systems with the same core/thread number, GUPS is about 40-80% fast and SSCA#2 about 17-30% fast. The dynamic load balanc- ing and software pipeline for optimizing SSCA#2 are intro- duced. Based on the experiment, the potential of Cell/BE for random access is analyzed in detail as well as its limita- tions of memory controller, atomic engine and TLB manage- ment.Our research shows although more programming effort are needed, Cell/BE has the potencial for irregular memory access applications., Comment: 8 pages, 10 figures

Published
2011

71. Unintended Consequence: Diversity as a Casualty of Eliminating United States Medical Licensing Examination Step 1 Scores

Author

Campos, Felipe M., primary, Grimm, Lars J., additional, Maxfield, Charles M., additional, Amin, Sabina, additional, Bader, David, additional, Beckett, Brooke, additional, Carter, Kevin, additional, Chapman, Teresa, additional, Chow, Bernard, additional, Derylo, Amanda, additional, Flaherty, Francis, additional, Fox, Michael, additional, Gould, Jennifer, additional, Groves, Robert, additional, Heitkamp, Darel, additional, Heymann, John, additional, Ho, Christopher, additional, Hughes, Marion, additional, Hull, Nathan, additional, Jafroodifar, Abtin, additional, Jay, Ann, additional, Kamer, Aaron, additional, Kelly, Hillary, additional, Kennedy, Tabassum, additional, Knippa, Emily, additional, Koontz, Nicholas, additional, Marx, Mary, additional, Milburn, James, additional, Mills, Megan, additional, Molina, Marco, additional, Morgan, Desiree, additional, Morgan, Rustain, additional, Omofoye, Toma, additional, Peterson, Ryan, additional, Romanelli, Donald, additional, Schubert, Johanna, additional, Schweitzer, Andrew, additional, Seekins, Jayne, additional, Stanfill, John, additional, Udager, Kara, additional, Vatakencherry, Geogy, additional, Wang, Morlie, additional, Weidenhaft, Mandy, additional, Williamson, Clint, additional, Wojtowycz, Andrij, additional, and Zarzour, Jessica, additional

Published
2023
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76. Rehospitalization Through Childhood and Adolescence: Association with Neonatal Morbidities in Infants of Very Low Birth Weight

Author

Heymann, Eli, Zangen, Shmuel, Smolkin, Tatyana, Mimouni, Francis, Bader, David, Rothschild, Avi, Strauss, Zipora, Felszer, Clari, Jeryes, Jamalia, Tov-Friedman, Smadar Even, Bar-Oz, Benjamin, Feldman, Michael, Saad, Nizar, Flidel-Rimon, Orna, Weisbrod, Meir, Lubin, Daniel, Litmanovitz, Ita, Kugelman, Amir, Shinwell, Eric, Klinger, Gil, Nijim, Yousif, Golan, Agneta, Mandel, Dror, Fleisher-Sheffer, Vered, Kohelet, David, Bakhrakh, Lev, Lerner-Geva, Liat, Kuint, Jacob, Chodick, Gabriel, Boyko, Valentina, Shalev, Varda, and Reichman, Brian

Published
2017
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78. Evaluation of a WRF dynamical downscaling simulation over California

Author

Caldwell, Peter, Chin, Hung-Neng S., Bader, David C., and Bala, Govindasamy

Subjects
Earth Sciences, Meteorology/Climatology
Abstract

This paper presents results from a 40 year Weather Research and Forecasting (WRF) based dynamical downscaling experiment performed at 12 km horizontal grid spacing, centered on the state of California, and forced by a 1° × 1.25° finite-volume current-climate Community Climate System Model ver. 3 (CCSM3) simulation. In-depth comparisons between modeled and observed regional-average precipitation, 2 m temperature, and snowpack are performed. The regional model reproduces the spatial distribution of precipitation quite well, but substantially overestimates rainfall along windward slopes. This is due to strong overprediction of precipitation intensity; precipitation frequency is actually underpredicted by the model. Moisture fluxes impinging on the coast seem to be well-represented over California, implying that precipitation bias is caused by processes internal to WRF. Positive-definite moisture advection and use of the Grell cumulus parameterization result in some decrease in precipitation bias, but other sources are needed to explain the full bias magnitude. Surface temperature is well simulated in all seasons except summer, when overly-dry soil moisture results in a several degree warm bias in both CCSM3 and WRF. Additionally, coastal temperatures appear to be too warm due to a coastal sea surface temperature bias inherited from CCSM3. Modeled snowfall/snowmelt agrees quite well with observations, but snow water equivalent is found to be much too low due to monthly reinitialization of all regional model fields from CCSM3 values.

Published
2009

85. Neonatal Outcomes of Very Low Birth Weight and Very Preterm Neonates: An International Comparison

Author

Badawi, Nadia, Marshall, Peter, Craven, Paul, Simmer, Karen, Stack, Jacqueline, Casalaz, Dan, Carse, Elizabeth, Cooke, Lucy, Shingde, Vijay, Cartwright, David, Hunt, Rod, Kilburn, Charles, Dargaville, Peter, Lui, Kei, Paradisis, Mary, Rieger, Ingrid, Kuschel, Carl, Numa, Andrew, Carlisle, Hazel, Koh, Guan, Andersen, Chad, Luig, Melissa, Austin, Nicola, Broadbent, Roland, Mildenhall, Lindsay, Battin, Malcolm, Bourchier, David, Richardson, Vaughan, Synnes, Anne, Rouvinez-Bouali, Nicole, Piedboeuf, Bruno, Bulleid, Barbara, Yee, Wendy, Singhal, Nalini, Harrison, Adele, Tan-Dy, Cherrie, Shivananda, Sandesh, Tan, Kenneth, James, Andrew, Seshia, Molly, Barrington, Keith, Lefebvre, Francine, McMillan, Doug, Andrews, Wayne, Kovacs, Lajos, Dow, Kimberly, Clarke, Maxine, Riley, Patricia, Shah, Prakesh, Ohlsson, Arne, Aziz, Khalid, Peliowski, Abraham, Cieslak, Zenon, Sorokan, Todd, Kalapesi, Zarin, Ninan, Abraham, Sankaran, Koravangattu, Faucher, Daniel, Cronin, Gerarda, Canning, Roderick, da Silva, Orlando, Lee, David, Ojah, Cecil, Dunn, Michael, Heymann, Eli, Zangen, Shmuel, Kushnir, Amir, Mimouni, Francis, Bader, David, Rothschild, Avi, Strauss, Zipora, Felszer, Clari, Jeryes, Jamalia, Even Tov-Friedman, Smadar, Bar-Oz, Benjamin, Feldman, Michael, Saad, Nizar, Flidel-Rimon, Orna, Weisbrod, Meir, Lubin, Daniel, Litmanovitz, Ita, Blazer, Shraga, Shinwell, Eric, Sirota, Leah, Nijim, Yousif, Golan, Agneta, Mandel, Dror, Fleisher-Sheffer, Vered, Kohelet, David, Bakhrakh, Lev, Hattori, Satoshi, Konishi, Shohei, Amizuka, Takasuke, Kasai, Takeo, Takahasi, Ritsuko, Arai, Hirokazu, Sato, Maki, Miyazono, Yayoi, Shimizu, Junichi, Suzumura, Hiroshi, Kono, Yumi, Inoue, Takahiro, Miyabayashi, Hiroshi, Sobajima, Hisanori, Ishiguro, Rika, Sato, Hiroyuki, Totsu, Satsuki, Ishii, Nozomi, Hosono, Shigeharu, Shiraishi, Mika, Miura, Humihiro, Nakao, Atsushi, Yoda, Hitoshi, Shimizu, Mitsumasa, Seki, Kazuo, Itani, Yasuhumi, Suzuki, Keiji, Nemoto, Atsushi, Nakamura, Tomohiko, Wada, Masaki, Nagayama, Yoshihisa, Numata, Osamu, Futatani, Takeshi, Ueno, Yasuhisa, Iwai, Kazuyuki, Kono, Yoshinori, Ooki, Shigeru, Nakazawa, Yusuke, Suzuki, Chizuko, Tanaka, Taihei, Bonno, Motoki, Nakamura, Kenji, Kihara, Minako, Sano, Hiroyuki, Shiraishi, Atsushi, Ohashi, Atsushi, Ichiba, Hiroyuki, Sumi, Kiyoaki, Yoshimoto, Seiji, Takahashi, Yukihiro, Okutani, Takahiro, Miura, Masumi, Kato, Fumihide, Watabe, Shinichi, Kageyama, Misao, Fukuhara, Rie, Hayashitani, Michiko, Hasegawa, Keiko, Koyano, Kosuke, Kobayashi, Shoko, Akiyoshi, Shinosuke, Nakata, Yusei, Kanda, Takeshi, Tadashi, Hisano, Kanda, Hiroshi, Nakamura, Masaki, Matsumoto, Naoko, Ochiai, Masayuki, Aoki, Mikihiro, Kawase, Akihiko, Iida, Koichi, Ishihara, Chie, Kohama, Moriyasu, Seara, M<ce:sup loc='post">a</ce:sup> José Fernández, Bermúdez, José M<ce:sup loc='post">a</ce:sup> Fraga, Martínez Gutiérrez, Andrés, Martínez Ayúcar, María Mercedes, Díaz, Carolina Vizcaíno, Quiles Durá, José Luis, González Santacruz, María, Siguile, M<ce:sup loc='post">a</ce:sup> Anne Feret, Fernández, Adela Rodríguez, Fernández Colomer, Belén, García López, Enrique, Figuera Aloy, Josep, Botet Mussons, Francesc, Anquela Sanz, Israel, Galiana, Gemma Ginovart, Moliner Calderon, Elisenda, Pujol, Antonio Natal, Vives, Alicia Mirada, Iriondo Sanz, Martín, Porta, Roser, Cogul, Eva Capdevila, Castells Vilella, Laura, Álvarez, Bruno Alonso, Montero Macarro, José María, Barrio Sacristán, Ana R., Cuesta, M<ce:sup loc='post">a</ce:sup> Jesús López, Tardío, Ortiz, Sánchez Puerta, Eugenia Valls, Benavente Fernández, Isabel, Romero, Juan Mena, Martinez Gimenez, María Dolores, Olmos, Ramón Aguilera, Segura, Ricardo Tosca, Cabañas, Juana M<ce:sup loc='post">a</ce:sup> Guzmán, Muñoz, M<ce:sup loc='post">a</ce:sup> Dolores Huertas, Trujillo, Alberto, Moltó Ripoll, Luis Fidel, Hurtado Suazo, José Antonio, Aldea Romero, Ana Elena, Grisolía, Luis Paisán, Garrido Ocana, Ana Isabel, Soblechero, Eduardo Garcia, Ruiz del Prado, M<ce:sup loc='post">a</ce:sup> Yolanda, Díez, Inés Esteba, González-Luis, Gema E., García-Muñoz Rodrigo, Fermín, Iglesias, Emilio Álvaro, Calvo, Fernando Fernandez, Solé Mir, Eduard, Martí, Jordi Garcia, Ortiz Movilla, Roberto, Vilaplana, Lucía Cabanillas, San Miguel, Marta García, Martín, Isabel Llana, Díaz, María Fernández, Pérez Rodríguez, Jesús, Salas, Sofía, Labian, Carmen Muñoz, González Armengod, Carmen, Comeche, Laura Domingo, Sánchez Tamayo, Tomás, García del Río, Manuel, Alonso Gallego, José Ángel, Lloreda Garcia, José María, González, Javier Vilas, Ocampo, Insunza, Nieves Balado, García González, Pilar, Granero Asencio, Mercedes, Sanz, Antonia López, Díaz, Carmen Macías, Ferrari Cortés, Araceli, Fuster Jorge, Pedro Amadeo, López Mendoza, Santiago, Ramírez, Sabina Romero, Font, M<ce:sup loc='post">a</ce:sup> del Mar Albújar, de Ureta Huertas, Alicia, Plana, Antonio Arroyos, Capell, Javier Estañ, Roqués, Vicente, Morcillo, F., Marín, Sara, Omaña, María Fernanda, Iturriaga, Gabriel Saitua, Kofron, Jiri, Brodd, Katarina Strand, Odlind, Andreas, Alberg, Lars, Arwehed, Sofia, Engström, Eva, Kasemo, Anna, Ekelund, Charlotte, Åhman, Lars, Ingemarsson, Fredrik, Österdahl, Laura, Thurn, Pernilla, Albinsson, Eva, Selander, Bo, Lundberg, Fredrik, Heimdahl, Ingela, Hafström, Ola, Wejryd, Erik, Kuusima-Löfbom, Johanna, Lund, Ellen-Elisabeth, Thorén, Annelie, Hallberg, Boubou, Broström, Eva Berggren, Hertzberg, Torbjörn, Stjernstedt, Björn, Robinson, Johan, Farooqi, Aijaz, Normann, Erik, Fredriksson, Magnus, Palm, Anders, Hedblom, Åsa, Sjöberg, Kenneth, Thorbjörnsson, Leif, Ohlin, Andreas, Florell, Rein, Smedsaas-Löfvenberg, Agneta, Meyer, Philipp, Anderegg, Claudia, Schulzke, Sven, Nelle, Mathias, Wagner, Bendicht, Bär, Walter, Kaczala, Grégoire, Pfister, Riccardo E., Tolsa, Jean-François, Roth, Matthias, Berger, Thomas M., Laubscher, Bernhard, Malzacher, Andreas, Micallef, John P., Hegi, Lukas, Bassler, Dirk, Arlettaz, Romaine, Bernet, Vera, Bag, Santanu, Kefas, Jonathan, Rackham, Oliver, Thirumurgan, Arumugavelu, Yoxall, Bill, McBride, Tim, Webb, Delyth, Amegavie, Laweh, Hassan, Ahmed, Ambadkar, Priyadarshan, Dyke, Mark, Babiker, Seif, Rubin, Susan, Ogilvy-Stuart, Amanda, Panasa, Nagesh, Settle, Paul, Moise, Jonathan, Edi-Osagie, Ngozi, Heal, Carrie, Birch, Jacqeline, Hasib, Abdul, Soe, Aung, Kumar, Niraj, Kisat, Hamudi, Vasu, Vimal, Lama, Meera, Gupta, Richa, Rawlingson, Chris, Wickham, Tim, Schwarz, Karin, Sommen, Van, Watkin, Sara, Gupta, Aashish, Aladangady, Narendra, Ali, Imdad, Alsford, Lesley, Mannan, Khalid, Rainer, Ebel, Wilson, Nicholas, Thomas, Mark, Mathur, Ramnik, Cruwys, Michele, Godambe, Sunit, Watts, Timothy, Kuna, Jauro, Chang, John, Filkin, Jon, Huddy, Charlotte, Shephard, Ruth, Zieba, Krzystof, Rao, Patti, Currie, Andrew, Manzoor, Azhar, Ahmed, Munir, Simmons, Phil, Nycyk, Julie, Gallagher, Andrew, Halahakoon, Chrisantha, Deshpande, Sanjeev, Mohite, Anand, Palmer, Kate, Gibson, Alan, Garbash, Mehdi, Lal, Mithilesh, Abu-Harb, Majd, McKeon-Carter, Róisín, Selter, Michael, Munyard, Paul, Lewis, Vaughan, Raman, Mala, Whincup, Graham, Mallik, Abdus, Amess, Philip, Godden, Charles, Reynolds, Peter, Misra, Indranil, Shettihalli, Naveen, De Halpert, Peter, Salgia, Sanjay, Sanghavi, Rekha, Wigfield, Ruth, Deketelaere, Abby, Khashu, Minesh, Hall, Michael, Groves, Charlotte, Brown, Nick, Brennan, Nick, Vamvakiti, Katia, Ratnayaka, Mal, Pirie, Simon, Jones, Stephen, Mannix, Paul, Harding, David, Eaton, Megan, Gibson, David, Miall, Lawrence, Shah, Prakesh S., Sjörs, Gunnar, Mirea, Lucia, Reichman, Brian, Adams, Mark, Modi, Neena, Darlow, Brian A., Kusuda, Satoshi, San Feliciano, Laura, Yang, Junmin, Håkansson, Stellan, Mori, Rintaro, Figueras-Aloy, Josep, and Lee, Shoo K.

Published
2016
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92. ClimSim: An open large-scale dataset for training high-resolution physics emulators in hybrid multi-scale climate simulators

Author

Yu, Sungduk, Hannah, Walter M., Peng, Liran, Bhouri, Mohamed Aziz, Gupta, Ritwik, Lin, Jerry, Lütjens, Björn, Will, Justus C., Beucler, Tom, Harrop, Bryce E., Hillman, Benjamin R., Jenney, Andrea M., Ferretti, Savannah L., Liu, Nana, Anandkumar, Anima, Brenowitz, Noah D., Eyring, Veronika, Gentine, Pierre, Mandt, Stephan, Pathak, Jaideep, Vondrick, Carl, Yu, Rose, Zanna, Laure, Abernathey, Ryan P., Ahmed, Fiaz, Bader, David C., Baldi, Pierre, Barnes, Elizabeth A., Behrens, Gunnar, Bretherton, Christopher S., Busecke, Julius J. M., Caldwell, Peter M., Chuang, Wayne, Han, Yilun, Huang, Yu, Iglesias-Suarez, Fernando, Jantre, Sanket, Kashinath, Karthik, Khairoutdinov, Marat, Kurth, Thorsten, Lutsko, Nicholas J., Ma, Po-Lun, Mooers, Griffin, Neelin, J. David, Randall, David A., Shamekh, Sara, Subramaniam, Akshay, Taylor, Mark A., Urban, Nathan M., Yuval, Janni, Zhang, Guang J., Zheng, Tian, and Pritchard, Michael S.

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Physics - Atmospheric and Oceanic Physics, Atmospheric and Oceanic Physics (physics.ao-ph), FOS: Physical sciences, Machine Learning (cs.LG)
Abstract

Modern climate projections lack adequate spatial and temporal resolution due to computational constraints. A consequence is inaccurate and imprecise prediction of critical processes such as storms. Hybrid methods that combine physics with machine learning (ML) have introduced a new generation of higher fidelity climate simulators that can sidestep Moore's Law by outsourcing compute-hungry, short, high-resolution simulations to ML emulators. However, this hybrid ML-physics simulation approach requires domain-specific treatment and has been inaccessible to ML experts because of lack of training data and relevant, easy-to-use workflows. We present ClimSim, the largest-ever dataset designed for hybrid ML-physics research. It comprises multi-scale climate simulations, developed by a consortium of climate scientists and ML researchers. It consists of 5.7 billion pairs of multivariate input and output vectors that isolate the influence of locally-nested, high-resolution, high-fidelity physics on a host climate simulator's macro-scale physical state. The dataset is global in coverage, spans multiple years at high sampling frequency, and is designed such that resulting emulators are compatible with downstream coupling into operational climate simulators. We implement a range of deterministic and stochastic regression baselines to highlight the ML challenges and their scoring. The data (https://huggingface.co/datasets/LEAP/ClimSim_high-res) and code (https://leap-stc.github.io/ClimSim) are released openly to support the development of hybrid ML-physics and high-fidelity climate simulations for the benefit of science and society.

Published
2023
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94. Measuring the Sensitivity of Graph Metrics to Missing Data

Author

Zakrzewska, Anita, Bader, David A., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Wyrzykowski, Roman, editor, Dongarra, Jack, editor, Karczewski, Konrad, editor, and Waśniewski, Jerzy, editor

Published
2014
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95. A Lin-Kernighan Heuristic for the DCJ Median Problem of Genomes with Unequal Contents

Author

Yin, Zhaoming, Tang, Jijun, Schaeffer, Stephen W., Bader, David A., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Cai, Zhipeng, editor, Zelikovsky, Alex, editor, and Bourgeois, Anu, editor

Published
2014
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