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1. Second-order group knockoffs with applications to genome-wide association studies

   https://doi.org/10.1093/bioinformatics/btae580  

   Chu, Benjamin B; Gu, Jiaqi; Chen, Zhaomeng; Morrison, Tim; Candès, Emmanuel; He, Zihuai; Sabatti, Chiara (October 2024, Bioinformatics)

   Gao, Xin (Ed.)

   Abstract MotivationConditional testing via the knockoff framework allows one to identify—among a large number of possible explanatory variables—those that carry unique information about an outcome of interest and also provides a false discovery rate guarantee on the selection. This approach is particularly well suited to the analysis of genome-wide association studies (GWAS), which have the goal of identifying genetic variants that influence traits of medical relevance. ResultsWhile conditional testing can be both more powerful and precise than traditional GWAS analysis methods, its vanilla implementation encounters a difficulty common to all multivariate analysis methods: it is challenging to distinguish among multiple, highly correlated regressors. This impasse can be overcome by shifting the object of inference from single variables to groups of correlated variables. To achieve this, it is necessary to construct “group knockoffs.” While successful examples are already documented in the literature, this paper substantially expands the set of algorithms and software for group knockoffs. We focus in particular on second-order knockoffs, for which we describe correlation matrix approximations that are appropriate for GWAS data and that result in considerable computational savings. We illustrate the effectiveness of the proposed methods with simulations and with the analysis of albuminuria data from the UK Biobank. Availability and implementationThe described algorithms are implemented in an open-source Julia package Knockoffs.jl. R and Python wrappers are available as knockoffsr and knockoffspy packages. 

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2. From the Dexterous Surgical Skill to the Battlefield—A Robotics Exploratory Study

   https://doi.org/10.1093/milmed/usaa253  

   Gonzalez, Glebys T; Kaur, Upinder; Rahman, Masudur; Venkatesh, Vishnunandan; Sanchez, Natalia; Hager, Gregory; Xue, Yexiang; Voyles, Richard; Wachs, Juan (January 2021, Military Medicine)

   null (Ed.)

   ABSTRACT Introduction Short response time is critical for future military medical operations in austere settings or remote areas. Such effective patient care at the point of injury can greatly benefit from the integration of semi-autonomous robotic systems. To achieve autonomy, robots would require massive libraries of maneuvers collected with the goal of training machine learning algorithms. Although this is attainable in controlled settings, obtaining surgical data in austere settings can be difficult. Hence, in this article, we present the Dexterous Surgical Skill (DESK) database for knowledge transfer between robots. The peg transfer task was selected as it is one of the six main tasks of laparoscopic training. In addition, we provide a machine learning framework to evaluate novel transfer learning methodologies on this database. Methods A set of surgical gestures was collected for a peg transfer task, composed of seven atomic maneuvers referred to as surgemes. The collected Dexterous Surgical Skill dataset comprises a set of surgical robotic skills using the four robotic platforms: Taurus II, simulated Taurus II, YuMi, and the da Vinci Research Kit. Then, we explored two different learning scenarios: no-transfer and domain-transfer. In the no-transfer scenario, the training and testing data were obtained from the same domain; whereas in the domain-transfer scenario, the training data are a blend of simulated and real robot data, which are tested on a real robot. Results Using simulation data to train the learning algorithms enhances the performance on the real robot where limited or no real data are available. The transfer model showed an accuracy of 81% for the YuMi robot when the ratio of real-tosimulated data were 22% to 78%. For the Taurus II and the da Vinci, the model showed an accuracy of 97.5% and 93%, respectively, training only with simulation data. Conclusions The results indicate that simulation can be used to augment training data to enhance the performance of learned models in real scenarios. This shows potential for the future use of surgical data from the operating room in deployable surgical robots in remote areas. 

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3. ARK: Robust knockoffs inference with coupling

   https://doi.org/10.1214/24-AOS2480  

   Fan, Yingying; Gao, Lan; Lv, Jinchi (April 2025, The Annals of Statistics)

   We investigate the robustness of the model-X knockoffs framework with respect to the misspecified or estimated feature distribution. We achieve such a goal by theoretically studying the feature selection performance of a practically implemented knockoffs algorithm, which we name as the approximate knockoffs (ARK) procedure, under the measures of the false discovery rate (FDR) and k-familywise error rate (k-FWER). The approximate knockoffs procedure differs from the model-X knockoffs procedure only in that the former uses the misspecified or estimated feature distribution. A key technique in our theoretical analyses is to couple the approximate knockoffs procedure with the model-X knockoffs procedure so that random variables in these two procedures can be close in realizations. We prove that if such coupled model-X knockoffs procedure exists, the approximate knockoffs procedure can achieve the asymptotic FDR or k-FWER control at the target level. We showcase three specific constructions of such coupled model-X knockoff variables, verifying their existence and justifying the robustness of the model-X knockoffs framework. Additionally, we formally connect our concept of knockoff variable coupling to a type of Wasserstein distance. 

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4. A transfer learning approach based on gradient boosting machine for diagnosis of Alzheimer’s disease

   https://doi.org/10.3389/fnagi.2022.966883  

   Shojaie, Mehdi; Cabrerizo, Mercedes; DeKosky, Steven T.; Vaillancourt, David E.; Loewenstein, David; Duara, Ranjan; Adjouadi, Malek (October 2022, Frontiers in Aging Neuroscience)

   Early detection of Alzheimer’s disease (AD) during the Mild Cognitive Impairment (MCI) stage could enable effective intervention to slow down disease progression. Computer-aided diagnosis of AD relies on a sufficient amount of biomarker data. When this requirement is not fulfilled, transfer learning can be used to transfer knowledge from a source domain with more amount of labeled data than available in the desired target domain. In this study, an instance-based transfer learning framework is presented based on the gradient boosting machine (GBM). In GBM, a sequence of base learners is built, and each learner focuses on the errors (residuals) of the previous learner. In our transfer learning version of GBM (TrGB), a weighting mechanism based on the residuals of the base learners is defined for the source instances. Consequently, instances with different distribution than the target data will have a lower impact on the target learner. The proposed weighting scheme aims to transfer as much information as possible from the source domain while avoiding negative transfer. The target data in this study was obtained from the Mount Sinai dataset which is collected and processed in a collaborative 5-year project at the Mount Sinai Medical Center. The Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset was used as the source domain. The experimental results showed that the proposed TrGB algorithm could improve the classification accuracy by 1.5 and 4.5% for CN vs. MCI and multiclass classification, respectively, as compared to the conventional methods. Also, using the TrGB model and transferred knowledge from the CN vs. AD classification of the source domain, the average score of early MCI vs. late MCI classification improved by 5%. 

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5. Targeting Development Aid with Machine Learning and Mobile Phone Data: Evidence from an Anti-Poverty Intervention in Afghanistan

   https://doi.org/10.1145/3378393.3402274  

   Aiken, Emily L.; Bedoya, Guadalupe; Coville, Aidan; Blumenstock, Joshua E. (June 2020, ACM SIGCAS Computing and Sustainable Societies (COMPASS 2020))

   null (Ed.)

   Recent papers demonstrate that non-traditional data, from mobile phones and other digital sensors, can be used to roughly estimate the wealth of individual subscribers. This paper asks a question more directly relevant to development policy: Can non-traditional data be used to more efficiently target development aid? By combining rich survey data from a "big push" anti-poverty program in Afghanistan with detailed mobile phone logs from program beneficiaries, we study the extent to which machine learning methods can accurately differentiate ultra-poor households eligible for program benefits from other households deemed ineligible. We show that supervised learning methods leveraging mobile phone data can identify ultra-poor households as accurately as standard survey-based measures of poverty, including consumption and wealth; and that combining survey-based measures with mobile phone data produces classifications more accurate than those based on a single data source. We discuss the implications and limitations of these methods for targeting extreme poverty in marginalized populations. 

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