In the treatment of ovarian cancer, precise residual disease prediction is significant for clinical and surgical decision-making. However, traditional methods are either invasive (e.g., laparoscopy) or time-consuming (e.g., manual analysis). Recently, deep learning methods make many efforts in automatic analysis of medical images. Despite the remarkable progress, most of them underestimated the importance of 3D image information of disease, which might brings a limited performance for residual disease prediction, especially in small-scale datasets. To this end, in this paper, we propose a novel Multi-View Attention Learning (MuVAL) method for residual disease prediction, which focuses on the comprehensive learning of 3D Computed Tomography (CT) images in a multi-view manner. Specifically, we first obtain multi-view of 3D CT images from transverse, coronal and sagittal views. To better represent the image features in a multi-view manner, we further leverage attention mechanism to help find the more relevant slices in each view. Extensive experiments on a dataset of 111 patients show that our method outperforms existing deep-learning methods.
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Single-particle traces of the diffusive motion of molecules, cells, or animals are by-now routinely measured, similar to stochastic records of stock prices or weather data. Deciphering the stochastic mechanism behind the recorded dynamics is vital in understanding the observed systems. Typically, the task is to decipher the exact type of diffusion and/or to determine system parameters. The tools used in this endeavor are currently revolutionized by modern machine-learning techniques. In this Perspective we provide an overview over recently introduced methods in machine-learning for diffusive time series, most notably, those successfully competing in the Anomalous-Diffusion-Challenge. As such methods are often criticized for their lack of interpretability, we focus on means to include uncertainty estimates and feature-based approaches, both improving interpretability and providing concrete insight into the learning process of the machine. We expand the discussion by examining predictions on different out-of-distribution data. We also comment on expected future developments.
Using administrative patient-care data such as Electronic Health Records (EHR) and medical/ pharmaceutical claims for population-based scientific research has become increasingly common. With vast sample sizes leading to very small standard errors, researchers need to pay more attention to potential biases in the estimates of association parameters of interest, specifically to biases that do not diminish with increasing sample size. Of these multiple sources of biases, in this paper, we focus on understanding selection bias. We present an analytic framework using directed acyclic graphs for guiding applied researchers to dissect how different sources of selection bias may affect estimates of the association between a binary outcome and an exposure (continuous or categorical) of interest. We consider four easy-to-implement weighting approaches to reduce selection bias with accompanying variance formulae. We demonstrate through a simulation study when they can rescue us in practice with analysis of real world data. We compare these methods using a data example where our goal is to estimate the well-known association of cancer and biological sex, using EHR from a longitudinal biorepository at the University of Michigan Healthcare system. We provide annotated R codes to implement these weighted methods with associated inference.
Diagnostic codes for Barrett's esophagus (BE), a precursor to esophageal cancer, lack granularity and precision for many research or clinical use cases. Laborious manual chart review is required to extract key diagnostic phenotypes from BE pathology reports. We developed a generalizable transformer-based method to automate data extraction. Using pathology reports from Columbia University Irving Medical Center with gastroenterologist-annotated targets, we performed binary dysplasia classification as well as granularized multi-class BE-related diagnosis classification. We utilized two clinically pre-trained large language models, with best model performance comparable to a highly tailored rule-based system developed using the same data. Binary dysplasia extraction achieves 0.964 F1-score, while the multi-class model achieves 0.911 F1-score. Our method is generalizable and faster to implement as compared to a tailored rule-based approach.
Many applications, e.g. in content recommendation, sports, or recruitment, leverage the comparisons of alternatives to score those alternatives. The classical Bradley-Terry model and its variants have been widely used to do so. The historical model considers binary comparisons (victory or defeat) between alternatives, while more recent developments allow finer comparisons to be taken into account. In this article, we introduce a probabilistic model encompassing a broad variety of paired comparisons that can take discrete or continuous values. We do so by considering a well-behaved subset of the exponential family, which we call the family of generalized Bradley-Terry (GBT) models, as it includes the classical Bradley-Terry model and many of its variants. Remarkably, we prove that all GBT models are guaranteed to yield a strictly convex negative log-likelihood. Moreover, assuming a Gaussian prior on alternatives' scores, we prove that the maximum a posteriori (MAP) of GBT models, whose existence, uniqueness and fast computation are thus guaranteed, varies monotonically with respect to comparisons (the more A beats B, the better the score of A) and is Lipschitz-resilient with respect to each new comparison (a single new comparison can only have a bounded effect on all the estimated scores). These desirable properties make GBT models appealing for practical use. We illustrate some features of GBT models on simulations.
Vessel image segmentation plays a pivotal role in medical diagnostics, aiding in the early detection and treatment of vascular diseases. While segmentation based on deep learning has shown promising results, effectively segmenting small structures and maintaining connectivity between them remains challenging. To address these limitations, we propose GAEI-UNet, a novel model that combines global attention and elastic interaction-based techniques. GAEI-UNet leverages global spatial and channel context information to enhance high-level semantic understanding within the U-Net architecture, enabling precise segmentation of small vessels. Additionally, we adopt an elastic interaction-based loss function to improve connectivity among these fine structures. By capturing the forces generated by misalignment between target and predicted shapes, our model effectively learns to preserve the correct topology of vessel networks. Evaluation on retinal vessel dataset -- DRIVE demonstrates the superior performance of GAEI-UNet in terms of SE and connectivity of small structures, without significantly increasing computational complexity. This research aims to advance the field of vessel image segmentation, providing more accurate and reliable diagnostic tools for the medical community. The implementation code is available on Code.
Ultrasound (US) imaging is indispensable in clinical practice. To diagnose certain diseases, sonographers must observe corresponding dynamic anatomic structures to gather comprehensive information. However, the limited availability of specific US video cases causes teaching difficulties in identifying corresponding diseases, which potentially impacts the detection rate of such cases. The synthesis of US videos may represent a promising solution to this issue. Nevertheless, it is challenging to accurately animate the intricate motion of dynamic anatomic structures while preserving image fidelity. To address this, we present a novel online feature-decoupling framework called OnUVS for high-fidelity US video synthesis. Our highlights can be summarized by four aspects. First, we introduced anatomic information into keypoint learning through a weakly-supervised training strategy, resulting in improved preservation of anatomical integrity and motion while minimizing the labeling burden. Second, to better preserve the integrity and textural information of US images, we implemented a dual-decoder that decouples the content and textural features in the generator. Third, we adopted a multiple-feature discriminator to extract a comprehensive range of visual cues, thereby enhancing the sharpness and fine details of the generated videos. Fourth, we constrained the motion trajectories of keypoints during online learning to enhance the fluidity of generated videos. Our validation and user studies on in-house echocardiographic and pelvic floor US videos showed that OnUVS synthesizes US videos with high fidelity.
Mounting evidence underscores the prevalent hierarchical organization of cancer tissues. At the foundation of this hierarchy reside cancer stem cells, a subset of cells endowed with the pivotal role of engendering the entire cancer tissue through cell differentiation. In recent times, substantial attention has been directed towards the phenomenon of cancer cell plasticity, where the dynamic interconversion between cancer stem cells and non-stem cancer cells has garnered significant interest. Since the task of detecting cancer cell plasticity from empirical data remains a formidable challenge, we propose a Bayesian statistical framework designed to infer phenotypic plasticity within cancer cells, utilizing temporal data on cancer stem cell proportions. Our approach is grounded in a stochastic model, adept at capturing the dynamic behaviors of cells. Leveraging Bayesian analysis, we explore the moment equation governing cancer stem cell proportions, derived from the Kolmogorov forward equation of our stochastic model. With improved Euler method for ordinary differential equations, a new statistical method for parameter estimation in nonlinear ordinary differential equations models is developed, which also provides novel ideas for the study of compositional data. Extensive simulations robustly validate the efficacy of our proposed method. To further corroborate our findings, we apply our approach to analyze published data from SW620 colon cancer cell lines. Our results harmonize with \emph{in situ} experiments, thereby reinforcing the utility of our method in discerning and quantifying phenotypic plasticity within cancer cells.
Conceptualizing Machine Learning for Dynamic Information Retrieval of Electronic Health Record Notes
The large amount of time clinicians spend sifting through patient notes and documenting in electronic health records (EHRs) is a leading cause of clinician burnout. By proactively and dynamically retrieving relevant notes during the documentation process, we can reduce the effort required to find relevant patient history. In this work, we conceptualize the use of EHR audit logs for machine learning as a source of supervision of note relevance in a specific clinical context, at a particular point in time. Our evaluation focuses on the dynamic retrieval in the emergency department, a high acuity setting with unique patterns of information retrieval and note writing. We show that our methods can achieve an AUC of 0.963 for predicting which notes will be read in an individual note writing session. We additionally conduct a user study with several clinicians and find that our framework can help clinicians retrieve relevant information more efficiently. Demonstrating that our framework and methods can perform well in this demanding setting is a promising proof of concept that they will translate to other clinical settings and data modalities (e.g., labs, medications, imaging).
We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
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