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126 results on '"Bau D"'

1. NeuroX: A Toolkit for Analyzing Individual Neurons in Neural Networks

Author

Dalvi, Fahim, Nortonsmith, Avery, Bau, D. Anthony, Belinkov, Yonatan, Sajjad, Hassan, Durrani, Nadir, and Glass, James

Subjects
Computer Science - Computation and Language
Abstract

We present a toolkit to facilitate the interpretation and understanding of neural network models. The toolkit provides several methods to identify salient neurons with respect to the model itself or an external task. A user can visualize selected neurons, ablate them to measure their effect on the model accuracy, and manipulate them to control the behavior of the model at the test time. Such an analysis has a potential to serve as a springboard in various research directions, such as understanding the model, better architectural choices, model distillation and controlling data biases., Comment: AAAI Conference on Artificial Intelligence (AAAI 2019), Demonstration track, pages 2

Published
2018

7. Rewriting a Deep Generative Model

Author

Bau, D, Liu, S, Wang, T, Zhu, JY, and Torralba, A

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, I.2.10, I.2.6, I.3.3, Computer Science - Graphics, Computer Vision and Pattern Recognition (cs.CV), Computer Science - Computer Vision and Pattern Recognition, Graphics (cs.GR), Machine Learning (cs.LG)
Abstract

A deep generative model such as a GAN learns to model a rich set of semantic and physical rules about the target distribution, but up to now, it has been obscure how such rules are encoded in the network, or how a rule could be changed. In this paper, we introduce a new problem setting: manipulation of specific rules encoded by a deep generative model. To address the problem, we propose a formulation in which the desired rule is changed by manipulating a layer of a deep network as a linear associative memory. We derive an algorithm for modifying one entry of the associative memory, and we demonstrate that several interesting structural rules can be located and modified within the layers of state-of-the-art generative models. We present a user interface to enable users to interactively change the rules of a generative model to achieve desired effects, and we show several proof-of-concept applications. Finally, results on multiple datasets demonstrate the advantage of our method against standard fine-tuning methods and edit transfer algorithms., ECCV 2020 (oral). Code at https://github.com/davidbau/rewriting. For videos and demos see https://rewriting.csail.mit.edu/

Published
2020

8. Rewriting a Deep Generative Model

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Bau, D, Liu, S, Wang, T, Zhu, JY, Torralba, A, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Bau, D, Liu, S, Wang, T, Zhu, JY, and Torralba, A

Abstract

© 2020, Springer Nature Switzerland AG. A deep generative model such as a GAN learns to model a rich set of semantic and physical rules about the target distribution, but up to now, it has been obscure how such rules are encoded in the network, or how a rule could be changed. In this paper, we introduce a new problem setting: manipulation of specific rules encoded by a deep generative model. To address the problem, we propose a formulation in which the desired rule is changed by manipulating a layer of a deep network as a linear associative memory. We derive an algorithm for modifying one entry of the associative memory, and we demonstrate that several interesting structural rules can be located and modified within the layers of state-of-the-art generative models. We present a user interface to enable users to interactively change the rules of a generative model to achieve desired effects, and we show several proof-of-concept applications. Finally, results on multiple datasets demonstrate the advantage of our method against standard fine-tuning methods and edit transfer algorithms.

Published
2021

11. The first glimpse of the endometrial microbiota in early pregnancy

Author

Moreno I, Garcia-Grau I, Bau D, Perez-Villaroya D, Gonzalez-Monfort M, Vilella F, Romero R, and Simon C

Subjects
endometrial microbiota, spontaneous abortion, microbiome, pregnancy, reproductive tract, sequencing, 16S rRNA, metagenomic, Lactobacillus crispatus, Lactobacillus iners
Abstract

Investigation of the microbial community in the female reproductive tract with the use of sequencing techniques has revealed that endometrial samples obtained through a transvaginal catheter are dominated by Lactobacillus species. Dysbiotic changes in the endometrial microbiota may be associated with implantation failure or early spontaneous abortion in patients who undergo assisted reproductive technology treatment. Whether or not there is an endometrial microbiota in early pregnancy is unknown. Herein we describe, the human endometrial microbiota in a patient who subsequently had an 8th week spontaneous clinical miscarriage with euploid embryos in the next cycle and, for the first time, during a successful pregnancy in which the endometrial fluid was sampled at 4 weeks of gestation. The microbial profile found on the endometrial sample before the spontaneous abortion had higher bacterial diversity and lower Lactobacillus abundance than the endometrial fluid from the healthy pregnancy. Functional metagenomics detected different Lactobacillus species between the 2 samples. Lactobacillus crispatus was present in the endometrium before the spontaneous abortion, as were other bacteria involved in dysbiosis, which had an unstable functional pattern characterized by transposases and insertion elements. Lactobacillus iners was the most prevalent microbe found in the endometrium during early pregnancy; its presence was associated with defense mechanisms and basal functions. These novel observations prompt future investigations to understand the potential implications of microbiology on healthy and pathologic human pregnancy.

Published
2020

15. Psychometric evaluation of the Australian interprofessional socialisation and valuing scale: An invariant measure for health practitioners and students.

Author

Bau Dilam Ardyansyah, Reinie Cordier, Margo Brewer, and Dave Parsons

Subjects
Medicine, Science
Abstract

ObjectivesThis study aimed to evaluate the psychometric properties of the Australian Interprofessional Socialisation and Valuing Scale (ISVS)-21 and provide an invariant measure for health practitioners and students to assess interprofessional socialisation.MethodsThe COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) were used as guidelines. This research began with a key step: conducting a pilot study to assess content validity, a requirement of COSMIN for item development. The ISVS-21 has not yet been validated in Australia. Content validity checks ensure the developed items accurately represent the measured construct in the intended cultural context. In addition to conducting more comprehensive tests of psychometric properties compared to previous studies on ISVS-21, this paper introduces something new by evaluating the internal structure of the instrument involving measurement invariance and hypothesis testing for construct validity based on several assumptions related to interprofessional socialisation and values. An invariant measure validates the use of the Australian ISVS-21 on practitioner and student equivalently, allowing the comparison of outcomes at both levels.ResultsThe evaluation of content validity indicated that the items were relevant, comprehensible (practitioners and students had an agreement score of >70% for all 21 items), and comprehensive to the concepts intended to be measured. Structural validity confirms ISVS-21 Australia as unidimensional, with good internal consistency reliabilities, Cronbach's α scores = 0.96 (practitioner) and 0.96 (student). Measurement invariance tests confirm ISVS-21 Australia is configural, metric and scalar invariance (ΔCFI ≤ 0.01) across the tested groups of practitioner and student, and therefore suitable for use by both cohorts in Australia. Age and length of work/study were discriminant factors for interprofessional socialisation in both cohorts; the professional background was a differentiating factor for practitioners but not for students. Hypotheses testing results support the COSMIN construct validity requirement for the measure, with 83.3% of assumptions tested accepted.ConclusionThe Australian ISVS has good psychometric properties based on evaluating the content validity, internal structure, and hypotheses testing for construct validity. In addition, Australian ISVS is an invariant measure for use by health practitioners and students and, therefore, confirmed as a quality measure to assess interprofessional socialisation for both cohorts in Australia.

Published
2024
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16. An evaluation of the psychometric properties of the Australian Collaborative Practice Assessment Tool.

Author

Bau Dilam Ardyansyah, Reinie Cordier, Margo Brewer, and Dave Parsons

Subjects
Medicine, Science
Abstract

ObjectivesThis study aimed to validate the Collaborative Practice Assessment Tool (CPAT) in the Australian setting and provide a quality instrument in terms of psychometric properties that can be used to measure interprofessional outcomes for both healthcare practitioners and students. The outcomes evaluated include the capacity to work in an interprofessional team, good interprofessional communication skills, leadership skills, ensuring clear division of tasks and roles in a team, effective conflict management, and being actively involved with patients and their families/communities in care.MethodsThe COSMIN (COnsensus-based Standards for the selection of health Measurement INstruments) taxonomy and standards were used as guides for evaluating the psychometric properties of the Australian CPAT, which include evaluations regarding instrument development requirements of sample target and size, content validity, internal structure (structural validity, internal consistency reliability and measurement invariance), and hypotheses testing. CPAT Australia was developed through two stages involving pilot studies and a validation study, both of which included healthcare practitioners and students as participants. A pilot study examined content validity regarding item relevance, item comprehensibility, and instrument comprehensiveness. The validation study was carried out to assess the internal structure of CPAT Australia for aspects of structural validity, internal consistency reliabilities, and configural, metric and scalar measurement invariance. The structural validity was explored using the following three steps: exploratory, confirmatory, and multi-group factor analysis. Construct validity was evaluated to confirm direct and indirect paths of assumptions based on a previously validated model. Data collected between August 2021 and May 2022.ResultsThe content validity evaluation confirmed that all items were relevant, understandable and comprehensive for measuring interprofessional collaborative care in Australia. Three hundred ninety-nine participants contributed to the validation study (n=152 practitioners; n=247 students). The original instrument model of 8-Factor 56-Item was improved in the Australian CPAT. Two items, Item 27 (Physicians assume the ultimate responsibility) and Item 49 (Final decision rest with the physician), were consistently rejected and therefore discarded. The internal structure of the 7-Factor 54-Item solution was confirmed as a suitable model with fit indices meeting COSMIN standards for a good model in practitioner and student cohorts. Configural, metric and scalar invariances were confirmed, indicating the invariance of the instruments when used for the practitioner and student cohorts. The construct validity evaluation indicated that 81.3% of direct and indirect assumptions were accepted, fulfilling the COSMIN requirement of >75% of proposed assumptions being accepted.ConclusionThe Australian CPAT with a 7-factor 54-item solution was confirmed as a quality measure for assessing interprofessional education and collaborative practice for both healthcare practitioners and students in Australia with robust psychometric properties.

Published
2024
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18. Application of Binary Permeability Fields for the Study of CO 2 Leakage from Geological Carbon Storage in Saline Aquifers of the Michigan Basin

Author

González-Nicolás, A., Bau, D., and Cody, B.M.

Abstract

The feasibility of geological carbon storage (GCS) sites depends on their capacity to retain safely CO2CO2 . While deep saline formations and depleted gas/oil reservoirs are good candidates to sequester CO2CO2 , gas/oil reservoirs typically have a limited storage capacity compared to ideal targets ( ∼∼ 1 Mt/year) considered for CO2CO2 disposal (Celia et al. in Water Resour Res 51(9):6846–6892, 2015. doi:10.1002/2015WR017609). In this respect, deep saline aquifers are considered more appropriate formations for GCS, but present the disadvantage of having limited characterization data. In particular, information about the continuity of the overlying sealing formations (caprock) is often sparse if it exists at all. In this work, a study of CO2CO2 leakage is conducted for a candidate GCS site located in the Michigan Basin, whose sealing properties of the caprock are practically unknown. Quantification of uncertainty on CO2CO2 leakage from the storage formation is achieved through a Monte Carlo simulation approach, relying on the use of a computationally efficient semi-analytical leakage model based upon the solution derived by Nordbotten et al. (Environ Sci Technol 43(3):743–749, 2009), which assumes leakage occurs across “passive” wells intersecting caprock layers. A categorical indicator Kriging simulator is developed and implemented to represent the caprock sealing properties and model the permeability uncertainty. Binary fields of caprock permeability are generated and exhibit mostly low permeability, with sparsely-occurring local high permeability areas where brine and CO2CO2 may leak out of the storage formation. In addition, the feasibility of extending the use of the semi-analytical model to large-area leakage pathways is studied. This work advances a methodology for preliminary uncertainty quantification of CO2CO2 leakage at sites of GCS with little or no information on the sealing properties of the caprock. The implemented analysis shows that, for the considered site, CO2CO2 leakage may not be negligible even for relatively low ( ∼∼ 1%) probabilities of finding permeable inclusions in the caprock and highlights the importance of being able to characterize caprock sealing properties over large areas.

Published
2017

19. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Author

Trussart, M, Yus, E, Martinez, S, Bau, D, Tahara, YO, Pengo, T, Widjaja, M, Kretschmer, S, Swoger, J, Djordjevic, S, Turnbull, L, Whitchurch, C, Miyata, M, Marti-Renom, MA, Lluch-Senar, M, Serrano, L, Trussart, M, Yus, E, Martinez, S, Bau, D, Tahara, YO, Pengo, T, Widjaja, M, Kretschmer, S, Swoger, J, Djordjevic, S, Turnbull, L, Whitchurch, C, Miyata, M, Marti-Renom, MA, Lluch-Senar, M, and Serrano, L

Abstract

DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.

Published
2017

20. Assessing decentralised policy implementation in Vietnam : The case of land recovery and resettlement in the Vung Ang Economic Zone

Author

de Wit, J.W., Viet Sang, L., Van Chien, L., Thu Hien, L., Viet Hung, H., Thi Anh Tuyet, D., Ngoc Bau, D., Hoa, Q., and Thi Thanh Tam, M.

Subjects
Vietnam, decentralisation, land acquisition and compensation policy, livelihoods
Abstract

From 2006 plans were implemented to create a deep-sea water port linked to an Economic Zone in the coastal Province of Ha Tinh, located in north central Vietnam. The multi-purpose Zone entitled ‘Vung Ang’, was to attract foreign investors, while the port would provide a link to nearby Laos and Thailand. The project obviously had large implications for the administrations at various levels of governance from Hanoi to the coastal communes and villages, but even more serious impacts on the people living in the affected areas. A large area of about 23,000 hectares was to be cleared, affecting the people of 9 communes, in some of which all inhabitants had to leave their houses and homesteads, to be relocated to completely new settlements about 10 miles inland. These tightly knit communities were not too happy with the prospect to leave their homes and land, the burial places of their ancestors, and the long term comforts of community support networks. While initial decision making process started at the highest levels of Vietnam Governance, the implementation of port and industrial park construction and the related relocation policy was delegated to Ha Tinh province, which is consistent with current decentralisation policies in Vietnam. Actual implementation was carried out by the affected District and Commune level officials – with support from the Communist Party led Mass Organisations – who were in charge of the planning and implementation of the relocation process. This entailed a complex and sensitive series of steps to inform affected households, prepare relocation areas and allocate compensation and alternative housing. This paper describes the implementation dynamics of relocation by depicting and assessing the roles of all stakeholders involved, including the impacts - for better or for worse – of the relocated households. It brings out the way local authorities dealt with affected people, including efforts linked to the ideal of grass-roots democracy. Key areas of contestation are uncovered, such as inadequate infrastructure and low compensation rates. The paper has a second objective to assess the degree to which decentralisation in Vietnam has been actually implemented, and how this affects policy making processes such as the Vung Ang port/industrial zone project. The paper concludes that the relocation policy was implemented in a fairly efficient and harmonious way – with a very intensive engagement of the entire provincial administrative machinery, but that it is too early to assess the livelihood opportunities of the relocated households.

Published
2012

22. Pencil code

Author

Bau, David, primary, Bau, D. Anthony, additional, Dawson, Mathew, additional, and Pickens, C. Sydney, additional

Published
2015
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33. Assessing decentralised policy implementation in Vietnam : The case of land recovery and resettlement in the Vung Ang Economic Zone

Author

Wit, J.W. (Joop) de, Viet Sang, L. (Luong), Van Chien, L. (Le), Thu Hien, L. (Luong), Viet Hung, H. (Ha), Thi Anh Tuyet, D. (Dang), Ngoc Bau, D. (Dao), Hoa, Q. (Quang), Thi Thanh Tam, M. (Mai), Wit, J.W. (Joop) de, Viet Sang, L. (Luong), Van Chien, L. (Le), Thu Hien, L. (Luong), Viet Hung, H. (Ha), Thi Anh Tuyet, D. (Dang), Ngoc Bau, D. (Dao), Hoa, Q. (Quang), and Thi Thanh Tam, M. (Mai)

Abstract

From 2006 plans were implemented to create a deep-sea water port linked to an Economic Zone in the coastal Province of Ha Tinh, located in north central Vietnam. The multi-purpose Zone entitled ‘Vung Ang’, was to attract foreign investors, while the port would provide a link to nearby Laos and Thailand. The project obviously had large implications for the administrations at various levels of governance from Hanoi to the coastal communes and villages, but even more serious impacts on the people living in the affected areas. A large area of about 23,000 hectares was to be cleared, affecting the people of 9 communes, in some of which all inhabitants had to leave their houses and homesteads, to be relocated to completely new settlements about 10 miles inland. These tightly knit communities were not too happy with the prospect to leave their homes and land, the burial places of their ancestors, and the long term comforts of community support networks. While initial decision making process started at the highest levels of Vietnam Governance, the implementation of port and industrial park construction and the related relocation policy was delegated to Ha Tinh province, which is consistent with current decentralisation policies in Vietnam. Actual implementation was carried out by the affected District and Commune level officials – with support from the Communist Party led Mass Organisations – who were in charge of the planning and implementation of the relocation process. This entailed a complex and sensitive series of steps to inform affected households, prepare relocation areas and allocate compensation and alternative housing. This paper describes the implementation dynamics of relocation by depicting and assessing the roles of all stakeholders involved, including the impacts - for better or for worse – of the relocated households. It brings out the way local authorities dealt with affected people, including efforts linked to the ideal of grass-roots democracy. Key areas

Published
2012

48. The contribution of XRCC3 genotypes to childhood acute lymphoblastic leukemia

Author

Pei JS, Chang WS, Hsu PC, Chen CC, Cheng SP, Wang YC, Tsai CW, Shen TC, and Bau DT

Subjects
acute lymphoblastic leukemia (ALL), childhood, genotype, XRCC3, polymorphism, Taiwan, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Jen-Sheng Pei,1,* Wen-Shin Chang,2,* Pei-Chen Hsu,1,* Chao-Chun Chen,1 Shun-Ping Cheng,3 Yun-Chi Wang,2 Chia-Wen Tsai,2,* Te-Chun Shen,2,4,* Da-Tian Bau2,5,6,* 1Department of Pediatrics, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan, Republic of China; 2Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan, Republic of China; 3Department of Physical Medicine and Rehabilitation, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan, Republic of China; 4Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan, Republic of China; 5Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, Republic of China; 6Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan, Republic of China *These authors contributed equally to this work Purpose: A growing body of evidence shows an association between DNA repair protein genotypes and susceptibility to various cancers. However, few studies have assessed the contribution of the genotype of XRCC3, a homologous repair gene, to the occurrence or prognosis of childhood acute lymphoblastic leukemia (ALL). In this study, we investigated the contribution of seven XRCC3 polymorphisms to childhood ALL.Patients and methods: We recruited 266 patients with childhood ALL and 266 healthy controls. Genomic DNA was isolated from peripheral blood samples. The XRCC3 rs1799794, rs45603942, rs1799796, rs861530, rs28903081, rs861539, and rs3212057 polymorphic genotypes of each subject were determined through conventional polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis.Results: Genotypes with the rs861539 polymorphism were significantly associated with the risk of childhood ALL. The allelic distribution analyses suggested a significant association between the T allele at rs861539 with an increased risk of childhood ALL in the Taiwanese population. Polymorphic variants of XRCC3 at rs3212057 or rs28903081 did not exist in the study population. XRCC3 rs1799794, rs45603942, rs1799796, and rs861530 were not significantly associated with the risk of childhood ALL in the Taiwanese population.Conclusion: Our findings suggest that XRCC3 genotypes with polymorphisms at rs861539 may play a role in determining individual susceptibility to childhood ALL in this Taiwanese population. The polymorphism may be a potential detector and predictor of childhood ALL. Keywords: acute lymphoblastic leukemia, ALL, childhood, genotype XRCC3, polymorphism, Taiwan

Published
2018

49. Interleukin-18 promoter genotype is associated with the risk of nasopharyngeal carcinoma in Taiwan

Author

Huang CY, Chang WS, Tsai CW, Hsia TC, Shen TC, Bau DT, and Shui HA

Subjects
genotype, IL-18, nasopharyngeal cancer (NPC), polymorphism, Taiwan, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Chung-Yu Huang,1,2 Wen-Shin Chang,3 Chia-Wen Tsai,3 Te-Chun Hsia,3 Te-Chun Shen,3,* Da-Tian Bau,3–5,* Hao-Ai Shui1,* 1Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan; 2Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan; 3Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan; 4Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; 5Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan *These authors contributed equally to this work Background: The incidence rate of nasopharyngeal carcinoma (NPC) has been documented to be high in Southeast Asia. Interleukin-18 (IL-18) is a multifunctional cytokine that augments interferon-γ production and acts as an important immunomediator in the development of several types of cancer.Patients and methods: This case–control study evaluated the role of IL-18 in NPC at the DNA level by genotyping its promoter polymorphisms at positions -656, -607, and -137 in a Taiwanese population. A total of 176 patients with NPC and age- and gender-matched 352 noncancer controls were included in this study.Results: The CC genotype of the IL-18-607 polymorphism was found to be associated with significantly decreased risks of NPC compared to the AA genotype (crude OR =0.50, 95% CI =0.29–0.84, P=0.0093). This significant difference persisted even in the dominant and recessive models. A significantly lower C allele frequency at position -607 was detected in the NPC group (41.8% vs 50.3%; OR =0.77; 95% CI =0.63–1.04, P=0.0089). Regarding IL-18-656 and -137 polymorphisms, there were no differential distributions of their genotypes between the NPC and control groups. After substratification of the subjects according to their smoking, alcohol consumption, and areca chewing status, the genotype distribution of the IL-18-607 polymorphism was found to be different only among nonsmokers between the NPC and control subgroups.Conclusion: This study suggests that IL-18 plays an important role in the carcinogenesis of NPC in Taiwan and that the genotype–phenotype correlation of IL-18-607 polymorphism and its contribution to NPC need to be investigated further. Keywords: genotype, IL-18, nasopharyngeal carcinoma (NPC), polymorphism, Taiwan

Published
2018

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