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4,538 results on '"Egyed A"'

1. Model-based Maintenance and Evolution with GenAI: A Look into the Future

Author

Marchezan, Luciano, Assunção, Wesley K. G., Herac, Edvin, and Egyed, Alexander

Subjects
Computer Science - Software Engineering
Abstract

Model-Based Engineering (MBE) has streamlined software development by focusing on abstraction and automation. The adoption of MBE in Maintenance and Evolution (MBM&E), however, is still limited due to poor tool support and a lack of perceived benefits. We argue that Generative Artificial Intelligence (GenAI) can be used as a means to address the limitations of MBM&E. In this sense, we argue that GenAI, driven by Foundation Models, offers promising potential for enhancing MBM&E tasks. With this possibility in mind, we introduce a research vision that contains a classification scheme for GenAI approaches in MBM&E considering two main aspects: (i) the level of augmentation provided by GenAI and (ii) the experience of the engineers involved. We propose that GenAI can be used in MBM&E for: reducing engineers' learning curve, maximizing efficiency with recommendations, or serving as a reasoning tool to understand domain problems. Furthermore, we outline challenges in this field as a research agenda to drive scientific and practical future solutions. With this proposed vision, we aim to bridge the gap between GenAI and MBM&E, presenting a structured and sophisticated way for advancing MBM&E practices.

Published
2024

2. Contemporary Software Modernization: Perspectives and Challenges to Deal with Legacy Systems

Author

Assunção, Wesley K. G., Marchezan, Luciano, Egyed, Alexander, and Ramler, Rudolf

Subjects
Computer Science - Software Engineering
Abstract

Software modernization is an inherent activity of software engineering, as technology advances and systems inevitably become outdated. The term "software modernization" emerged as a research topic in the early 2000s, with a differentiation from traditional software evolution. Studies on this topic became popular due to new programming paradigms, technologies, and architectural styles. Given the pervasive nature of software today, modernizing legacy systems is paramount to provide users with competitive and innovative products and services. Despite the large amount of work available in the literature, there are significant limitations: (i) proposed approaches are strictly specific to one scenario or technology, lacking flexibility; (ii) most of the proposed approaches are not aligned with the current modern software development scenario; and (iii) due to a myriad of proposed modernization approaches, practitioners may be misguided on how to modernize legacies. In this work, our goal is to call attention to the need for advances in research and practices toward a well-defined software modernization domain. The focus is on enabling organizations to preserve the knowledge represented in legacy systems while taking advantages of disruptive and emerging technologies. Based on this goal, we put the different perspectives of software modernization in the context of contemporary software development. We also present a research agenda with 10 challenges to motivate new studies.

Published
2024

3. Gemini 1.5: Unlocking multimodal understanding across millions of tokens of context

Author

Gemini Team, Georgiev, Petko, Lei, Ving Ian, Burnell, Ryan, Bai, Libin, Gulati, Anmol, Tanzer, Garrett, Vincent, Damien, Pan, Zhufeng, Wang, Shibo, Mariooryad, Soroosh, Ding, Yifan, Geng, Xinyang, Alcober, Fred, Frostig, Roy, Omernick, Mark, Walker, Lexi, Paduraru, Cosmin, Sorokin, Christina, Tacchetti, Andrea, Gaffney, Colin, Daruki, Samira, Sercinoglu, Olcan, Gleicher, Zach, Love, Juliette, Voigtlaender, Paul, Jain, Rohan, Surita, Gabriela, Mohamed, Kareem, Blevins, Rory, Ahn, Junwhan, Zhu, Tao, Kawintiranon, Kornraphop, Firat, Orhan, Gu, Yiming, Zhang, Yujing, Rahtz, Matthew, Faruqui, Manaal, Clay, Natalie, Gilmer, Justin, Co-Reyes, JD, Penchev, Ivo, Zhu, Rui, Morioka, Nobuyuki, Hui, Kevin, Haridasan, Krishna, Campos, Victor, Mahdieh, Mahdis, Guo, Mandy, Hassan, Samer, Kilgour, Kevin, Vezer, Arpi, Cheng, Heng-Tze, de Liedekerke, Raoul, Goyal, Siddharth, Barham, Paul, Strouse, DJ, Noury, Seb, Adler, Jonas, Sundararajan, Mukund, Vikram, Sharad, Lepikhin, Dmitry, Paganini, Michela, Garcia, Xavier, Yang, Fan, Valter, Dasha, Trebacz, Maja, Vodrahalli, Kiran, Asawaroengchai, Chulayuth, Ring, Roman, Kalb, Norbert, Soares, Livio Baldini, Brahma, Siddhartha, Steiner, David, Yu, Tianhe, Mentzer, Fabian, He, Antoine, Gonzalez, Lucas, Xu, Bibo, Kaufman, Raphael Lopez, Shafey, Laurent El, Oh, Junhyuk, Hennigan, Tom, Driessche, George van den, Odoom, Seth, Lucic, Mario, Roelofs, Becca, Lall, Sid, Marathe, Amit, Chan, Betty, Ontanon, Santiago, He, Luheng, Teplyashin, Denis, Lai, Jonathan, Crone, Phil, Damoc, Bogdan, Ho, Lewis, Riedel, Sebastian, Lenc, Karel, Yeh, Chih-Kuan, Chowdhery, Aakanksha, Xu, Yang, Kazemi, Mehran, Amid, Ehsan, Petrushkina, Anastasia, Swersky, Kevin, Khodaei, Ali, Chen, Gowoon, Larkin, Chris, Pinto, Mario, Yan, Geng, Badia, Adria Puigdomenech, Patil, Piyush, Hansen, Steven, Orr, Dave, Arnold, Sebastien M. R., Grimstad, Jordan, Dai, Andrew, Douglas, Sholto, Sinha, Rishika, Yadav, Vikas, Chen, Xi, Gribovskaya, Elena, Austin, Jacob, Zhao, Jeffrey, Patel, Kaushal, Komarek, Paul, Austin, Sophia, Borgeaud, Sebastian, Friso, Linda, Goyal, Abhimanyu, Caine, Ben, Cao, Kris, Chung, Da-Woon, Lamm, Matthew, Barth-Maron, Gabe, Kagohara, Thais, Olszewska, Kate, Chen, Mia, Shivakumar, Kaushik, Agarwal, Rishabh, Godhia, Harshal, Rajwar, Ravi, Snaider, Javier, Dotiwalla, Xerxes, Liu, Yuan, Barua, Aditya, Ungureanu, Victor, Zhang, Yuan, Batsaikhan, Bat-Orgil, Wirth, Mateo, Qin, James, Danihelka, Ivo, Doshi, Tulsee, Chadwick, Martin, Chen, Jilin, Jain, Sanil, Le, Quoc, Kar, Arjun, Gurumurthy, Madhu, Li, Cheng, Sang, Ruoxin, Liu, Fangyu, Lamprou, Lampros, Munoz, Rich, Lintz, Nathan, Mehta, Harsh, Howard, Heidi, Reynolds, Malcolm, Aroyo, Lora, Wang, Quan, Blanco, Lorenzo, Cassirer, Albin, Griffith, Jordan, Das, Dipanjan, Lee, Stephan, Sygnowski, Jakub, Fisher, Zach, Besley, James, Powell, Richard, Ahmed, Zafarali, Paulus, Dominik, Reitter, David, Borsos, Zalan, Joshi, Rishabh, Pope, Aedan, Hand, Steven, Selo, Vittorio, Jain, Vihan, Sethi, Nikhil, Goel, Megha, Makino, Takaki, May, Rhys, Yang, Zhen, Schalkwyk, Johan, Butterfield, Christina, Hauth, Anja, Goldin, Alex, Hawkins, Will, Senter, Evan, Brin, Sergey, Woodman, Oliver, Ritter, Marvin, Noland, Eric, Giang, Minh, Bolina, Vijay, Lee, Lisa, Blyth, Tim, Mackinnon, Ian, Reid, Machel, Sarvana, Obaid, Silver, David, Chen, Alexander, Wang, Lily, Maggiore, Loren, Chang, Oscar, Attaluri, Nithya, Thornton, Gregory, Chiu, Chung-Cheng, Bunyan, Oskar, Levine, Nir, Chung, Timothy, Eltyshev, Evgenii, Si, Xiance, Lillicrap, Timothy, Brady, Demetra, Aggarwal, Vaibhav, Wu, Boxi, Xu, Yuanzhong, McIlroy, Ross, Badola, Kartikeya, Sandhu, Paramjit, Moreira, Erica, Stokowiec, Wojciech, Hemsley, Ross, Li, Dong, Tudor, Alex, Shyam, Pranav, Rahimtoroghi, Elahe, Haykal, Salem, Sprechmann, Pablo, Zhou, Xiang, Mincu, Diana, Li, Yujia, Addanki, Ravi, Krishna, Kalpesh, Wu, Xiao, Frechette, Alexandre, Eyal, Matan, Dafoe, Allan, Lacey, Dave, Whang, Jay, Avrahami, Thi, Zhang, Ye, Taropa, Emanuel, Lin, Hanzhao, Toyama, Daniel, Rutherford, Eliza, Sano, Motoki, Choe, HyunJeong, Tomala, Alex, Safranek-Shrader, Chalence, Kassner, Nora, Pajarskas, Mantas, Harvey, Matt, Sechrist, Sean, Fortunato, Meire, Lyu, Christina, Elsayed, Gamaleldin, Kuang, Chenkai, Lottes, James, Chu, Eric, Jia, Chao, Chen, Chih-Wei, Humphreys, Peter, Baumli, Kate, Tao, Connie, Samuel, Rajkumar, Santos, Cicero Nogueira dos, Andreassen, Anders, Rakićević, Nemanja, Grewe, Dominik, Kumar, Aviral, Winkler, Stephanie, Caton, Jonathan, Brock, Andrew, Dalmia, Sid, Sheahan, Hannah, Barr, Iain, Miao, Yingjie, Natsev, Paul, Devlin, Jacob, Behbahani, Feryal, Prost, Flavien, Sun, Yanhua, Myaskovsky, Artiom, Pillai, Thanumalayan Sankaranarayana, Hurt, Dan, Lazaridou, Angeliki, Xiong, Xi, Zheng, Ce, Pardo, Fabio, Li, Xiaowei, Horgan, Dan, Stanton, Joe, Ambar, Moran, Xia, Fei, Lince, Alejandro, Wang, Mingqiu, Mustafa, Basil, Webson, Albert, Lee, Hyo, Anil, Rohan, Wicke, Martin, Dozat, Timothy, Sinha, Abhishek, Piqueras, Enrique, Dabir, Elahe, Upadhyay, Shyam, Boral, Anudhyan, Hendricks, Lisa Anne, Fry, Corey, Djolonga, Josip, Su, Yi, Walker, Jake, Labanowski, Jane, Huang, Ronny, Misra, Vedant, Chen, Jeremy, Skerry-Ryan, RJ, Singh, Avi, Rijhwani, Shruti, Yu, Dian, Castro-Ros, Alex, Changpinyo, Beer, Datta, Romina, Bagri, Sumit, Hrafnkelsson, Arnar Mar, Maggioni, Marcello, Zheng, Daniel, Sulsky, Yury, Hou, Shaobo, Paine, Tom Le, Yang, Antoine, Riesa, Jason, Rogozinska, Dominika, Marcus, Dror, Badawy, Dalia El, Zhang, Qiao, Wang, Luyu, Miller, Helen, Greer, Jeremy, Sjos, Lars Lowe, Nova, Azade, Zen, Heiga, Chaabouni, Rahma, Rosca, Mihaela, Jiang, Jiepu, Chen, Charlie, Liu, Ruibo, Sainath, Tara, Krikun, Maxim, Polozov, Alex, Lespiau, Jean-Baptiste, Newlan, Josh, Cankara, Zeyncep, Kwak, Soo, Xu, Yunhan, Chen, Phil, Coenen, Andy, Meyer, Clemens, Tsihlas, Katerina, Ma, Ada, Gottweis, Juraj, Xing, Jinwei, Gu, Chenjie, Miao, Jin, Frank, Christian, Cankara, Zeynep, Ganapathy, Sanjay, Dasgupta, Ishita, Hughes-Fitt, Steph, Chen, Heng, Reid, David, Rong, Keran, Fan, Hongmin, van Amersfoort, Joost, Zhuang, Vincent, Cohen, Aaron, Gu, Shixiang Shane, Mohananey, Anhad, Ilic, Anastasija, Tobin, Taylor, Wieting, John, Bortsova, Anna, Thacker, Phoebe, Wang, Emma, Caveness, Emily, Chiu, Justin, Sezener, Eren, Kaskasoli, Alex, Baker, Steven, Millican, Katie, Elhawaty, Mohamed, Aisopos, Kostas, Lebsack, Carl, Byrd, Nathan, Dai, Hanjun, Jia, Wenhao, Wiethoff, Matthew, Davoodi, Elnaz, Weston, Albert, Yagati, Lakshman, Ahuja, Arun, Gao, Isabel, Pundak, Golan, Zhang, Susan, Azzam, Michael, Sim, Khe Chai, Caelles, Sergi, Keeling, James, Sharma, Abhanshu, Swing, Andy, Li, YaGuang, Liu, Chenxi, Bostock, Carrie Grimes, Bansal, Yamini, Nado, Zachary, Anand, Ankesh, Lipschultz, Josh, Karmarkar, Abhijit, Proleev, Lev, Ittycheriah, Abe, Yeganeh, Soheil Hassas, Polovets, George, Faust, Aleksandra, Sun, Jiao, Rrustemi, Alban, Li, Pen, Shivanna, Rakesh, Liu, Jeremiah, Welty, Chris, Lebron, Federico, Baddepudi, Anirudh, Krause, Sebastian, Parisotto, Emilio, Soricut, Radu, Xu, Zheng, Bloxwich, Dawn, Johnson, Melvin, Neyshabur, Behnam, Mao-Jones, Justin, Wang, Renshen, Ramasesh, Vinay, Abbas, Zaheer, Guez, Arthur, Segal, Constant, Nguyen, Duc Dung, Svensson, James, Hou, Le, York, Sarah, Milan, Kieran, Bridgers, Sophie, Gworek, Wiktor, Tagliasacchi, Marco, Lee-Thorp, James, Chang, Michael, Guseynov, Alexey, Hartman, Ale Jakse, Kwong, Michael, Zhao, Ruizhe, Kashem, Sheleem, Cole, Elizabeth, Miech, Antoine, Tanburn, Richard, Phuong, Mary, Pavetic, Filip, Cevey, Sebastien, Comanescu, Ramona, Ives, Richard, Yang, Sherry, Du, Cosmo, Li, Bo, Zhang, Zizhao, Iinuma, Mariko, Hu, Clara Huiyi, Roy, Aurko, Bijwadia, Shaan, Zhu, Zhenkai, Martins, Danilo, Saputro, Rachel, Gergely, Anita, Zheng, Steven, Jia, Dawei, Antonoglou, Ioannis, Sadovsky, Adam, Gu, Shane, Bi, Yingying, Andreev, Alek, Samangooei, Sina, Khan, Mina, Kocisky, Tomas, Filos, Angelos, Kumar, Chintu, Bishop, Colton, Yu, Adams, Hodkinson, Sarah, Mittal, Sid, Shah, Premal, Moufarek, Alexandre, Cheng, Yong, Bloniarz, Adam, Lee, Jaehoon, Pejman, Pedram, Michel, Paul, Spencer, Stephen, Feinberg, Vladimir, Xiong, Xuehan, Savinov, Nikolay, Smith, Charlotte, Shakeri, Siamak, Tran, Dustin, Chesus, Mary, Bohnet, Bernd, Tucker, George, von Glehn, Tamara, Muir, Carrie, Mao, Yiran, Kazawa, Hideto, Slone, Ambrose, Soparkar, Kedar, Shrivastava, Disha, Cobon-Kerr, James, Sharman, Michael, Pavagadhi, Jay, Araya, Carlos, Misiunas, Karolis, Ghelani, Nimesh, Laskin, Michael, Barker, David, Li, Qiujia, Briukhov, Anton, Houlsby, Neil, Glaese, Mia, Lakshminarayanan, Balaji, Schucher, Nathan, Tang, Yunhao, Collins, Eli, Lim, Hyeontaek, Feng, Fangxiaoyu, Recasens, Adria, Lai, Guangda, Magni, Alberto, De Cao, Nicola, Siddhant, Aditya, Ashwood, Zoe, Orbay, Jordi, Dehghani, Mostafa, Brennan, Jenny, He, Yifan, Xu, Kelvin, Gao, Yang, Saroufim, Carl, Molloy, James, Wu, Xinyi, Arnold, Seb, Chang, Solomon, Schrittwieser, Julian, Buchatskaya, Elena, Radpour, Soroush, Polacek, Martin, Giordano, Skye, Bapna, Ankur, Tokumine, Simon, Hellendoorn, Vincent, Sottiaux, Thibault, Cogan, Sarah, Severyn, Aliaksei, Saleh, Mohammad, Thakoor, Shantanu, Shefey, Laurent, Qiao, Siyuan, Gaba, Meenu, Chang, Shuo-yiin, Swanson, Craig, Zhang, Biao, Lee, Benjamin, Rubenstein, Paul Kishan, Song, Gan, Kwiatkowski, Tom, Koop, Anna, Kannan, Ajay, Kao, David, Schuh, Parker, Stjerngren, Axel, Ghiasi, Golnaz, Gibson, Gena, Vilnis, Luke, Yuan, Ye, Ferreira, Felipe Tiengo, Kamath, Aishwarya, Klimenko, Ted, Franko, Ken, Xiao, Kefan, Bhattacharya, Indro, Patel, Miteyan, Wang, Rui, Morris, Alex, Strudel, Robin, Sharma, Vivek, Choy, Peter, Hashemi, Sayed Hadi, Landon, Jessica, Finkelstein, Mara, Jhakra, Priya, Frye, Justin, Barnes, Megan, Mauger, Matthew, Daun, Dennis, Baatarsukh, Khuslen, Tung, Matthew, Farhan, Wael, Michalewski, Henryk, Viola, Fabio, Quitry, Felix de Chaumont, Lan, Charline Le, Hudson, Tom, Wang, Qingze, Fischer, Felix, Zheng, Ivy, White, Elspeth, Dragan, Anca, Alayrac, Jean-baptiste, Ni, Eric, Pritzel, Alexander, Iwanicki, Adam, Isard, Michael, Bulanova, Anna, Zilka, Lukas, Dyer, Ethan, Sachan, Devendra, Srinivasan, Srivatsan, Muckenhirn, Hannah, Cai, Honglong, Mandhane, Amol, Tariq, Mukarram, Rae, Jack W., Wang, Gary, Ayoub, Kareem, FitzGerald, Nicholas, Zhao, Yao, Han, Woohyun, Alberti, Chris, Garrette, Dan, Krishnakumar, Kashyap, Gimenez, Mai, Levskaya, Anselm, Sohn, Daniel, Matak, Josip, Iturrate, Inaki, Chang, Michael B., Xiang, Jackie, Cao, Yuan, Ranka, Nishant, Brown, Geoff, Hutter, Adrian, Mirrokni, Vahab, Chen, Nanxin, Yao, Kaisheng, Egyed, Zoltan, Galilee, Francois, Liechty, Tyler, Kallakuri, Praveen, Palmer, Evan, Ghemawat, Sanjay, Liu, Jasmine, Tao, David, Thornton, Chloe, Green, Tim, Jasarevic, Mimi, Lin, Sharon, Cotruta, Victor, Tan, Yi-Xuan, Fiedel, Noah, Yu, Hongkun, Chi, Ed, Neitz, Alexander, Heitkaemper, Jens, Sinha, Anu, Zhou, Denny, Sun, Yi, Kaed, Charbel, Hulse, Brice, Mishra, Swaroop, Georgaki, Maria, Kudugunta, Sneha, Farabet, Clement, Shafran, Izhak, Vlasic, Daniel, Tsitsulin, Anton, Ananthanarayanan, Rajagopal, Carin, Alen, Su, Guolong, Sun, Pei, V, Shashank, Carvajal, Gabriel, Broder, Josef, Comsa, Iulia, Repina, Alena, Wong, William, Chen, Warren Weilun, Hawkins, Peter, Filonov, Egor, Loher, Lucia, Hirnschall, Christoph, Wang, Weiyi, Ye, Jingchen, Burns, Andrea, Cate, Hardie, Wright, Diana Gage, Piccinini, Federico, Zhang, Lei, Lin, Chu-Cheng, Gog, Ionel, Kulizhskaya, Yana, Sreevatsa, Ashwin, Song, Shuang, Cobo, Luis C., Iyer, Anand, Tekur, Chetan, Garrido, Guillermo, Xiao, Zhuyun, Kemp, Rupert, Zheng, Huaixiu Steven, Li, Hui, Agarwal, Ananth, Ngani, Christel, Goshvadi, Kati, Santamaria-Fernandez, Rebeca, Fica, Wojciech, Chen, Xinyun, Gorgolewski, Chris, Sun, Sean, Garg, Roopal, Ye, Xinyu, Eslami, S. M. Ali, Hua, Nan, Simon, Jon, Joshi, Pratik, Kim, Yelin, Tenney, Ian, Potluri, Sahitya, Thiet, Lam Nguyen, Yuan, Quan, Luisier, Florian, Chronopoulou, Alexandra, Scellato, Salvatore, Srinivasan, Praveen, Chen, Minmin, Koverkathu, Vinod, Dalibard, Valentin, Xu, Yaming, Saeta, Brennan, Anderson, Keith, Sellam, Thibault, Fernando, Nick, Huot, Fantine, Jung, Junehyuk, Varadarajan, Mani, Quinn, Michael, Raul, Amit, Le, Maigo, Habalov, Ruslan, Clark, Jon, Jalan, Komal, Bullard, Kalesha, Singhal, Achintya, Luong, Thang, Wang, Boyu, Rajayogam, Sujeevan, Eisenschlos, Julian, Jia, Johnson, Finchelstein, Daniel, Yakubovich, Alex, Balle, Daniel, Fink, Michael, Agarwal, Sameer, Li, Jing, Dvijotham, Dj, Pal, Shalini, Kang, Kai, Konzelmann, Jaclyn, Beattie, Jennifer, Dousse, Olivier, Wu, Diane, Crocker, Remi, Elkind, Chen, Jonnalagadda, Siddhartha Reddy, Lee, Jong, Holtmann-Rice, Dan, Kallarackal, Krystal, Liu, Rosanne, Vnukov, Denis, Vats, Neera, Invernizzi, Luca, Jafari, Mohsen, Zhou, Huanjie, Taylor, Lilly, Prendki, Jennifer, Wu, Marcus, Eccles, Tom, Liu, Tianqi, Kopparapu, Kavya, Beaufays, Francoise, Angermueller, Christof, Marzoca, Andreea, Sarcar, Shourya, Dib, Hilal, Stanway, Jeff, Perbet, Frank, Trdin, Nejc, Sterneck, Rachel, Khorlin, Andrey, Li, Dinghua, Wu, Xihui, Goenka, Sonam, Madras, David, Goldshtein, Sasha, Gierke, Willi, Zhou, Tong, Liu, Yaxin, Liang, Yannie, White, Anais, Li, Yunjie, Singh, Shreya, Bahargam, Sanaz, Epstein, Mark, Basu, Sujoy, Lao, Li, Ozturel, Adnan, Crous, Carl, Zhai, Alex, Lu, Han, Tung, Zora, Gaur, Neeraj, Walton, Alanna, Dixon, Lucas, Zhang, Ming, Globerson, Amir, Uy, Grant, Bolt, Andrew, Wiles, Olivia, Nasr, Milad, Shumailov, Ilia, Selvi, Marco, Piccinno, Francesco, Aguilar, Ricardo, McCarthy, Sara, Khalman, Misha, Shukla, Mrinal, Galic, Vlado, Carpenter, John, Villela, Kevin, Zhang, Haibin, Richardson, Harry, Martens, James, Bosnjak, Matko, Belle, Shreyas Rammohan, Seibert, Jeff, Alnahlawi, Mahmoud, McWilliams, Brian, Singh, Sankalp, Louis, Annie, Ding, Wen, Popovici, Dan, Simicich, Lenin, Knight, Laura, Mehta, Pulkit, Gupta, Nishesh, Shi, Chongyang, Fatehi, Saaber, Mitrovic, Jovana, Grills, Alex, Pagadora, Joseph, Petrova, Dessie, Eisenbud, Danielle, Zhang, Zhishuai, Yates, Damion, Mittal, Bhavishya, Tripuraneni, Nilesh, Assael, Yannis, Brovelli, Thomas, Jain, Prateek, Velimirovic, Mihajlo, Akbulut, Canfer, Mu, Jiaqi, Macherey, Wolfgang, Kumar, Ravin, Xu, Jun, Qureshi, Haroon, Comanici, Gheorghe, Wiesner, Jeremy, Gong, Zhitao, Ruddock, Anton, Bauer, Matthias, Felt, Nick, GP, Anirudh, Arnab, Anurag, Zelle, Dustin, Rothfuss, Jonas, Rosgen, Bill, Shenoy, Ashish, Seybold, Bryan, Li, Xinjian, Mudigonda, Jayaram, Erdogan, Goker, Xia, Jiawei, Simsa, Jiri, Michi, Andrea, Yao, Yi, Yew, Christopher, Kan, Steven, Caswell, Isaac, Radebaugh, Carey, Elisseeff, Andre, Valenzuela, Pedro, McKinney, Kay, Paterson, Kim, Cui, Albert, Latorre-Chimoto, Eri, Kim, Solomon, Zeng, William, Durden, Ken, Ponnapalli, Priya, Sosea, Tiberiu, Choquette-Choo, Christopher A., Manyika, James, Robenek, Brona, Vashisht, Harsha, Pereira, Sebastien, Lam, Hoi, Velic, Marko, Owusu-Afriyie, Denese, Lee, Katherine, Bolukbasi, Tolga, Parrish, Alicia, Lu, Shawn, Park, Jane, Venkatraman, Balaji, Talbert, Alice, Rosique, Lambert, Cheng, Yuchung, Sozanschi, Andrei, Paszke, Adam, Kumar, Praveen, Austin, Jessica, Li, Lu, Salama, Khalid, Kim, Wooyeol, Dukkipati, Nandita, Baryshnikov, Anthony, Kaplanis, Christos, Sheng, XiangHai, Chervonyi, Yuri, Unlu, Caglar, Casas, Diego de Las, Askham, Harry, Tunyasuvunakool, Kathryn, Gimeno, Felix, Poder, Siim, Kwak, Chester, Miecnikowski, Matt, Dimitriev, Alek, Parisi, Aaron, Liu, Dangyi, Tsai, Tomy, Shevlane, Toby, Kouridi, Christina, Garmon, Drew, Goedeckemeyer, Adrian, Brown, Adam R., Vijayakumar, Anitha, Elqursh, Ali, Jazayeri, Sadegh, Huang, Jin, Carthy, Sara Mc, Hoover, Jay, Kim, Lucy, Kumar, Sandeep, Chen, Wei, Biles, Courtney, Bingham, Garrett, Rosen, Evan, Wang, Lisa, Tan, Qijun, Engel, David, Pongetti, Francesco, de Cesare, Dario, Hwang, Dongseong, Yu, Lily, Pullman, Jennifer, Narayanan, Srini, Levin, Kyle, Gopal, Siddharth, Li, Megan, Aharoni, Asaf, Trinh, Trieu, Lo, Jessica, Casagrande, Norman, Vij, Roopali, Matthey, Loic, Ramadhana, Bramandia, Matthews, Austin, Carey, CJ, Johnson, Matthew, Goranova, Kremena, Shah, Rohin, Ashraf, Shereen, Dasgupta, Kingshuk, Larsen, Rasmus, Wang, Yicheng, Vuyyuru, Manish Reddy, Jiang, Chong, Ijazi, Joana, Osawa, Kazuki, Smith, Celine, Boppana, Ramya Sree, Bilal, Taylan, Koizumi, Yuma, Xu, Ying, Altun, Yasemin, Shabat, Nir, Bariach, Ben, Korchemniy, Alex, Choo, Kiam, Ronneberger, Olaf, Iwuanyanwu, Chimezie, Zhao, Shubin, Soergel, David, Hsieh, Cho-Jui, Cai, Irene, Iqbal, Shariq, Sundermeyer, Martin, Chen, Zhe, Bursztein, Elie, Malaviya, Chaitanya, Biadsy, Fadi, Shroff, Prakash, Dhillon, Inderjit, Latkar, Tejasi, Dyer, Chris, Forbes, Hannah, Nicosia, Massimo, Nikolaev, Vitaly, Greene, Somer, Georgiev, Marin, Wang, Pidong, Martin, Nina, Sedghi, Hanie, Zhang, John, Banzal, Praseem, Fritz, Doug, Rao, Vikram, Wang, Xuezhi, Zhang, Jiageng, Patraucean, Viorica, Du, Dayou, Mordatch, Igor, Jurin, Ivan, Liu, Lewis, Dubey, Ayush, Mohan, Abhi, Nowakowski, Janek, Ion, Vlad-Doru, Wei, Nan, Tojo, Reiko, Raad, Maria Abi, Hudson, Drew A., Keshava, Vaishakh, Agrawal, Shubham, Ramirez, Kevin, Wu, Zhichun, Nguyen, Hoang, Liu, Ji, Sewak, Madhavi, Petrini, Bryce, Choi, DongHyun, Philips, Ivan, Wang, Ziyue, Bica, Ioana, Garg, Ankush, Wilkiewicz, Jarek, Agrawal, Priyanka, Guo, Danhao, Xue, Emily, Shaik, Naseer, Leach, Andrew, Khan, Sadh MNM, Wiesinger, Julia, Jerome, Sammy, Chakladar, Abhishek, Wang, Alek Wenjiao, Ornduff, Tina, Abu, Folake, Ghaffarkhah, Alireza, Wainwright, Marcus, Cortes, Mario, Liu, Frederick, Maynez, Joshua, Terzis, Andreas, Samangouei, Pouya, Mansour, Riham, Kępa, Tomasz, Aubet, François-Xavier, Algymr, Anton, Banica, Dan, Weisz, Agoston, Orban, Andras, Senges, Alexandre, Andrejczuk, Ewa, Geller, Mark, Santo, Niccolo Dal, Anklin, Valentin, Merey, Majd Al, Baeuml, Martin, Strohman, Trevor, Bai, Junwen, Petrov, Slav, Wu, Yonghui, Hassabis, Demis, Kavukcuoglu, Koray, Dean, Jeffrey, and Vinyals, Oriol

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

In this report, we introduce the Gemini 1.5 family of models, representing the next generation of highly compute-efficient multimodal models capable of recalling and reasoning over fine-grained information from millions of tokens of context, including multiple long documents and hours of video and audio. The family includes two new models: (1) an updated Gemini 1.5 Pro, which exceeds the February version on the great majority of capabilities and benchmarks; (2) Gemini 1.5 Flash, a more lightweight variant designed for efficiency with minimal regression in quality. Gemini 1.5 models achieve near-perfect recall on long-context retrieval tasks across modalities, improve the state-of-the-art in long-document QA, long-video QA and long-context ASR, and match or surpass Gemini 1.0 Ultra's state-of-the-art performance across a broad set of benchmarks. Studying the limits of Gemini 1.5's long-context ability, we find continued improvement in next-token prediction and near-perfect retrieval (>99%) up to at least 10M tokens, a generational leap over existing models such as Claude 3.0 (200k) and GPT-4 Turbo (128k). Finally, we highlight real-world use cases, such as Gemini 1.5 collaborating with professionals on completing their tasks achieving 26 to 75% time savings across 10 different job categories, as well as surprising new capabilities of large language models at the frontier; when given a grammar manual for Kalamang, a language with fewer than 200 speakers worldwide, the model learns to translate English to Kalamang at a similar level to a person who learned from the same content.

Published
2024

4. Development of a nasal spray containing xylometazoline hydrochloride and iota-carrageenan for the symptomatic relief of nasal congestion caused by rhinitis and sinusitis

Author

Graf C, Bernkop-Schnürch A, Egyed A, Koller C, Prieschl-Grassauer E, and Morokutti-Kurz M

Subjects
antiviral, permeation, toxicity, vasoconstriction, Medicine (General), R5-920
Abstract

Christine Graf,1 Andreas Bernkop-Schnürch,2 Alena Egyed,1 Christiane Koller,1 Eva Prieschl-Grassauer,1 Martina Morokutti-Kurz1 1Marinomed Biotech AG, Vienna, Austria; 2ThioMatriX, Innsbruck, Austria Introduction: Xylometazoline hydrochloride (HCl) is a nasal decongestant that causes vasoconstriction in the nasal submucosa. It has been used for more than 50 years for the treatment of nasal congestion caused by rhinitis/sinusitis. Iota-carrageenan is effective against a broad variety of respiratory viruses, which are the most common cause of infections of the upper respiratory tract. Therefore, it is used as the active component in the antiviral nasal spray ­Coldamaris prophylactic (1.2 mg/mL iota-carrageenan in 0.5% NaCl) and other medical device nasal sprays that are approved and marketed in the EU. Recently, we developed a nasal spray formulation containing both xylometazoline HCl (0.05%) and iota-carrageenan (0.12%) that provides decongestion and antiviral protection of the nasal mucosa at the same time. Results: A set of in vitro experiments revealed that the vasoconstrictive properties of xylometazoline HCl and the antiviral effectiveness of iota-carrageenan against human rhinovirus (hRV) 1a, hRV8 and human coronavirus OC43 were maintained in the formulation containing these two compounds. Permeation experiments using bovine nasal mucosa showed that iota-carrageenan had no significant influence on the permeation of xylometazoline HCl. Finally, in the local tolerance and toxicity study, it was shown that the formulation was well tolerated at the application site with no occurrence of erythema or edema in the nostrils of all rabbits or any signs of toxicity in any of the organs and tissues inspected. Conclusion: Investigations on compatibility of xylometazoline HCl and iota-carrageenan demonstrated that the substances do not influence each other, allowing both to fulfill their known specific clinical efficacy (xylometazoline HCl) and effectiveness (iota-carrageenan). Keywords: antiviral, permeation, toxicity, vasoconstriction

Published
2018

5. TRIAD: Automated Traceability Recovery based on Biterm-enhanced Deduction of Transitive Links among Artifacts

Author

Gao, Hui, Kuang, Hongyu, Assunção, Wesley K. G., Mayr-Dorn, Christoph, Rong, Guoping, Zhang, He, Ma, Xiaoxing, and Egyed, Alexander

Subjects
Computer Science - Software Engineering
Abstract

Traceability allows stakeholders to extract and comprehend the trace links among software artifacts introduced across the software life cycle, to provide significant support for software engineering tasks. Despite its proven benefits, software traceability is challenging to recover and maintain manually. Hence, plenty of approaches for automated traceability have been proposed. Most rely on textual similarities among software artifacts, such as those based on Information Retrieval (IR). However, artifacts in different abstraction levels usually have different textual descriptions, which can greatly hinder the performance of IR-based approaches (e.g., a requirement in natural language may have a small textual similarity to a Java class). In this work, we leverage the consensual biterms and transitive relationships (i.e., inner- and outer-transitive links) based on intermediate artifacts to improve IR-based traceability recovery. We first extract and filter biterms from all source, intermediate, and target artifacts. We then use the consensual biterms from the intermediate artifacts to extend the biterms of both source and target artifacts, and finally deduce outer and inner-transitive links to adjust text similarities between source and target artifacts. We conducted a comprehensive empirical evaluation based on five systems widely used in other literature to show that our approach can outperform four state-of-the-art approaches, and how its performance is affected by different conditions of source, intermediate, and target artifacts. The results indicate that our approach can outperform baseline approaches in AP over 15% and MAP over 10% on average., Comment: Accepted by the 46th International Conference on Software Engineering (ICSE 2024)

Published
2023
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6. Defining and executing temporal constraints for evaluating engineering artifact compliance

Author

Ratiu, Cosmina-Cristina, Mayr-Dorn, Christoph, and Egyed, Alexander

Subjects
Computer Science - Software Engineering
Abstract

Engineering processes for safety-critical systems describe the steps and sequence that guide engineers from refining user requirements into executable code, as well as producing the artifacts, traces, and evidence that the resulting system is of high quality. Process compliance focuses on ensuring that the actual engineering work is followed as closely as possible to the described engineering processes. To this end, temporal constraints describe the ideal sequence of steps. Checking these process constraints, however, is still a daunting task that requires a lot of manual work and delivers feedback to engineers only late in the process. In this paper, we present an automated constraint checking approach that can incrementally check temporal constraints across inter-related engineering artifacts upon every artifact change thereby enabling timely feedback to engineers on process deviations. Temporal constraints are expressed in the Object Constraint Language (OCL) extended with operators from Linear Temporal Logic (LTL). We demonstrate the ability of our approach to support a wide range of higher level temporal patterns. We further show that for constraints in an industry-derived use case, the average evaluation time for a single constraint takes around 0.2 milliseconds.

Published
2023

8. Non-Hermitian dynamics and nonreciprocity of optically coupled nanoparticles

Author

Reisenbauer, Manuel, Rudolph, Henning, Egyed, Livia, Hornberger, Klaus, Zasedatelev, Anton V., Abuzarli, Murad, Stickler, Benjamin A., and Delić, Uroš

Subjects
Physics - Optics, Condensed Matter - Mesoscale and Nanoscale Physics, Quantum Physics
Abstract

Non-Hermitian dynamics, as observed in photonic, atomic, electrical, and optomechanical platforms, holds great potential for sensing applications and signal processing. Recently, fully tunable nonreciprocal optical interaction has been demonstrated between levitated nanoparticles. Here, we use this tunability to investigate the collective non-Hermitian dynamics of two nonreciprocally and nonlinearly interacting nanoparticles. We observe parity-time symmetry breaking and, for sufficiently strong coupling, a collective mechanical lasing transition, where the particles move along stable limit cycles. This work opens up a research avenue of nonequilibrium multi-particle collective effects, tailored by the dynamic control of individual sites in a tweezer array.

Published
2023
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9. Validation-Driven Development

Author

Stock, Sebastian, Mashkoor, Atif, and Egyed, Alexander

Subjects
Computer Science - Software Engineering, Computer Science - Logic in Computer Science
Abstract

Formal methods play a fundamental role in asserting the correctness of requirements specifications. However, historically, formal method experts have primarily focused on verifying those specifications. Although equally important, validation of requirements specifications often takes the back seat. This paper introduces a validation-driven development (VDD) process that prioritizes validating requirements in formal development. The VDD process is built upon problem frames - a requirements analysis approach - and validation obligations (VOs) - the concept of breaking down the overall validation of a specification and linking it to refinement steps. The effectiveness of the VDD process is demonstrated through a case study in the aviation industry.

Published
2023

12. PromptORE -- A Novel Approach Towards Fully Unsupervised Relation Extraction

Author

Genest, Pierre-Yves, Portier, Pierre-Edouard, Egyed-Zsigmond, Elöd, and Goix, Laurent-Walter

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Information Retrieval, Computer Science - Machine Learning
Abstract

Unsupervised Relation Extraction (RE) aims to identify relations between entities in text, without having access to labeled data during training. This setting is particularly relevant for domain specific RE where no annotated dataset is available and for open-domain RE where the types of relations are a priori unknown. Although recent approaches achieve promising results, they heavily depend on hyperparameters whose tuning would most often require labeled data. To mitigate the reliance on hyperparameters, we propose PromptORE, a ''Prompt-based Open Relation Extraction'' model. We adapt the novel prompt-tuning paradigm to work in an unsupervised setting, and use it to embed sentences expressing a relation. We then cluster these embeddings to discover candidate relations, and we experiment different strategies to automatically estimate an adequate number of clusters. To the best of our knowledge, PromptORE is the first unsupervised RE model that does not need hyperparameter tuning. Results on three general and specific domain datasets show that PromptORE consistently outperforms state-of-the-art models with a relative gain of more than 40% in B 3 , V-measure and ARI. Qualitative analysis also indicates PromptORE's ability to identify semantically coherent clusters that are very close to true relations.

Published
2023
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13. Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin

Author

Noémi Borbély, Dániel Dudás, Attila Tapasztó, Eszter Dudás-Boda, Veronika Csáky, Bea Szeifert, Balázs Gusztáv Mende, Balázs Egyed, Anna Szécsényi-Nagy, and Horolma Pamjav

Subjects
Medicine, Science
Abstract

Abstract This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe.

Published
2024
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23. Using Consensual Biterms from Text Structures of Requirements and Code to Improve IR-Based Traceability Recovery

Author

Gao, Hui, Kuang, Hongyu, Sun, Kexin, Ma, Xiaoxing, Egyed, Alexander, Mäder, Patrick, Rong, Guoping, Shao, Dong, and Zhang, He

Subjects
Computer Science - Software Engineering
Abstract

Traceability approves trace links among software artifacts based on whether two artifacts are related by system functionalities. The traces are valuable for software development, but are difficult to obtain manually. To cope with the costly and fallible manual recovery, automated approaches are proposed to recover traces through textual similarities among software artifacts, such as those based on Information Retrieval (IR). However, the low quality & quantity of artifact texts negatively impact the calculated IR values, thus greatly hindering the performance of IR-based approaches. In this study, we propose to extract co-occurred word pairs from the text structures of both requirements and code (i.e., consensual biterms) to improve IR-based traceability recovery. We first collect a set of biterms based on the part-of-speech of requirement texts, and then filter them through the code texts. We then use these consensual biterms to both enrich the input corpus for IR techniques and enhance the calculations of IR values. A nine-system-based evaluation shows that in general, when solely used to enhance IR techniques, our approach can outperform pure IR-based approaches and another baseline by 21.9% & 21.8% in AP, and 9.3% & 7.2% in MAP, respectively. Moreover, when used to collaborate with another enhancing strategy from different perspectives, it can outperform this baseline by 5.9% in AP and 4.8% in MAP., Comment: Accepted by the 37th IEEE/ACM International Conference on Automated Software Engineering (ASE 2022)

Published
2022
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24. Changes in bone marrow fibrosis during momelotinib or ruxolitinib therapy do not correlate with efficacy outcomes in patients with myelofibrosis

Author

Stephen T. Oh, Srdan Verstovsek, Vikas Gupta, Uwe Platzbecker, Timothy Devos, Jean‐Jacques Kiladjian, Donal P. McLornan, Andrew Perkins, Maria Laura Fox, Mary Frances McMullin, Adam J. Mead, Miklos Egyed, Jiri Mayer, Tomasz Sacha, Jun Kawashima, Mei Huang, Bryan Strouse, and Ruben Mesa

Subjects
bone marrow fibrosis, JAK inhibitor, momelotinib, myelofibrosis, ruxolitinib, Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

Abstract Bone marrow fibrosis (BMF) is a pathological feature of myelofibrosis, with higher grades associated with poor prognosis. Limited data exist on the association between outcomes and BMF changes. We present BMF data from Janus kinase (JAK) inhibitor–naive patients from SIMPLIFY‐1 (NCT01969838), a double‐blind, randomized, phase 3 study of momelotinib vs ruxolitinib. Baseline and week 24 bone marrow biopsies were graded from 0 to 3 as per World Health Organization criteria. Other assessments included Total Symptom Score, spleen volume, transfusion independence status, and hemoglobin levels. Paired samples were available from 144 and 160 patients randomized to momelotinib and ruxolitinib. With momelotinib and ruxolitinib, transfusion independence was achieved by 87% and 44% of patients with BMF improvement of ≥1 grade and 76% and 56% of those with stable/worsening BMF; there was no association between BMF changes and transfusion independence for either arm (momelotinib, p = .350; ruxolitinib, p = .096). Regardless of BMF changes, hemoglobin levels also generally increased on momelotinib but decreased on ruxolitinib. In addition, no associations between BMF changes and spleen (momelotinib, p = .126; ruxolitinib, p = .407)/symptom (momelotinib, p = .617; ruxolitinib, p = .833) outcomes were noted, and no improvement in overall survival was observed with ≥1‐grade BMF improvement (momelotinib, p = .395; ruxolitinib, p = .407). These data suggest that the anemia benefit of momelotinib is not linked to BMF changes, and question the use of BMF assessment as a surrogate marker for clinical benefit with JAK inhibitors.

Published
2024
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25. Trace Refinement in B and Event-B

Author

Stock, Sebastian, Mashkoor, Atif, Leuschel, Michael, and Egyed, Alexander

Subjects
Computer Science - Logic in Computer Science
Abstract

Traces are used to show whether a model complies with the intended behavior. A modeler can use trace checking to ensure the preservation of the model behavior during the refinement process. In this paper, we present a trace refinement technique and tool called BERT that allows designers to ensure the behavioral integrity of high-level traces at the concrete level. The proposed technique is evaluated within the context of the B and Event-B methods on industrial-strength case studies from the automotive domain.

Published
2022

26. Balanced Knowledge Distribution among Software Development Teams -- Observations from Open-Source and Closed-Source Software Development

Author

Shafiq, Saad, Mayr-Dorn, Christoph, Mashkoor, Atif, and Egyed, Alexander

Subjects
Computer Science - Software Engineering, Computer Science - Information Retrieval
Abstract

In software development teams, developer turnover is among the primary reasons for project failures as it leads to a great void of knowledge and strain for the newcomers. Unfortunately, no established methods exist to measure how knowledge is distributed among development teams. Knowing how this knowledge evolves and is owned by key developers in a project helps managers reduce risks caused by turnover. To this end, this paper introduces a novel, realistic representation of domain knowledge distribution: the ConceptRealm. To construct the ConceptRealm, we employ a latent Dirichlet allocation model to represent textual features obtained from 300k issues and 1.3M comments from 518 open-source projects. We analyze whether the newly emerged issues and developers share similar concepts or how aligned the developers' concepts are with the team over time. We also investigate the impact of leaving members on the frequency of concepts. Finally, we evaluate the soundness of our approach to closed-source software, thus allowing the validation of the results from a practical standpoint. We find out that the ConceptRealm can represent the high-level domain knowledge within a team and can be utilized to predict the alignment of developers with issues. We also observe that projects exhibit many keepers independent of project maturity and that abruptly leaving keepers harm the team's concept familiarity., Comment: 33 pages, 17 figures, journal submission

Published
2022
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27. Application of Validation Obligations to Security Concerns

Author

Stock, Sebastian, Mashkoor, Atif, and Egyed, Alexander

Subjects
Computer Science - Logic in Computer Science
Abstract

Our lives become increasingly dependent on safety- and security-critical systems, so formal techniques are advocated for engineering such systems. One of such techniques is validation obligations that enable formalizing requirements early in development to ensure their correctness. Furthermore, validation obligations help hold requirements consistent in an evolving model and create assurances about the model's completeness. Although initially proposed for safety properties, this paper shows how the technique of validation obligations enables us to also reason about security concerns through an example from the medical domain.

Published
2022

28. Formalization of Advanced VOs semantics and VO Refinement

Author

Stock, Sebastian, Vu, Fabian, Geleßus, David, Mashkoor, Atif, Leuschel, Michael, and Egyed, Alexander

Subjects
Computer Science - Logic in Computer Science
Abstract

This document lays out the foundations for VO and requirement refinement, abstractions of models, and instantiations. Also, VOs on abstractions and instantiations are considered.

Published
2022

35. PersonALL: a genetic scoring guide for personalized risk assessment in pediatric B-cell precursor acute lymphoblastic leukemia

Author

Bedics, Gábor, Egyed, Bálint, Kotmayer, Lili, Benard-Slagter, Anne, de Groot, Karel, Bekő, Anna, Hegyi, Lajos László, Bátai, Bence, Krizsán, Szilvia, Kriván, Gergely, Erdélyi, Dániel J., Müller, Judit, Haltrich, Irén, Kajtár, Béla, Pajor, László, Vojcek, Ágnes, Ottóffy, Gábor, Ujfalusi, Anikó, Szegedi, István, Tiszlavicz, Lilla Györgyi, Bartyik, Katalin, Csanádi, Krisztina, Péter, György, Simon, Réka, Hauser, Péter, Kelemen, Ágnes, Sebestyén, Endre, Jakab, Zsuzsanna, Matolcsy, András, Kiss, Csongor, Kovács, Gábor, Savola, Suvi, Bödör, Csaba, and Alpár, Donát

Published
2023
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36. Dog Domestication Strongly Relied on Translation Regulation According to Differential Gene Expression Analysis

Author

David Jonas, Kitti Tatrai, Sara Sandor, Balazs Egyed, and Eniko Kubinyi

Subjects
RNA sequencing, dog, wolf, domestication, Veterinary medicine, SF600-1100, Zoology, QL1-991
Abstract

Domestication of dogs from their shared ancestors with wolves occurred more than 15,000 years ago and affected many characteristics of the species. We analyzed the blood RNA sequence data of 12 dogs and 11 wolves from Europe and Asia to shed more light on the domestication history of dogs. We implemented a differential gene expression analysis, a weighted gene correlation network analysis, gene ontology and genetic pathway analyses. We found that both the sample origin (Europe or Asia) and the species had a significant effect on the blood gene expression profiles of the animals. We identified 1567 differentially expressed genes between wolves and dogs and found several significantly overrepresented gene ontology terms, such as RNA polymerase II transcription regulatory region sequence-specific DNA binding or translation. We identified 11 significant gene co-expression networks, hosting a total of 4402 genes, related to DNA replication, metabolism of RNA or metabolism of proteins, for example. Our findings suggest that gene expression regulation played a cardinal role in dog domestication. We recommend further diversifying the analyzed dog and wolf populations in the future by including individuals from different dog breeds and geographical origins, in order to enhance the specificity of detecting significant, true positive genes related to domestication as well as to reduce the false positive rate.

Published
2024
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37. Emergence and Comparative Genome Analysis of Salmonella Ohio Strains from Brown Rats, Poultry, and Swine in Hungary

Author

Ama Szmolka, Zsuzsanna Sréterné Lancz, Fanni Rapcsák, and László Egyed

Subjects
Salmonella Ohio, core genome MLST, whole-genome sequencing, food-producing animals, brown rat, poultry, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

Rats are particularly important from an epidemiological point of view, because they are regarded as reservoirs for diverse zoonotic pathogens including enteric bacteria. This study is the first to report the emergence of Salmonella serovar Ohio in brown rats (Rattus norvegicus) and food-producing animals in Hungary. We first reveal the genomic diversity of the strains and their phylogenomic relationships in the context of the international collection of S. Ohio genomes. This pathogen was detected in 4.3% (4/92) of rats, captured from multiple sites in Hungary. A whole-genome-based genotype comparison of S. Ohio, Infantis, Enteritidis, and Typhimurium strains showed that 76.4% (117/153) of the virulence and antimicrobial resistance genes were conserved among these serovars, and none of the genes were specific to S. Ohio. All S. Ohio strains lacked virulence and resistance plasmids. The cgMLST phylogenomic comparison highlighted a close genetic relationship between rat and poultry strains of S. Ohio from Hungary. These strains clustered together with the international S. Ohio genomes from aquatic environments. Overall, this study contributes to our understanding of the epidemiology of Salmonella spp. in brown rats and highlights the importance of monitoring to minimize the public health risk of rodent populations. However, further research is needed to understand the route of infection and evolution of this serovar.

Published
2024
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39. Exploring firm performance in Central and Eastern European regions: a foundational approach

Author

Ildikó Egyed and Zsuzsanna Zsibók

Subjects
foundational economy, regional policy, firm-level data, labour productivity, central and eastern europe, Geography (General), G1-922
Abstract

Economic development in post-transition countries is dominated by the performance of capital cities, although second-tier cities are also important drivers of development. However, peripheral regions struggle with problems of adaptation and response, often leading to brain drain and economic decline. Industrial strategies highlight those tradable sectors of the economy that favour leading edge KIBS firms and advanced manufacturing, while neglecting the residentiary economy that is more sheltered from competition and provides jobs in local production and services sectors. Our research is inspired by the burgeoning literature of the ‘foundational economy’ approach to economic development, focusing on mundane economic activities providing essential goods and services, and we investigate the differences of economic performance across the NUTS3 regions in selected CEE countries. We study regionally aggregated, firm-level financial and employment data including sectoral classification of the companies with 10+ employees. Our position is that a well-functioning foundational economy is necessary for the whole local economy to work efficiently in the long run. Moreover, increasing productivity in the foundational economy should lead to more regionally balanced growth than an exclusive focus on the ‘frontier firms’ that are highly concentrated spatially as the regional productivity gap in the case of certain foundational activities is not necessarily large.

Published
2023
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43. Do Communities in Developer Interaction Networks align with Subsystem Developer Teams? An Empirical Study of Open Source Systems

Author

Ashraf, Usman, Mayr-Dorn, Christoph, Mashkoor, Atif, Egyed, Alexander, and Panichella, Sebastiano

Subjects
Computer Science - Software Engineering
Abstract

Studies over the past decade demonstrated that developers contributing to open source software systems tend to self-organize in "emerging" communities. This latent community structure has a significant impact on software quality. While several approaches address the analysis of developer interaction networks, the question of whether these emerging communities align with the developer teams working on various subsystems remains unanswered. Work on socio-technical congruence implies that people that work on the same task or artifact need to coordinate and thus communicate, potentially forming stronger interaction ties. Our empirical study of 10 open source projects revealed that developer communities change considerably across a project's lifetime (hence implying that relevant relations between developers change) and that their alignment with subsystem developer teams is mostly low. However, subsystems teams tend to remain more stable. These insights are useful for practitioners and researchers to better understand developer interaction structure of open source systems., Comment: ICSSP/ICGSE 2021

Published
2021

44. Team-oriented Consistency Checking of Heterogeneous Engineering Artifacts

Author

Tröls, Michael Alexander, Mashkoor, Atif, and Egyed, Alexander

Subjects
Computer Science - Software Engineering, D.2.4
Abstract

Consistency checking of interdependent heterogeneous engineering artifacts, such as requirements, specifications, and code, is a challenging task in large-scale engineering projects. The lack of team-oriented solutions allowing a multitude of project stakeholders to collaborate in a consistent manner is thus becoming a critical problem. In this context, this work proposes an approach for team-oriented consistency checking of collaboratively developed heterogeneous engineering artifacts., Comment: 2 pages, 1 figure, ICSE Poster Exhibit

Published
2021

45. TaskAllocator: A Recommendation Approach for Role-based Tasks Allocation in Agile Software Development

Author

Shafiq, Saad, Mashkoor, Atif, Mayr-Dorn, Christoph, and Egyed, Alexander

Subjects
Computer Science - Software Engineering
Abstract

In this paper, we propose a recommendation approach -- TaskAllocator -- in order to predict the assignment of incoming tasks to potential befitting roles. The proposed approach, identifying team roles rather than individual persons, allows project managers to perform better tasks allocation in case the individual developers are over-utilized or moved on to different roles/projects. We evaluated our approach on ten agile case study projects obtained from the Taiga.io repository. In order to determine the TaskAllocator's performance, we have conducted a benchmark study by comparing it with contemporary machine learning models. The applicability of the TaskAllocator was assessed through a plugin that can be integrated with JIRA and provides recommendations about suitable roles whenever a new task is added to the project. Lastly, the source code of the plugin and the dataset employed have been made public., Comment: 11 pages, 9 figures

Published
2021

46. Validation Obligations: A Novel Approach to Check Compliance between Requirements and their Formal Specification

Author

Mashkoor, Atif, Leuschel, Michael, and Egyed, Alexander

Subjects
Computer Science - Software Engineering, Computer Science - Formal Languages and Automata Theory
Abstract

Traditionally, practitioners use formal methods pre-dominately for one half of the quality-assurance process: verification (do we build the software right?). The other half -- validation (do we build the right software?) -- has been given comparatively little attention. While verification is the core of refinement-based formal methods, where each new refinement step must preserve all properties of its abstract model, validation is usually postponed until the latest stages of the development, when models can be automatically executed. Thus mistakes in requirements or in their interpretation are caught too late: usually at the end of the development process. In this paper, we present a novel approach to check compliance between requirements and their formal refinement-based specification during the earlier stages of development. Our proposed approach -- "validation obligations" -- is based on the simple idea that both verification and validation are an integral part of all refinement steps of a system., Comment: ICSE 2021 - NIER

Published
2021

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