Proceedings of machine learning research最新文献

{"title":"Alleviating tiling effect by random walk sliding window in high-resolution histological whole slide image synthesis.","authors":"Shunxing Bao, Ho Hin Lee, Qi Yang, Lucas W Remedios, Ruining Deng, Can Cui, Leon Y Cai, Kaiwen Xu, Xin Yu, Sophie Chiron, Yike Li, Nathan Heath Patterson, Yaohong Wang, Jia Li, Qi Liu, Ken S Lau, Joseph T Roland, Lori A Coburn, Keith T Wilson, Bennett A Landman, Yuankai Huo","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Multiplex immunofluorescence (MxIF) is an advanced molecular imaging technique that can simultaneously provide biologists with multiple (i.e., more than 20) molecular markers on a single histological tissue section. Unfortunately, due to imaging restrictions, the more routinely used hematoxylin and eosin (H&E) stain is typically unavailable with MxIF on the same tissue section. As biological H&E staining is not feasible, previous efforts have been made to obtain H&E whole slide image (WSI) from MxIF via deep learning empowered virtual staining. However, the tiling effect is a long-lasting problem in high-resolution WSI-wise synthesis. The MxIF to H&E synthesis is no exception. Limited by computational resources, the cross-stain image synthesis is typically performed at the patch-level. Thus, discontinuous intensities might be visually identified along with the patch boundaries assembling all individual patches back to a WSI. In this work, we propose a deep learning based unpaired high-resolution image synthesis method to obtain virtual H&E WSIs from MxIF WSIs (each with 27 markers/stains) with reduced tiling effects. Briefly, we first extend the CycleGAN framework by adding simultaneous nuclei and mucin segmentation supervision as spatial constraints. Then, we introduce a random walk sliding window shifting strategy during the optimized inference stage, to alleviate the tiling effects. The validation results show that our spatially constrained synthesis method achieves a 56% performance gain for the downstream cell segmentation task. The proposed inference method reduces the tiling effects by using 50% fewer computation resources without compromising performance. The proposed random sliding window inference method is a plug-and-play module, which can be generalized for other high-resolution WSI image synthesis applications. The source code with our proposed model are available at https://github.com/MASILab/RandomWalkSlidingWindow.git.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"227 ","pages":"1406-1422"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11238901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592304","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":"Data Consistent Deep Rigid MRI Motion Correction.","authors":"Nalini M Singh, Neel Dey, Malte Hoffmann, Bruce Fischl, Elfar Adalsteinsson, Robert Frost, Adrian V Dalca, Polina Golland","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Motion artifacts are a pervasive problem in MRI, leading to misdiagnosis or mischaracterization in population-level imaging studies. Current retrospective rigid intra-slice motion correction techniques jointly optimize estimates of the image and the motion parameters. In this paper, we use a deep network to reduce the joint image-motion parameter search to a search over rigid motion parameters alone. Our network produces a reconstruction as a function of two inputs: corrupted k-space data and motion parameters. We train the network using simulated, motion-corrupted k-space data generated with known motion parameters. At test-time, we estimate unknown motion parameters by minimizing a data consistency loss between the motion parameters, the network-based image reconstruction given those parameters, and the acquired measurements. Intra-slice motion correction experiments on simulated and realistic 2D fast spin echo brain MRI achieve high reconstruction fidelity while providing the benefits of explicit data consistency optimization. Our code is publicly available at https://www.github.com/nalinimsingh/neuroMoCo.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"227 ","pages":"368-381"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11482239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482672","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":"MULTIPAR: Supervised Irregular Tensor Factorization with Multi-task Learning for Computational Phenotyping.","authors":"Yifei Ren, Jian Lou, Li Xiong, Joyce C Ho, Xiaoqian Jiang, Sivasubramanium Venkatraman Bhavani","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Tensor factorization has received increasing interest due to its intrinsic ability to capture latent factors in multi-dimensional data with many applications including Electronic Health Records (EHR) mining. PARAFAC2 and its variants have been proposed to address irregular tensors where one of the tensor modes is not aligned, e.g., different patients in EHRs may have different length of records. PARAFAC2 has been successfully applied to EHRs for extracting meaningful medical concepts (phenotypes). Despite recent advancements, current models' predictability and interpretability are not satisfactory, which limits its utility for downstream analysis. In this paper, we propose MULTIPAR: a supervised irregular tensor factorization with multi-task learning for computational phenotyping. MULTIPAR is flexible to incorporate both static (e.g. in-hospital mortality prediction) and continuous or dynamic (e.g. the need for ventilation) tasks. By supervising the tensor factorization with downstream prediction tasks and leveraging information from multiple related predictive tasks, MULTIPAR can yield not only more meaningful phenotypes but also better predictive performance for downstream tasks. We conduct extensive experiments on two real-world temporal EHR datasets to demonstrate that MULTIPAR is scalable and achieves better tensor fit with more meaningful subgroups and stronger predictive performance compared to existing state-of-the-art methods. The implementation of MULTIPAR is available.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"225 ","pages":"498-511"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775499","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":"A Probabilistic Method to Predict Classifier Accuracy on Larger Datasets given Small Pilot Data.","authors":"Ethan Harvey, Wansu Chen, David M Kent, Michael C Hughes","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Practitioners building classifiers often start with a smaller pilot dataset and plan to grow to larger data in the near future. Such projects need a toolkit for extrapolating how much classifier accuracy may improve from a 2x, 10x, or 50x increase in data size. While existing work has focused on finding a single \"best-fit\" curve using various functional forms like power laws, we argue that modeling and assessing the <i>uncertainty</i> of predictions is critical yet has seen less attention. In this paper, we propose a Gaussian process model to obtain probabilistic extrapolations of accuracy or similar performance metrics as dataset size increases. We evaluate our approach in terms of error, likelihood, and coverage across six datasets. Though we focus on medical tasks and image modalities, our open source approach generalizes to any kind of classifier.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"225 ","pages":"129-144"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11826957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434464","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":"GANcMRI: Cardiac magnetic resonance video generation and physiologic guidance using latent space prompting.","authors":"Milos Vukadinovic, Alan C Kwan, Debiao Li, David Ouyang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Generative artificial intelligence can be applied to medical imaging on tasks such as privacy-preserving image generation and superresolution and denoising of existing images. Few prior approaches have used cardiac magnetic resonance imaging (cMRI) as a modality given the complexity of videos (the addition of the temporal dimension) as well as the limited scale of publicly available datasets. We introduce GANcMRI, a generative adversarial network that can synthesize cMRI videos with physiological guidance based on latent space prompting. GANcMRI uses a StyleGAN framework to learn the latent space from individual video frames and leverages the timedependent trajectory between end-systolic and end-diastolic frames in the latent space to predict progression and generate motion over time. We proposed various methods for modeling latent time-dependent trajectories and found that our Frame-to-frame approach generates the best motion and video quality. GANcMRI generated high-quality cMRI image frames that are indistinguishable by cardiologists, however, artifacts in video generation allow cardiologists to still recognize the difference between real and generated videos. The generated cMRI videos can be prompted to apply physiologybased adjustments which produces clinically relevant phenotypes recognizable by cardiologists. GANcMRI has many potential applications such as data augmentation, education, anomaly detection, and preoperative planning.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"225 ","pages":"594-606"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10783442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139426220","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":"Diffusion Models To Predict 3D Late Mechanical Activation From Sparse 2D Cardiac MRIs.","authors":"Nivetha Jayakumar, Jiarui Xing, Tonmoy Hossain, Fred Epstein, Kenneth Bilchick, Miaomiao Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Identifying regions of late mechanical activation (LMA) of the left ventricular (LV) myocardium is critical in determining the optimal pacing site for cardiac resynchronization therapy in patients with heart failure. Several deep learning-based approaches have been developed to predict 3D LMA maps of LV myocardium from a stack of sparse 2D cardiac magnetic resonance imaging (MRIs). However, these models often loosely consider the geometric shape structure of the myocardium. This makes the reconstructed activation maps suboptimal; hence leading to a reduced accuracy of predicting the late activating regions of hearts. In this paper, we propose to use shape-constrained diffusion models to better reconstruct a 3D LMA map, given a limited number of 2D cardiac MRI slices. In contrast to previous methods that primarily rely on spatial correlations of image intensities for 3D reconstruction, our model leverages object shape as priors learned from the training data to guide the reconstruction process. To achieve this, we develop a joint learning network that simultaneously learns a mean shape under deformation models. Each reconstructed image is then considered as a deformed variant of the mean shape. To validate the performance of our model, we train and test the proposed framework on a publicly available mesh dataset of 3D myocardium and compare it with state-of-the-art deep learning-based reconstruction models. Experimental results show that our model achieves superior performance in reconstructing the 3D LMA maps as compared to the state-of-the-art models.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"225 ","pages":"190-200"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10958778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208466","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":"A Meta-Evaluation of Faithfulness Metrics for Long-Form Hospital-Course Summarization.","authors":"Griffin Adams, Jason Zucker, Noémie Elhadad","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Long-form clinical summarization of hospital admissions has real-world significance because of its potential to help both clinicians and patients. The factual consistency of summaries-their faithfulness-is critical to their safe usage in clinical settings. To better understand the limitations of state-of-the-art natural language processing (NLP) systems, as well as the suitability of existing evaluation metrics, we benchmark faithfulness metrics against fine-grained human annotations for model-generated summaries of a patient's Brief Hospital Course. We create a corpus of patient hospital admissions and summaries for a cohort of HIV patients, each with complex medical histories. Annotators are presented with summaries and source notes, and asked to categorize manually highlighted summary elements (clinical entities like conditions and medications as well as actions like \"following up\") into one of three categories: \"Incorrect,\" \"Missing,\" and \"Not in Notes.\" We meta-evaluate a broad set of faithfulness metrics-proposed for the general NLP domain-by measuring the correlation of metric scores to clinician ratings. Across metrics, we explore the importance of domain adaptation (e.g. the impact of in-domain pre-training and metric fine-tuning), the use of source-summary alignments, and the effects of distilling a single metric from an ensemble. We find that off-the-shelf metrics with no exposure to clinical text correlate well to clinician ratings yet overly rely on copy-and-pasted text. As a practical guide, we observe that most metrics correlate best to clinicians when provided with one summary sentence at a time and a minimal set of supporting sentences from the notes before discharge.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"219 ","pages":"2-30"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11441639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142334002","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":"Detecting Heart Disease from Multi-View Ultrasound Images via Supervised Attention Multiple Instance Learning.","authors":"Zhe Huang, Benjamin S Wessler, Michael C Hughes","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Aortic stenosis (AS) is a degenerative valve condition that causes substantial morbidity and mortality. This condition is under-diagnosed and under-treated. In clinical practice, AS is diagnosed with expert review of transthoracic echocardiography, which produces dozens of ultrasound images of the heart. Only some of these views show the aortic valve. To automate screening for AS, deep networks must learn to mimic a human expert's ability to identify views of the aortic valve then aggregate across these relevant images to produce a study-level diagnosis. We find previous approaches to AS detection yield insufficient accuracy due to relying on inflexible averages across images. We further find that off-the-shelf attention-based multiple instance learning (MIL) performs poorly. We contribute a new end-to-end MIL approach with two key methodological innovations. First, a supervised attention technique guides the learned attention mechanism to favor relevant views. Second, a novel self-supervised pretraining strategy applies contrastive learning on the representation of the whole study instead of individual images as commonly done in prior literature. Experiments on an open-access dataset and a temporally-external heldout set show that our approach yields higher accuracy while reducing model size.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"219 ","pages":"285-307"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10923076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140095343","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":"Fairness-Aware Class Imbalanced Learning on Multiple Subgroups.","authors":"Davoud Ataee Tarzanagh, Bojian Hou, Boning Tong, Qi Long, Li Shen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We present a novel Bayesian-based optimization framework that addresses the challenge of generalization in overparameterized models when dealing with imbalanced subgroups and limited samples per subgroup. Our proposed tri-level optimization framework utilizes <i>local</i> predictors, which are trained on a small amount of data, as well as a fair and class-balanced predictor at the middle and lower levels. To effectively overcome saddle points for minority classes, our lower-level formulation incorporates sharpness-aware minimization. Meanwhile, at the upper level, the framework dynamically adjusts the loss function based on validation loss, ensuring a close alignment between the <i>global</i> predictor and local predictors. Theoretical analysis demonstrates the framework's ability to enhance classification and fairness generalization, potentially resulting in improvements in the generalization bound. Empirical results validate the superior performance of our tri-level framework compared to existing state-of-the-art approaches. The source code can be found at https://github.com/PennShenLab/FACIMS.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"216 ","pages":"2123-2133"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11003754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140857599","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":"Maximum Likelihood Estimation of Flexible Survival Densities with Importance Sampling.","authors":"Mert Ketenci, Shreyas Bhave, Noémie Elhadad, Adler Perotte","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Survival analysis is a widely-used technique for analyzing time-to-event data in the presence of censoring. In recent years, numerous survival analysis methods have emerged which scale to large datasets and relax traditional assumptions such as proportional hazards. These models, while being performant, are very sensitive to model hyperparameters including: (1) number of bins and bin size for discrete models and (2) number of cluster assignments for mixture-based models. Each of these choices requires extensive tuning by practitioners to achieve optimal performance. In addition, we demonstrate in empirical studies that: (1) optimal bin size may drastically differ based on the metric of interest (e.g., concordance vs brier score), and (2) mixture models may suffer from mode collapse and numerical instability. We propose a survival analysis approach which eliminates the need to tune hyperparameters such as mixture assignments and bin sizes, reducing the burden on practitioners. We show that the proposed approach matches or outperforms baselines on several real-world datasets.</p>","PeriodicalId":74504,"journal":{"name":"Proceedings of machine learning research","volume":"219 ","pages":"360-380"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11441640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142334003","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}