{"title":"Py-Tetrad and RPy-Tetrad: A New Python Interface with R Support for Tetrad Causal Search.","authors":"Joseph D Ramsey, Bryan Andrews","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We give novel Python and R interfaces for the (Java) Tetrad project for causal modeling, search, and estimation. The Tetrad project is a mainstay in the literature, having been under consistent development for over 30 years. Some of its algorithms are now classics, like PC and FCI; others are recent developments. It is increasingly the case, however, that researchers need to access the underlying Java code from Python or R. Existing methods for doing this are inadequate. We provide new, up-to-date methods using the JPype Python-Java interface and the Reticulate Python-R interface, directly solving these issues. With the addition of some simple tools and the provision of working examples for both Python and R, using JPype and Reticulate to interface Python and R with Tetrad is straightforward and intuitive.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"223 ","pages":"40-51"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fair Survival Time Prediction via Mutual Information Minimization.","authors":"Hyungrok Do, Yuxin Chang, Yoon Sang Cho, Padhraic Smyth, Judy Zhong","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Survival analysis is a general framework for predicting the time until a specific event occurs, often in the presence of censoring. Although this framework is widely used in practice, few studies to date have considered fairness for time-to-event outcomes, despite recent significant advances in the algorithmic fairness literature more broadly. In this paper, we propose a framework to achieve demographic parity in survival analysis models by minimizing the mutual information between predicted time-to-event and sensitive attributes. We show that our approach effectively minimizes mutual information to encourage statistical independence of time-to-event predictions and sensitive attributes. Furthermore, we propose four types of disparity assessment metrics based on common survival analysis metrics. Through experiments on multiple benchmark datasets, we demonstrate that by minimizing the dependence between the prediction and the sensitive attributes, our method can systematically improve the fairness of survival predictions and is robust to censoring.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"219 ","pages":"128-149"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140861818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Typed Markers and Context for Clinical Temporal Relation Extraction.","authors":"Cheng Cheng, Jeremy C Weiss","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Reliable extraction of temporal relations from clinical notes is a growing need in many clinical research domains. Our work introduces typed markers to the task of clinical temporal relation extraction. We demonstrate that the addition of medical entity information to clinical text as tags with context sentences then input to a transformer-based architecture can outperform more complex systems requiring feature engineering and temporal reasoning. We propose several strategies of typed marker creation that incorporate entity type information at different granularities, with extensive experiments to test their effectiveness. Our system establishes the best result on I2B2, a clinical benchmark dataset for temporal relation extraction, with a F1 at 83.5% that provides a substantial 3.3% improvement over the previous best system.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"219 ","pages":"94-109"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10929572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140112398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"EASL: A Framework for Designing, Implementing, and Evaluating ML Solutions in Clinical Healthcare Settings.","authors":"Eric Prince, Todd C Hankinson, Carsten Görg","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We introduce the Explainable Analytical Systems Lab (EASL) framework, an end-to-end solution designed to facilitate the development, implementation, and evaluation of clinical machine learning (ML) tools. EASL is highly versatile and applicable to a variety of contexts and includes resources for data management, ML model development, visualization and user interface development, service hosting, and usage analytics. To demonstrate its practical applications, we present the EASL framework in the context of a case study: designing and evaluating a deep learning classifier to predict diagnoses from medical imaging. The framework is composed of three modules, each with their own set of resources. The Workbench module stores data and develops initial ML models, the Canvas module contains a medical imaging viewer and web development framework, and the Studio module hosts the ML model and provides web analytics and support for conducting user studies. EASL encourages model developers to take a holistic view by integrating the model development, implementation, and evaluation into one framework, and thus ensures that models are both effective and reliable when used in a clinical setting. EASL contributes to our understanding of machine learning applied to healthcare by providing a comprehensive framework that makes it easier to develop and evaluate ML tools within a clinical setting.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"219 ","pages":"612-630"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Causal Inference With Outcome-Dependent Missingness And Self-Censoring.","authors":"Jacob M Chen, Daniel Malinsky, Rohit Bhattacharya","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We consider missingness in the context of causal inference when the outcome of interest may be missing. If the outcome directly affects its own missingness status, i.e., it is \"self-censoring\", this may lead to severely biased causal effect estimates. Miao et al. [2015] proposed the shadow variable method to correct for bias due to self-censoring; however, verifying the required model assumptions can be difficult. Here, we propose a test based on a randomized incentive variable offered to encourage reporting of the outcome that can be used to verify identification assumptions that are sufficient to correct for both self-censoring and confounding bias. Concretely, the test confirms whether a given set of pre-treatment covariates is sufficient to block all backdoor paths between the treatment and outcome as well as all paths between the treatment and missingness indicator after conditioning on the outcome. We show that under these conditions, the causal effect is identified by using the treatment as a shadow variable, and it leads to an intuitive inverse probability weighting estimator that uses a product of the treatment and response weights. We evaluate the efficacy of our test and downstream estimator via simulations.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"216 ","pages":"358-368"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Karine Karine, Predrag Klasnja, Susan A Murphy, Benjamin M Marlin
{"title":"Assessing the Impact of Context Inference Error and Partial Observability on RL Methods for Just-In-Time Adaptive Interventions.","authors":"Karine Karine, Predrag Klasnja, Susan A Murphy, Benjamin M Marlin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Just-in-Time Adaptive Interventions (JITAIs) are a class of personalized health interventions developed within the behavioral science community. JITAIs aim to provide the right type and amount of support by iteratively selecting a sequence of intervention options from a pre-defined set of components in response to each individual's time varying state. In this work, we explore the application of reinforcement learning methods to the problem of learning intervention option selection policies. We study the effect of context inference error and partial observability on the ability to learn effective policies. Our results show that the propagation of uncertainty from context inferences is critical to improving intervention efficacy as context uncertainty increases, while policy gradient algorithms can provide remarkable robustness to partially observed behavioral state information.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"216 ","pages":"1047-1057"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10506656/pdf/nihms-1926373.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10309493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mehdi Azabou, Venkataraman Ganesh, Shantanu Thakoor, Chi-Heng Lin, Lakshmi Sathidevi, Ran Liu, M. Vaĺko, Petar Velickovic, Eva L. Dyer
{"title":"Half-Hop: A graph upsampling approach for slowing down message passing","authors":"Mehdi Azabou, Venkataraman Ganesh, Shantanu Thakoor, Chi-Heng Lin, Lakshmi Sathidevi, Ran Liu, M. Vaĺko, Petar Velickovic, Eva L. Dyer","doi":"10.48550/arXiv.2308.09198","DOIUrl":"https://doi.org/10.48550/arXiv.2308.09198","url":null,"abstract":"Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding \"slow nodes\" at each edge that can mediate communication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"202 1","pages":"1341-1360"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45894268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Conditional Normalizing Flow for Accelerated Multi-Coil MR Imaging.","authors":"Jeffrey Wen, Rizwan Ahmad, Philip Schniter","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"202 ","pages":"36926-36939"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10712023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138814682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Haoxu Huang, Samyak Rawlekar, Sumit Chopra, Cem M Deniz
{"title":"Radiology Reports Improve Visual Representations Learned from Radiographs.","authors":"Haoxu Huang, Samyak Rawlekar, Sumit Chopra, Cem M Deniz","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Although human's ability to visually understand the structure of the World plays a crucial role in perceiving the World and making appropriate decisions, human perception does not solely rely on vision but amalgamates the information from acoustic, verbal, and visual stimuli. An active area of research has been revolving around designing an efficient framework that adapts to multiple modalities and ideally improves the performance of existing tasks. While numerous frameworks have proved effective on natural datasets like ImageNet, a limited number of studies have been carried out in the biomedical domain. In this work, we extend the available frameworks for natural data to biomedical data by leveraging the abundant, unstructured multi-modal data available as radiology images and reports. We attempt to answer the question, \"For multi-modal learning, self-supervised learning and joint learning using both learning strategies, which one improves the visual representation for downstream chest radiographs classification tasks the most?\". Our experiments indicated that in limited labeled data settings with 1% and 10% labeled data, the joint learning with multi-modal and self-supervised models outperforms self-supervised learning and is at par with multi-modal learning. Additionally, we found that multi-modal learning is generally more robust on out-of-distribution datasets. The code is publicly available online.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"227 ","pages":"1385-1405"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11234265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ba-Hien Tran, Babak Shahbaba, Stephan Mandt, Maurizio Filippone
{"title":"Fully Bayesian Autoencoders with Latent Sparse Gaussian Processes.","authors":"Ba-Hien Tran, Babak Shahbaba, Stephan Mandt, Maurizio Filippone","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We present a fully Bayesian autoencoder model that treats both local latent variables and global decoder parameters in a Bayesian fashion. This approach allows for flexible priors and posterior approximations while keeping the inference costs low. To achieve this, we introduce an amortized MCMC approach by utilizing an implicit stochastic network to learn sampling from the posterior over local latent variables. Furthermore, we extend the model by incorporating a Sparse Gaussian Process prior over the latent space, allowing for a fully Bayesian treatment of inducing points and kernel hyperparameters and leading to improved scalability. Additionally, we enable Deep Gaussian Process priors on the latent space and the handling of missing data. We evaluate our model on a range of experiments focusing on dynamic representation learning and generative modeling, demonstrating the strong performance of our approach in comparison to existing methods that combine Gaussian Processes and autoencoders.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"202 ","pages":"34409-34430"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11031196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140856806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}