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5,280 results on '"Gu, Jian"'

1. A Semantic-based Layer Freezing Approach to Efficient Fine-Tuning of Language Models

Author

Gu, Jian, Aleti, Aldeida, Chen, Chunyang, and Zhang, Hongyu

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

Finetuning language models (LMs) is crucial for adapting the models to downstream data and tasks. However, full finetuning is usually costly. Existing work, such as parameter-efficient finetuning (PEFT), often focuses on \textit{how to finetune} but neglects the issue of \textit{where to finetune}. As a pioneering work on answering where to finetune (at the layer level), we conduct a semantic analysis of the LM inference process. We first propose a virtual transition of the latent representation and then trace its factual transition. Based on the deviation in transitions, we estimate the gain of finetuning each model layer, and further, narrow down the scope for finetuning. We perform extensive experiments across well-known LMs and datasets. The results show that our approach is effective and efficient, and outperforms the existing baselines. Our approach is orthogonal to existing efficient techniques, such as PEFT methods, offering practical values on LM finetuning., Comment: 13 pages, 5 figures, under peer-review

Published
2024

2. Heavy-quark dominance and fine structure of excited heavy baryons $\Sigma_{Q}$, $\Xi '_{Q}$ and $\Omega_{Q}$

Author

Li, Zhen-Yu, Yu, Guo-Liang, Wang, Zhi-Gang, and Gu, Jian-Zhong

Subjects
High Energy Physics - Phenomenology
Abstract

In the framework of the relativized quark model, the calculation of spin-orbit interactions is improved by considering the contribution from the light quark cluster in a singly heavy baryon. It modifies the energy level splitting of the orbital excitation significantly and causes the emergence of fine structures for $\Sigma_{Q}$, $\Xi '_{Q}$ and $\Omega_{Q}$ baryons. Based on this improvement, we systematically analyze the fine structures and retest the heavy quark dominance mechanism. This mechanism is found to be violated in the $1P$-wave states of the $\Sigma_{c}$, $\Xi '_{c}$ and $\Omega_{c}$ baryons although it remains effective overall, which may help to understand the nature of the heavy quarks and strong interactions. With the predicted fine structures, we make the precise assignments of those observed heavy baryons which once could not be accurately explained due to their close mass values. The method used in this work is instructive and applicable for the study of more complex exotic hadrons, such as the heavy tetraquarks and pentaquarks., Comment: 10 pages, 3 figures, 2 tables

Published
2024

3. Genome-wide association study identifies high-impact susceptibility loci for HCC in North America.

Author

Hassan, Manal, Li, Donghui, Han, Younghun, Byun, Jinyoung, Hatia, Rikita, Long, Erping, Choi, Jiyeon, Kelley, Robin, Cleary, Sean, Lok, Anna, Bracci, Paige, Permuth, Jennifer, Bucur, Roxana, Yuan, Jian-Min, Singal, Amit, Jalal, Prasun, Ghobrial, R, Santella, Regina, Kono, Yuko, Shah, Dimpy, Nguyen, Mindie, Liu, Geoffrey, Parikh, Neehar, Kim, Richard, Wu, Hui-Chen, El-Serag, Hashem, Chang, Ping, Li, Yanan, Chun, Yun, Lee, Sunyoung, Gu, Jian, Hawk, Ernest, Sun, Ryan, Huff, Chad, Rashid, Asif, Amin, Hesham, Beretta, Laura, Wolff, Robert, Antwi, Samuel, Patt, Yehuda, Hwang, Lu-Yu, Klein, Alison, Zhang, Karen, Schmidt, Mikayla, White, Donna, Goss, John, Khaderi, Saira, Marrero, Jorge, Cigarroa, Francisco, Shah, Pankil, Kaseb, Ahmed, Roberts, Lewis, and Amos, Christopher

Subjects
Humans, Genome-Wide Association Study, Liver Neoplasms, Genetic Predisposition to Disease, Carcinoma, Hepatocellular, Male, Female, Middle Aged, North America, Case-Control Studies, Polymorphism, Single Nucleotide, Aged, Genetic Loci, White People
Abstract

BACKGROUND AND AIMS: Despite the substantial impact of environmental factors, individuals with a family history of liver cancer have an increased risk for HCC. However, genetic factors have not been studied systematically by genome-wide approaches in large numbers of individuals from European descent populations (EDP). APPROACH AND RESULTS: We conducted a 2-stage genome-wide association study (GWAS) on HCC not affected by HBV infections. A total of 1872 HCC cases and 2907 controls were included in the discovery stage, and 1200 HCC cases and 1832 controls in the validation. We analyzed the discovery and validation samples separately and then conducted a meta-analysis. All analyses were conducted in the presence and absence of HCV. The liability-scale heritability was 24.4% for overall HCC. Five regions with significant ORs (95% CI) were identified for nonviral HCC: 3p22.1, MOBP , rs9842969, (0.51, [0.40-0.65]); 5p15.33, TERT , rs2242652, (0.70, (0.62-0.79]); 19q13.11, TM6SF2 , rs58542926, (1.49, [1.29-1.72]); 19p13.11 MAU2 , rs58489806, (1.53, (1.33-1.75]); and 22q13.31, PNPLA3 , rs738409, (1.66, [1.51-1.83]). One region was identified for HCV-induced HCC: 6p21.31, human leukocyte antigen DQ beta 1, rs9275224, (0.79, [0.74-0.84]). A combination of homozygous variants of PNPLA3 and TERT showing a 6.5-fold higher risk for nonviral-related HCC compared to individuals lacking these genotypes. This observation suggests that gene-gene interactions may identify individuals at elevated risk for developing HCC. CONCLUSIONS: Our GWAS highlights novel genetic susceptibility of nonviral HCC among European descent populations from North America with substantial heritability. Selected genetic influences were observed for HCV-positive HCC. Our findings indicate the importance of genetic susceptibility to HCC development.

Published
2024

5. Molecular and physiological changes in the SpaceX Inspiration4 civilian crew

Author

Jones, Christopher W., Overbey, Eliah G., Lacombe, Jerome, Ecker, Adrian J., Meydan, Cem, Ryon, Krista, Tierney, Braden, Damle, Namita, MacKay, Matthew, Afshin, Evan E., Foox, Jonathan, Park, Jiwoon, Nelson, Theodore M., Suhail Mohamad, Mir, Byhaqui, Syed Gufran Ahmad, Aslam, Burhan, Tali, Ummer Akbar, Nisa, Liaqun, Menon, Priya V., Patel, Chintan O., Khan, Sharib A., Ebert, Doug J., Everson, Aaron, Schubert, Michael C., Ali, Nabila N., Sarma, Mallika S., Kim, JangKeun, Houerbi, Nadia, Grigorev, Kirill, Garcia Medina, J. Sebastian, Summers, Alexander J., Gu, Jian, Altin, John A., Fattahi, Ali, Hirzallah, Mohammad I., Wu, Jimmy H., Stahn, Alexander C., Beheshti, Afshin, Klotz, Remi, Ortiz, Veronica, Yu, Min, Patras, Laura, Matei, Irina, Lyden, David, Melnick, Ari, Banerjee, Neil, Mullane, Sean, Kleinman, Ashley S., Loesche, Michael, Menon, Anil S., Donoviel, Dorit B., Urquieta, Emmanuel, Mateus, Jaime, Sargsyan, Ashot E., Shelhamer, Mark, Zenhausern, Frederic, Bershad, Eric M., Basner, Mathias, and Mason, Christopher E.

Published
2024
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6. Realizing Disentanglement in LM Latent Space via Vocabulary-Defined Semantics

Author

Gu, Jian, Aleti, Aldeida, Chen, Chunyang, and Zhang, Hongyu

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

Understanding the latent space of language models (LMs) is important for improving the performance and interpretability of LMs. Existing analyses often fail to provide insights that take advantage of the semantic properties of language models and often overlook crucial aspects of language model adaptation. In response, we introduce a pioneering approach called vocabulary-defined semantics, which establishes a reference frame grounded in LM vocabulary within the LM latent space. We propose a novel technique to compute disentangled logits and gradients in latent space, not entangled ones on vocabulary. Further, we perform semantical clustering on data representations as a novel way of LM adaptation. Through extensive experiments across diverse text understanding datasets, our approach outperforms state-of-the-art methods of retrieval-augmented generation and parameter-efficient finetuning, showcasing its effectiveness and efficiency., Comment: under peer-review

Published
2024

7. Neuron Patching: Semantic-based Neuron-level Language Model Repair for Code Generation

Author

Gu, Jian, Aleti, Aldeida, Chen, Chunyang, and Zhang, Hongyu

Subjects
Computer Science - Software Engineering, Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

Large Language Models (LLMs) have already gained widespread adoption in software engineering, particularly in code generation tasks. However, updating these models with new knowledge can be prohibitively expensive, yet it is essential to maximize their utility, such as implementing a hotfix technique to address urgent or critical LLM errors. In this paper, we propose \textsc{MENT}, a novel and effective model editing approach to repair LLMs in coding tasks. \textsc{MENT} is effective, efficient, and reliable, capable of correcting a neural model by patching just one or two neurons. As pioneering work on neuron-level model editing of generative models, we formalize the editing process and introduce the involved concepts. We also introduce new measures to evaluate its generalization ability and establish a benchmark for further study. Our approach is evaluated on three coding tasks: line-level code generation, shellcode generation, and intent-to-bash translation. The experimental results demonstrate that the proposed approach significantly outperforms the state-of-the-art in both effectiveness and efficiency measures. Furthermore, we showcase the applications of \textsc{MENT} for LLM reasoning in software engineering. By editing LLM knowledge, the directly or indirectly dependent behaviors of API invocation in the chain-of-thought change accordingly. This illustrates the significance of repairing LLMs in the context of software engineering., Comment: 12 pages, 7 figures, 7 tables, under peer-review

Published
2023

8. Heavy quark dominance in orbital excitation of singly and doubly heavy baryons

Author

Li, Zhen-Yu, Yu, Guo-Liang, Wang, Zhi-Gang, and Gu, Jian-Zhong

Subjects
High Energy Physics - Phenomenology
Abstract

A mechanism of the heavy quark dominance in the orbital excitation is proposed in this paper which is testified to be reasonable for singly and doubly heavy baryons. In the relativistic quark model, an analysis of the Hamiltonian figures out the mechanism that the excitation mode with lower energy levels is always associated with the heavy quark(s), and the splitting of the energy levels is suppressed by the heavy quark(s). So, the heavy quarks dominate the orbital excitation of singly and doubly heavy baryons. Furthermore, a physical understanding of this mechanism is given in a semi-classical way. Accordingly, the predicted mass spectra of singly and doubly heavy baryons confirm the rationality of this mechanism. In addition, an interesting consequence of this mechanism is that a heavy-light meson is more likely to be produced in the strong decay of the high-orbital excited states, which is supported by experiments. This mechanism is rooted in the breakdown of the mass symmetry. Therefore, it may be also valid for other multi-quark systems, such as the tetraquarks Qqqq and QQqq, or the pentaquarks Qqqqq and QQqqq., Comment: 12 pages, 7 figures, 5 tables

Published
2023
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13. Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions

Author

Purdue, Mark P., Dutta, Diptavo, Machiela, Mitchell J., Gorman, Bryan R., Winter, Timothy, Okuhara, Dayne, Cleland, Sara, Ferreiro-Iglesias, Aida, Scheet, Paul, Liu, Aoxing, Wu, Chao, Antwi, Samuel O., Larkin, James, Zequi, Stênio C., Sun, Maxine, Hikino, Keiko, Hajiran, Ali, Lawson, Keith A., Cárcano, Flavio, Blanchet, Odile, Shuch, Brian, Nepple, Kenneth G., Margue, Gaëlle, Sundi, Debasish, Diver, W. Ryan, Folgueira, Maria A. A. K., van Bokhoven, Adrie, Neffa, Florencia, Brown, Kevin M., Hofmann, Jonathan N., Rhee, Jongeun, Yeager, Meredith, Cole, Nathan R., Hicks, Belynda D., Manning, Michelle R., Hutchinson, Amy A., Rothman, Nathaniel, Huang, Wen-Yi, Linehan, W. Marston, Lori, Adriana, Ferragu, Matthieu, Zidane-Marinnes, Merzouka, Serrano, Sérgio V., Magnabosco, Wesley J., Vilas, Ana, Decia, Ricardo, Carusso, Florencia, Graham, Laura S., Anderson, Kyra, Bilen, Mehmet A., Arciero, Cletus, Pellegrin, Isabelle, Ricard, Solène, Scelo, Ghislaine, Banks, Rosamonde E., Vasudev, Naveen S., Soomro, Naeem, Stewart, Grant D., Adeyoju, Adebanji, Bromage, Stephen, Hrouda, David, Gibbons, Norma, Patel, Poulam, Sullivan, Mark, Protheroe, Andrew, Nugent, Francesca I., Fournier, Michelle J., Zhang, Xiaoyu, Martin, Lisa J., Komisarenko, Maria, Eisen, Timothy, Cunningham, Sonia A., Connolly, Denise C., Uzzo, Robert G., Zaridze, David, Mukeria, Anush, Holcatova, Ivana, Hornakova, Anna, Foretova, Lenka, Janout, Vladimir, Mates, Dana, Jinga, Viorel, Rascu, Stefan, Mijuskovic, Mirjana, Savic, Slavisa, Milosavljevic, Sasa, Gaborieau, Valérie, Abedi-Ardekani, Behnoush, McKay, James, Johansson, Mattias, Phouthavongsy, Larry, Hayman, Lindsay, Li, Jason, Lungu, Ilinca, Bezerra, Stephania M., Souza, Aline G., Sares, Claudia T. G., Reis, Rodolfo B., Gallucci, Fabio P., Cordeiro, Mauricio D., Pomerantz, Mark, Lee, Gwo-Shu M., Freedman, Matthew L., Jeong, Anhyo, Greenberg, Samantha E., Sanchez, Alejandro, Thompson, R. Houston, Sharma, Vidit, Thiel, David D., Ball, Colleen T., Abreu, Diego, Lam, Elaine T., Nahas, William C., Master, Viraj A., Patel, Alpa V., Bernhard, Jean-Christophe, Freedman, Neal D., Bigot, Pierre, Reis, Rui M., Colli, Leandro M., Finelli, Antonio, Manley, Brandon J., Terao, Chikashi, Choueiri, Toni K., Carraro, Dirce M., Houlston, Richard, Eckel-Passow, Jeanette E., Abbosh, Philip H., Ganna, Andrea, Brennan, Paul, Gu, Jian, and Chanock, Stephen J.

Published
2024
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14. Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction

Author

Jia, Guochong, Ping, Jie, Guo, Xingyi, Yang, Yaohua, Tao, Ran, Li, Bingshan, Ambs, Stefan, Barnard, Mollie E., Chen, Yu, Garcia-Closas, Montserrat, Gu, Jian, Hu, Jennifer J., Huo, Dezheng, John, Esther M., Li, Christopher I., Li, James L., Nathanson, Katherine L., Nemesure, Barbara, Olopade, Olufunmilayo I., Pal, Tuya, Press, Michael F., Sanderson, Maureen, Sandler, Dale P., Shu, Xiao-Ou, Troester, Melissa A., Yao, Song, Adejumo, Prisca O., Ahearn, Thomas, Brewster, Abenaa M., Hennis, Anselm J. M., Makumbi, Timothy, Ndom, Paul, O’Brien, Katie M., Olshan, Andrew F., Oluwasanu, Mojisola M., Reid, Sonya, Butler, Ebonee N., Huang, Maosheng, Ntekim, Atara, Qian, Huijun, Zhang, Haoyu, Ambrosone, Christine B., Cai, Qiuyin, Long, Jirong, Palmer, Julie R., Haiman, Christopher A., and Zheng, Wei

Published
2024
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19. Using genome and transcriptome data from African-ancestry female participants to identify putative breast cancer susceptibility genes

Author

Ping, Jie, Jia, Guochong, Cai, Qiuyin, Guo, Xingyi, Tao, Ran, Ambrosone, Christine, Huo, Dezheng, Ambs, Stefan, Barnard, Mollie E., Chen, Yu, Garcia-Closas, Montserrat, Gu, Jian, Hu, Jennifer J., John, Esther M., Li, Christopher I., Nathanson, Katherine, Nemesure, Barbara, Olopade, Olufunmilayo I., Pal, Tuya, Press, Michael F., Sanderson, Maureen, Sandler, Dale P., Yoshimatsu, Toshio, Adejumo, Prisca O., Ahearn, Thomas, Brewster, Abenaa M., Hennis, Anselm J. M., Makumbi, Timothy, Ndom, Paul, O’Brien, Katie M., Olshan, Andrew F., Oluwasanu, Mojisola M., Reid, Sonya, Yao, Song, Butler, Ebonee N., Huang, Maosheng, Ntekim, Atara, Li, Bingshan, Troester, Melissa A., Palmer, Julie R., Haiman, Christopher A., Long, Jirong, and Zheng, Wei

Published
2024
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23. Constructing prediction models for the moderate/severe bronchopulmonary dysplasia in extremely preterm infants at different days after birth

Author

GU Jian, FAN Yuwei, LONG Huan, XIA Changshun, FAN Siying, LI Yuan, ZHONG Yi, ZHONG Xinqi

Subjects
extremely preterm infant, bronchopulmonary dysplasia, risk factor, prediction model, Medicine
Abstract

Objective To construct prediction models for moderate/severe bronchopulmonary dysplasia （BPD） in extremely preterm infants at different days after birth. Methods The preterm infants with BPD at a gestational age of < 28 weeks at the Third Affiliated Hospital of Guangzhou Medical University from September 2017 to December 2019 were retrospectively selected. They were divided into the mild-BPD group and moderate/severe-BPD group. The significant variables screened by using single-factor analysis were subject to risk assessment analysis by multivariate Logistic regression analysis. Early prediction models were established， and the predictive performance was validated and evaluated. Results Ninety extremely preterm infants were included in this study， including 58 cases （64.4%） in the mild-BPD group and 32 cases （35.6%） in the moderate/severe-BPD group. Multiple Logistic regression analysis showed birth weight， maternal pre-pregnancy body mass index （BMI） ≥ 25 kg/m2， 1-minute Apgar score≤7 after birth and pneumonia were the influencing factors for moderate/severe BPD at 7 days after birth. Preeclampsia， maternal pre-pregnancy BMI≥25 kg/m2， pneumonia and hsPDA were the risk factors for moderate/severe BPD at 14 days postnatal age. Preeclampsia， maternal pre-pregnancy BMI≥25 kg/m2， days of invasive mechanical ventilation and hsPDA were the risk factors for moderate/severe BPD at 28 days after birth. The area under the receiver operating characteristic （ROC） curve of the prediction models for 7， 14 and 28 days after birth were 0.864 （95% CI 0.776-0.952）， 0.860 （95% CI 0.774-0.946） and 0.863 （95% CI 0.783-0.944）， respectively. A nomogram was constructed based on high risk factors， the calibrated curve was close to the reference line， and the predicted value was close to the actual value， indicating good calibration of the model. Conclusions The risk factors for moderate/severe BPD in preterm infants vary slightly on 7， 14 and 28 days after birth， mainly the birth weight， maternal pre-pregnancy BMI ≥ 25 kg/m2， 1-minute Apgar score≤7， pneumonia， preeclampsia， hsPDA and days of invasive mechanical ventilation. The predictive models based on different factors at different time points have good predictive value， which can provide guidance for clinical practice.

Published
2024
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24. Research on the Evaluation of Online Teaching Quality for International Students from Universities in China under the Epidemic

Author

Diping, Zhang, Shuang, Ao, and Ya, Gu Jian

Abstract

The teaching of foreign students in China has become an important part of online teaching and one of the implementation problems during the epidemic. In order to better understand the online teaching situation and quality of foreign students in China, and to better carry out the online teaching of foreign students in China, this article firstly constructs the online teaching quality evaluation index system based on the investigation and analysis of the current situation of online teaching for foreign students in China. Secondly, further uses the analytic hierarchy process to determine the weight of each index, and finally uses the fuzzy comprehensive evaluation method to comprehensively evaluate the online teaching quality of foreign students in China. The research results show that the quality of online teaching for foreign students from Zhejiang Province is good. This research provides a model that can be used for reference for the follow-up online teaching of international students in China.

Published
2021

25. Mass spectra of bottom-charm baryons

Author

Li, Zhen-Yu, Yu, Guo-Liang, Wang, Zhi-Gang, Gu, Jian-Zhong, and Shen, Hong-Tao

Subjects
High Energy Physics - Phenomenology
Abstract

In this paper, we investigate the mass spectra of bottom-charm baryons systematically, where the relativistic quark model and the infinitesimally shifted Gaussian basis function method are employed. Our calculation shows that the $\rho$-mode appears lower in energy than the other excited modes. According to this feature, the allowed quantum states are selected and a systematic study of the mass spectra for $\Xi_{bc}^{'}$ ($\Xi_{bc}$) and $\Omega_{bc}^{'}$ ($\Omega_{bc}$) families is performed. The root mean square radii and quark radial probability density distributions of these baryons are analyzed as well. Next, the Regge trajectories in the $(J,M^{2})$ plane are successfully constructed based on the mass spectra. At last, we present the structures of the mass spectra, and analyze the difficulty and opportunity in searching for the ground states of bottom-charm baryons in experiment., Comment: 19 pages, 9 figures, 6 tables. arXiv admin note: text overlap with arXiv:2210.13085

Published
2022
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27. Study on the Microcrack Friction Ignition Mechanism of Explosive Charge

Author

Liu, Wei, Wang, Guoping, Gu, Jian, Rui, Xiaoting, Li, Chao, Wang, Yan, Zhao, Xin, Chaari, Fakher, Series Editor, Gherardini, Francesco, Series Editor, Ivanov, Vitalii, Series Editor, Haddar, Mohamed, Series Editor, Cavas-Martínez, Francisco, Editorial Board Member, di Mare, Francesca, Editorial Board Member, Kwon, Young W., Editorial Board Member, Trojanowska, Justyna, Editorial Board Member, Xu, Jinyang, Editorial Board Member, Rui, Xiaoting, editor, and Liu, Caishan, editor

Published
2024
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28. Mass spectra of double-bottom baryons

Author

Li, Zhen-Yu, Yu, Guo-Liang, Wang, Zhi-Gang, Gu, Jian-Zhong, and Shen, Hong-Tao

Subjects
High Energy Physics - Phenomenology
Abstract

Based on the relativistic quark model and the infinitesimally shifted Gaussian basis function method, we investigate the mass spectra of double bottom baryons systematically. In the $\rho$-mode which appears lower in energy than the other excited modes, we obtain the allowed quantum states and perform a systematic study of the mass spectra of the $\Xi_{bb}$ and $\Omega_{bb}$ families. We analyze the root mean square radii and quark radial probability density distributions to deeply understand the structure of the heavy baryons. Meanwhile, the mass spectra allow us to successfully construct the Regge trajectories in the $(J,M^{2})$ plane. We also predict the masses of the ground states of double bottom baryons and discuss the differences between the structures of our spectra and those from other theoretical methods. At last, the shell structure of the double bottom baryon spectra is shown, from which one could get a bird's-eye view of the mass spectra., Comment: 16 pages, 9 figures, 5 tables. arXiv admin note: text overlap with arXiv:2207.04167

Published
2022
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29. Towards Top-Down Automated Development in Limited Scopes: A Neuro-Symbolic Framework from Expressibles to Executables

Author

Gu, Jian and Gall, Harald C.

Subjects
Computer Science - Software Engineering, Computer Science - Machine Learning, Computer Science - Programming Languages
Abstract

Deep code generation is a topic of deep learning for software engineering (DL4SE), which adopts neural models to generate code for the intended functions. Since end-to-end neural methods lack domain knowledge and software hierarchy awareness, they tend to perform poorly w.r.t project-level tasks. To systematically explore the potential improvements of code generation, we let it participate in the whole top-down development from \emph{expressibles} to \emph{executables}, which is possible in limited scopes. In the process, it benefits from massive samples, features, and knowledge. As the foundation, we suggest building a taxonomy on code data, namely code taxonomy, leveraging the categorization of code information. Moreover, we introduce a three-layer semantic pyramid (SP) to associate text data and code data. It identifies the information of different abstraction levels, and thus introduces the domain knowledge on development and reveals the hierarchy of software. Furthermore, we propose a semantic pyramid framework (SPF) as the approach, focusing on software of high modularity and low complexity. SPF divides the code generation process into stages and reserves spots for potential interactions. In addition, we conceived preliminary applications in software development to confirm the neuro-symbolic framework., Comment: 5 pages, 3 figures, 2 tables, accepted by ESEC/FSE 2023, the camera-ready version

Published
2022
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31. Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants

Author

Wang, Anqi, Shen, Jiayi, Rodriguez, Alex A., Saunders, Edward J., Chen, Fei, Janivara, Rohini, Darst, Burcu F., Sheng, Xin, Xu, Yili, Chou, Alisha J., Benlloch, Sara, Dadaev, Tokhir, Brook, Mark N., Plym, Anna, Sahimi, Ali, Hoffman, Thomas J., Takahashi, Atushi, Matsuda, Koichi, Momozawa, Yukihide, Fujita, Masashi, Laisk, Triin, Figuerêdo, Jéssica, Muir, Kenneth, Ito, Shuji, Liu, Xiaoxi, Uchio, Yuji, Kubo, Michiaki, Kamatani, Yoichiro, Lophatananon, Artitaya, Wan, Peggy, Andrews, Caroline, Lori, Adriana, Choudhury, Parichoy P., Schleutker, Johanna, Tammela, Teuvo L. J., Sipeky, Csilla, Auvinen, Anssi, Giles, Graham G., Southey, Melissa C., MacInnis, Robert J., Cybulski, Cezary, Wokolorczyk, Dominika, Lubinski, Jan, Rentsch, Christopher T., Cho, Kelly, Mcmahon, Benjamin H., Neal, David E., Donovan, Jenny L., Hamdy, Freddie C., Martin, Richard M., Nordestgaard, Borge G., Nielsen, Sune F., Weischer, Maren, Bojesen, Stig E., Røder, Andreas, Stroomberg, Hein V., Batra, Jyotsna, Chambers, Suzanne, Horvath, Lisa, Clements, Judith A., Tilly, Wayne, Risbridger, Gail P., Gronberg, Henrik, Aly, Markus, Szulkin, Robert, Eklund, Martin, Nordstrom, Tobias, Pashayan, Nora, Dunning, Alison M., Ghoussaini, Maya, Travis, Ruth C., Key, Tim J., Riboli, Elio, Park, Jong Y., Sellers, Thomas A., Lin, Hui-Yi, Albanes, Demetrius, Weinstein, Stephanie, Cook, Michael B., Mucci, Lorelei A., Giovannucci, Edward, Lindstrom, Sara, Kraft, Peter, Hunter, David J., Penney, Kathryn L., Turman, Constance, Tangen, Catherine M., Goodman, Phyllis J., Thompson, Jr., Ian M., Hamilton, Robert J., Fleshner, Neil E., Finelli, Antonio, Parent, Marie-Élise, Stanford, Janet L., Ostrander, Elaine A., Koutros, Stella, Beane Freeman, Laura E., Stampfer, Meir, Wolk, Alicja, Håkansson, Niclas, Andriole, Gerald L., Hoover, Robert N., Machiela, Mitchell J., Sørensen, Karina Dalsgaard, Borre, Michael, Blot, William J., Zheng, Wei, Yeboah, Edward D., Mensah, James E., Lu, Yong-Jie, Zhang, Hong-Wei, Feng, Ninghan, Mao, Xueying, Wu, Yudong, Zhao, Shan-Chao, Sun, Zan, Thibodeau, Stephen N., McDonnell, Shannon K., Schaid, Daniel J., West, Catharine M. L., Barnett, Gill, Maier, Christiane, Schnoeller, Thomas, Luedeke, Manuel, Kibel, Adam S., Drake, Bettina F., Cussenot, Olivier, Cancel-Tassin, Geraldine, Menegaux, Florence, Truong, Thérèse, Koudou, Yves Akoli, John, Esther M., Grindedal, Eli Marie, Maehle, Lovise, Khaw, Kay-Tee, Ingles, Sue A., Stern, Mariana C., Vega, Ana, Gómez-Caamaño, Antonio, Fachal, Laura, Rosenstein, Barry S., Kerns, Sarah L., Ostrer, Harry, Teixeira, Manuel R., Paulo, Paula, Brandão, Andreia, Watya, Stephen, Lubwama, Alexander, Bensen, Jeannette T., Butler, Ebonee N., Mohler, James L., Taylor, Jack A., Kogevinas, Manolis, Dierssen-Sotos, Trinidad, Castaño-Vinyals, Gemma, Cannon-Albright, Lisa, Teerlink, Craig C., Huff, Chad D., Pilie, Patrick, Yu, Yao, Bohlender, Ryan J., Gu, Jian, Strom, Sara S., Multigner, Luc, Blanchet, Pascal, Brureau, Laurent, Kaneva, Radka, Slavov, Chavdar, Mitev, Vanio, Leach, Robin J., Brenner, Hermann, Chen, Xuechen, Holleczek, Bernd, Schöttker, Ben, Klein, Eric A., Hsing, Ann W., Kittles, Rick A., Murphy, Adam B., Logothetis, Christopher J., Kim, Jeri, Neuhausen, Susan L., Steele, Linda, Ding, Yuan Chun, Isaacs, William B., Nemesure, Barbara, Hennis, Anselm J. M., Carpten, John, Pandha, Hardev, Michael, Agnieszka, De Ruyck, Kim, De Meerleer, Gert, Ost, Piet, Xu, Jianfeng, Razack, Azad, Lim, Jasmine, Teo, Soo-Hwang, Newcomb, Lisa F., Lin, Daniel W., Fowke, Jay H., Neslund-Dudas, Christine M., Rybicki, Benjamin A., Gamulin, Marija, Lessel, Davor, Kulis, Tomislav, Usmani, Nawaid, Abraham, Aswin, Singhal, Sandeep, Parliament, Matthew, Claessens, Frank, Joniau, Steven, Van den Broeck, Thomas, Gago-Dominguez, Manuela, Castelao, Jose Esteban, Martinez, Maria Elena, Larkin, Samantha, Townsend, Paul A., Aukim-Hastie, Claire, Bush, William S., Aldrich, Melinda C., Crawford, Dana C., Srivastava, Shiv, Cullen, Jennifer, Petrovics, Gyorgy, Casey, Graham, Wang, Ying, Tettey, Yao, Lachance, Joseph, Tang, Wei, Biritwum, Richard B., Adjei, Andrew A., Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Yamoah, Kosj, Govindasami, Koveela, Chokkalingam, Anand P., Keaton, Jacob M., Hellwege, Jacklyn N., Clark, Peter E., Jalloh, Mohamed, Gueye, Serigne M., Niang, Lamine, Ogunbiyi, Olufemi, Shittu, Olayiwola, Amodu, Olukemi, Adebiyi, Akindele O., Aisuodionoe-Shadrach, Oseremen I., Ajibola, Hafees O., Jamda, Mustapha A., Oluwole, Olabode P., Nwegbu, Maxwell, Adusei, Ben, Mante, Sunny, Darkwa-Abrahams, Afua, Diop, Halimatou, Gundell, Susan M., Roobol, Monique J., Jenster, Guido, van Schaik, Ron H. N., Hu, Jennifer J., Sanderson, Maureen, Kachuri, Linda, Varma, Rohit, McKean-Cowdin, Roberta, Torres, Mina, Preuss, Michael H., Loos, Ruth J. F., Zawistowski, Matthew, Zöllner, Sebastian, Lu, Zeyun, Van Den Eeden, Stephen K., Easton, Douglas F., Ambs, Stefan, Edwards, Todd L., Mägi, Reedik, Rebbeck, Timothy R., Fritsche, Lars, Chanock, Stephen J., Berndt, Sonja I., Wiklund, Fredrik, Nakagawa, Hidewaki, Witte, John S., Gaziano, J. Michael, Justice, Amy C., Mancuso, Nick, Terao, Chikashi, Eeles, Rosalind A., Kote-Jarai, Zsofia, Madduri, Ravi K., Conti, David V., and Haiman, Christopher A.

Published
2023
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32. A report on monitoring of coagulation indicators and treatment of microthrombus formation in AML (M4 type) after hematopoietic stem cell transplantation: a case report

Author

SHEN Lianjun, WU Wei, JI Wei, WANG Hong, SUN Xing, SHI Qingqing, SUN Mei, GU Jian, NI Jun

Subjects
coagulation indicators, closely related haploidentical hematopoietic stem cell transplantation, micro-thrombus formation, color doppler ultrasound, Medicine
Abstract

This article reports a case of acute myelomonocytic leukemia (AML-M4, CBFB gene positive) with lower limb microthrombus formation after haploidentical hematopoietic stem cell transplantation, and summarizes the experience of diagnosis and treatment. The patient received achieved complete remission (CR) after routine chemotherapy, but relapsed 2 years later and underwent a haploidentical hematopoietic stem cell transplantation. During routine treatment after transplantation, the patient’s coagulation related indicators, including D-dimer (D-D), antithrombin Ⅲ (AT-Ⅲ), von Willebrand factor (vWF), fibrinogen degradation products (FDP) and fibrin monomer (FM), were dynamically observed. The patient experienced jaundice and elevated transaminases around 100 days after transplantation, and underwent plasma exchange treatment three times through the right lower limb femoral vein catheterization. After removing the venous catheter for one week, there was left ankle concavea pitting edema of the left ankle. Vascular ultrasound examination indicated the formation of microthrombus in the superficial venous plexus of the gastrocnemius muscle in the left lower limb. D-D, vWF, FDP, FM and other indicators were increased, while AT-Ⅲ levels was decreased. After 2 weeks of oral administration of 5 mg/d berritol for antithrombotic treatment, the above coagulation indicators gradually returned to normal, and the left lower limb intermuscular venous plexus thrombosis and limb swelling disappeared. Therefore, dynamic monitoring of coagulation indicators, such as D-D, AT-Ⅲ, vWF, FDP, and FM may serve as diagnostic indicators for predict transplant related microthrombus and hypercoagulable status, providing an experimental basis for effective anticoagulant treatment in clinical practice.

Published
2024
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33. Analytical and Experimental Investigation of Asymmetric Floating Phenomena of Uniform Bodies

Author

Gu Jian, Fernandes Antonio Carlos, Chai Wei, Bu Shu Xia, and Han Xiangxi

Subjects
hydrostatic stability, floating equilibrium, asymmetric floating state, experimental validation, Naval architecture. Shipbuilding. Marine engineering, VM1-989
Abstract

Uniform symmetric bodies can be observed floating asymmetrically under certain circumstances. Previous explanations of this are mostly abstract and lack experimental verification, making their understanding and application difficult. This article presents in detail alternative insights into the floating equilibria of uniform prisms and parabolic cylinders. The intrinsic characteristics of the equilibrium curves are investigated, and several equilibria different from those in the literature are found. The inflection points in the equilibrium curves are analyzed quantitatively due to their significance for floating states. Furthermore, experiments have been conducted for the square prism which validate the derived equilibrium curve, and provide a practical impression of the asymmetric floating phenomenon of symmetric bodies. These results have the potential to be applied in naval and ocean engineering, such as in the design of vessels and floating offshore structures.

Published
2024
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34. Systematic analysis of strange single heavy baryons $\Xi_{c}$ and $\Xi_{b}$

Author

Li, Zhen-Yu, Yu, Guo-Liang, Wang, Zhi-Gang, Gu, Jian-Zhong, and Lu, Jie

Subjects
High Energy Physics - Phenomenology
Abstract

Motivated by the experimental progress in the study of heavy baryons, we investigate the mass spectra of strange single heavy baryons in the $\lambda$-mode, where the relativistic quark model and the infinitesimally shifted Gaussian basis function method are employed. It is shown that the experimental data can be well reproduced by the predicted masses. The root mean square radii and radial probability density distributions of the wave functions are analyzed in detail. Meanwhile, the mass spectra allow us to successfully construct the Regge trajectories in the $(J,M^{2})$ plane. We also preliminarily assign quantum numbers to the recently observed baryons, including $\Xi_{c}(3055)$, $\Xi_{c}(3080)$, $\Xi_{c}(2930)$, $\Xi_{c}(2923)$, $\Xi_{c}(2939)$, $\Xi_{c}(2965)$, $\Xi_{c}(2970)$, $\Xi_{c}(3123)$, $\Xi_{b}(6100)$, $\Xi_{b}(6227)$, $\Xi_{b}(6327)$ and $\Xi_{b}(6333)$. At last, the spectral structure of the strange single heavy baryons is shown. Accordingly, we predict several new baryons that might be observed in forthcoming experiments., Comment: 27 pages, 11 figures, 8 tables

Published
2022
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36. Efficient Virtual View Selection for 3D Hand Pose Estimation

Author

Cheng, Jian, Wan, Yanguang, Zuo, Dexin, Ma, Cuixia, Gu, Jian, Tan, Ping, Wang, Hongan, Deng, Xiaoming, and Zhang, Yinda

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

3D hand pose estimation from single depth is a fundamental problem in computer vision, and has wide applications.However, the existing methods still can not achieve satisfactory hand pose estimation results due to view variation and occlusion of human hand. In this paper, we propose a new virtual view selection and fusion module for 3D hand pose estimation from single depth.We propose to automatically select multiple virtual viewpoints for pose estimation and fuse the results of all and find this empirically delivers accurate and robust pose estimation. In order to select most effective virtual views for pose fusion, we evaluate the virtual views based on the confidence of virtual views using a light-weight network via network distillation. Experiments on three main benchmark datasets including NYU, ICVL and Hands2019 demonstrate that our method outperforms the state-of-the-arts on NYU and ICVL, and achieves very competitive performance on Hands2019-Task1, and our proposed virtual view selection and fusion module is both effective for 3D hand pose estimation., Comment: Accepted by AAAI2022

Published
2022

40. Transcriptome- and proteome-wide association studies identify genes associated with renal cell carcinoma

Author

Purdue, Mark P., Dutta, Diptavo, Machiela, Mitchell J., Gorman, Bryan R., Winter, Timothy, Okuhara, Dayne, Cleland, Sara, Ferreiro-Iglesias, Aida, Scheet, Paul, Liu, Aoxing, Wu, Chao, Antwi, Samuel O., Larkin, James, Zequi, Stênio C., Sun, Maxine, Hikino, Keiko, Hajiran, Ali, Lawson, Keith A., Cárcano, Flavio, Blanchet, Odile, Shuch, Brian, Nepple, Kenneth G., Margue, Gaëlle, Sundi, Debasish, Diver, W. Ryan, Folgueira, Maria A.A.K., van Bokhoven, Adrie, Neffa, Florencia, Brown, Kevin M., Hofmann, Jonathan N., Rhee, Jongeun, Yeager, Meredith, Cole, Nathan R., Hicks, Belynda D., Manning, Michelle R., Hutchinson, Amy A., Rothman, Nathaniel, Huang, Wen-Yi, Linehan, W. Marston, Lori, Adriana, Ferragu, Matthieu, Zidane-Marinnes, Merzouka, Serrano, Sérgio, Magnabosco, Wesley J., BioBank Japan Project Consortium, Vilas, Ana, Decia, Ricardo, Carusso, Florencia, Graham, Laura S., Anderson, Kyra, Bilen, Mehmet A., Arciero, Cletus, Pellegrin, Isabelle, Ricard, Solène, FinnGen, Scelo, Ghislaine, Banks, Rosamonde E., Vasudev, Naveen S., Soomro, Naeem, Stewart, Grant D., Adeyoju, Adebanji, Bromage, Stephen, Hrouda, David, Gibbons, Norma, Patel, Poulam, Sullivan, Mark, Protheroe, Andrew, Nugent, Francesca I., Fournier, Michelle J., Zhang, Xiaoyu, Martin, Lisa J., Komisarenko, Maria, Eisen, Timothy, Cunningham, Sonia A., Connolly, Denise C., Uzzo, Robert G., Zaridze, David, Mukeria, Anush, Holcatova, Ivana, Hornakova, Anna, Foretova, Lenka, Janout, Vladimir, Mates, Dana, Jinga, Viorel, Rascu, Stefan, Mijuskovic, Mirjana, Savic, Slavisa, Milosavljevic, Sasa, Gaborieau, Valérie, Abedi-Ardekani, Behnoush, McKay, James, Johansson, Mattias, Phouthavongsy, Larry, Hayman, Lindsay, Li, Jason, Lungu, Ilinca, Bezerra, Stephania M., de Souza, Aline G., Sares, Claudia T.G., Reis, Rodolfo B., Gallucci, Fabio P., Cordeiro, Mauricio D., Pomerantz, Mark, Lee, Gwo-Shu M., Freedman, Matthew L., Jeong, Anhyo, Greenberg, Samantha E., Sanchez, Alejandro, Thompson, R. Houston, Sharma, Vidit, Thiel, David D., Ball, Colleen T., Abreu, Diego, Lam, Elaine T., Nahas, William C., Master, Viraj A., Patel, Alpa V., Bernhard, Jean-Christophe, Freedman, Neal D., Bigot, Pierre, Reis, Rui M., Colli, Leandro M., Finelli, Antonio, Manley, Brandon J., Terao, Chikashi, Choueiri, Toni K., Carraro, Dirce M., Houlston, Richard, Eckel-Passow, Jeanette E., Abbosh, Philip H., Ganna, Andrea, Brennan, Paul, Gu, Jian, Chanock, Stephen J., Guo, Xinyu, Winter, Timothy D., Jahagirdar, Om, Ha, Eunji, and Susztak, Katalin

Published
2024
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41. Assemble Foundation Models for Automatic Code Summarization

Author

Gu, Jian, Salza, Pasquale, and Gall, Harald C.

Subjects
Computer Science - Software Engineering, Computer Science - Machine Learning
Abstract

Automatic code summarization is beneficial to daily software development since it could help reduce the requirement of manual writing. Currently, artificial intelligence is undergoing a paradigm shift. The foundation models pretrained on massive data and finetuned to downstream tasks surpass specially customized models. This trend inspired us to consider reusing foundation models instead of learning from scratch. Thereby, we propose a flexible and robust approach for automatic code summarization, based on neural models. We assemble available foundation models, such as CodeBERT and GPT-2, into a single neural model named AdaMo. Moreover, we utilize Gaussian noise as the simulation of contextual information to optimize the latent representation. Furthermore, we introduce two adaptive schemes from the perspective of knowledge transfer, namely continuous pretraining and intermediate finetuning, and design intermediate stage tasks for general sequence-to-sequence learning. Finally, we evaluate AdaMo against a benchmark dataset for code summarization, by comparing it with state-of-the-art models., Comment: 12 pages, 2 figures, 8 tables, accepted by SANER 2022, the camera-ready version

Published
2022

43. Pressure-induced evolution of structures and phase transition of technetium diboride.

Author

Wang, Yi X., Wu, H., Xie, Wu N., Wang, Xiao F., Sun, Shao W., and Gu, Jian B.

Subjects
PHASE transitions, PARTICLE swarm optimization, TECHNETIUM, PHASE diagrams, STRUCTURAL stability
Abstract

Using the particle swarm optimization algorithm, we conducted an extensive search for the high-pressure stable structure of technetium diboride (TcB2) within the pressure range of 0–400 GPa. At zero pressure, the P63/mmc (hP6-TcB2) structure is considered the ground state configuration. As the pressure increases, a structural transition from hP6-TcB2 to P6/mmm (hP3-TcB2) occurs at approximately 174.9 GPa. We discuss the bonding between the two distinct phases and analyze the contribution of different atomic bonds to maintaining their structural stability. Meanwhile, the temperature–pressure phase diagram of TcB2 was successfully determined for the first time through the quasi-harmonic approximation method. It is predicted that the transition pressure from hP6-TcB2 to hP3-TcB2 can be reduced to about 164 GPa at a room temperature of 300 K. These results provide valuable insights into the behavior of TcB2 under different temperature and pressure conditions and open up new possibilities for exploring its potential applications in a variety of environments. [ABSTRACT FROM AUTHOR]

Published
2024
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47. On the Effectiveness of Transfer Learning for Code Search

Author

Salza, Pasquale, Schwizer, Christoph, Gu, Jian, and Gall, Harald C.

Subjects
Computer Science - Software Engineering
Abstract

The Transformer architecture and transfer learning have marked a quantum leap in natural language processing, improving the state of the art across a range of text-based tasks. This paper examines how these advancements can be applied to and improve code search. To this end, we pre-train a BERT-based model on combinations of natural language and source code data and fine-tune it on pairs of StackOverflow question titles and code answers. Our results show that the pre-trained models consistently outperform the models that were not pre-trained. In cases where the model was pre-trained on natural language "and" source code data, it also outperforms an information retrieval baseline based on Lucene. Also, we demonstrated that the combined use of an information retrieval-based approach followed by a Transformer leads to the best results overall, especially when searching into a large search pool. Transfer learning is particularly effective when much pre-training data is available and fine-tuning data is limited. We demonstrate that natural language processing models based on the Transformer architecture can be directly applied to source code analysis tasks, such as code search. With the development of Transformer models designed more specifically for dealing with source code data, we believe the results of source code analysis tasks can be further improved., Comment: Accepted for publication in the IEEE Transactions on Software Engineering (TSE)

Published
2021
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