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Penberthy, Lynne

Publications and source records attributed to Penberthy, Lynne.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Development of message passing-based graph convolutional networks for classifying cancer pathology reports

Abstract Background Applying graph convolutional networks (GCN) to the classification of free-form natural language texts leveraged by graph-of-words features (TextGCN) was studied and confirmed to be an effective means of describing complex natural language texts. However, the text classification models based on the TextGCN possess weaknesses in terms of memory consumption and model dissemination and distribution. In this paper, we present a fast message passing network (FastMPN), implementing a GCN with message passing architecture that provides versatility and flexibility by allowing trainable node embedding and edge weights, helping the GCN model find the better solution. We applied the FastMPN model to the task of clinical information extraction from cancer pathology reports, extracting the following six properties: main site, subsite, laterality, histology, behavior, and grade. Results We evaluated the clinical task performance of the FastMPN models in terms of micro- and macro-averaged F1 scores. A comparison was performed with the multi-task convolutional neural network (MT-CNN) model. Results show that the FastMPN model is equivalent to or better than the MT-CNN. Conclusions Our implementation revealed that our FastMPN model, which is based on the PyTorch platform, can train a large corpus (667,290 training samples) with 202,373 unique words in less than 3 minutes per epoch using one NVIDIA V100 hardware accelerator. Our experiments demonstrated that using this implementation, the clinical task performance scores of information extraction related to tumors from cancer pathology reports were highly competitive.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Landscape analysis of environmental data sources for linkage with SEER cancer patients database

Abstract One of the challenges associated with understanding environmental impacts on cancer risk and outcomes is estimating potential exposures of individuals diagnosed with cancer to adverse environmental conditions over the life course. Historically, this has been partly due to the lack of reliable measures of cancer patients’ potential environmental exposures before a cancer diagnosis. The emerging sources of cancer-related spatiotemporal environmental data and residential history information, coupled with novel technologies for data extraction and linkage, present an opportunity to integrate these data into the existing cancer surveillance data infrastructure, thereby facilitating more comprehensive assessment of cancer risk and outcomes. In this paper, we performed a landscape analysis of the available environmental data sources that could be linked to historical residential address information of cancer patients’ records collected by the National Cancer Institute’s Surveillance, Epidemiology, and End Results Program. The objective is to enable researchers to use these data to assess potential exposures at the time of cancer initiation through the time of diagnosis and even after diagnosis. The paper addresses the challenges associated with data collection and completeness at various spatial and temporal scales, as well as opportunities and directions for future research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Machine learning and deep learning tools for the automated capture of cancer surveillance data

The National Cancer Institute and the Department of Energy strategic partnership applies advanced computing and predictive machine learning and deep learning models to automate the capture of information from unstructured clinical text for inclusion in cancer registries. Applications include extraction of key data elements from pathology reports, determination of whether a pathology or radiology report is related to cancer, extraction of relevant biomarker information, and identification of recurrence. With the growing complexity of cancer diagnosis and treatment, capturing essential information with purely manual methods is increasingly difficult. These new methods for applying advanced computational capabilities to automate data extraction represent an opportunity to close critical information gaps and create a nimble, flexible platform on which new information sources, such as genomics, can be added. This will ultimately provide a deeper understanding of the drivers of cancer and outcomes in the population and increase the timeliness of reporting. These advances will enable better understanding of how real-world patients are treated and the outcomes associated with those treatments in the context of our complex medical and social environment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Topological Interpretability for Deep Learning

With the growing adoption of AI-based systems across everyday life, the need to understand their decision-making mechanisms is correspondingly increasing. The level at which we can trust the statistical inferences made from AI-based decision systems is an increasing concern, especially in high-risk systems such as criminal justice or medical diagnosis, where incorrect inferences may have tragic consequences. Despite their successes in providing solutions to problems involving real-world data, deep learning (DL) models cannot quantify the certainty of their predictions. These models are frequently quite confident, even when their solutions are incorrect. This work presents a method to infer prominent features in two DL classification models trained on clinical and non-clinical text by employing techniques from topological and geometric data analysis. We create a graph of a model's feature space and cluster the inputs into the graph's vertices by the similarity of features and prediction statistics. We then extract subgraphs demonstrating high-predictive accuracy for a given label. These subgraphs contain a wealth of information about features that the DL model has recognized as relevant to its decisions. We infer these features for a given label using a distance metric between probability measures, and demonstrate the stability of our method compared to the LIME and SHAP interpretability methods. This work establishes that we may gain insights into the decision mechanism of a DL model. This method allows us to ascertain if the model is making its decisions based on information germane to the problem or identifies extraneous patterns within the data.

Spannaus, Adam↗
DOE OSTI2023

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports

One of the goals of the Surveillance, Epidemiology, and End Results (SEER) program is to estimate incidence, prevalence, and mortality of all cancers. To that end, cancer registries across the country maintain a massive database of cancer pathology reports which contain rich information to understand cancer trends. However, these reports are stored in the form of unstructured text, and human annotators are required to read and extract relevant information. In this article, we show that existing deep learning models for automating information extraction from cancer pathology reports can be significantly improved by using ensemble model distillation. We found that by training multiple predictive models and transferring their knowledge to a single, low-resource model, we can reduce the number of highly confident wrong predictions. Our results show that our implemented methods could save 1000s of manual annotation hours.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Automatic information extraction from childhood cancer pathology reports

The International Classification of Childhood Cancer (ICCC) facilitates the effective classification of a heterogeneous group of cancers in the important pediatric population. However, there has been no development of machine learning models for the ICCC classification. We developed deep learning-based information extraction models from cancer pathology reports based on the ICD-O-3 coding standard. In this article, we describe extending the models to perform ICCC classification. We developed 2 models, ICD-O-3 classification and ICCC recoding (Model 1) and direct ICCC classification (Model 2), and 4 scenarios subject to the training sample size. We evaluated these models with a corpus consisting of 29206 reports with age at diagnosis between 0 and 19 from 6 state cancer registries. Our findings suggest that the direct ICCC classification (Model 2) is substantially better than reusing the ICD-O-3 classification model (Model 1). Applying the uncertainty quantification mechanism to assess the confidence of the algorithm in assigning a code demonstrated that the model achieved a micro-F1 score of 0.987 while abstaining (not sufficiently confident to assign a code) on only 14.8% of ambiguous pathology reports. Our experimental results suggest that the machine learning-based automatic information extraction from childhood cancer pathology reports in the ICCC is a reliable means of supplementing human annotators at state cancer registries by reading and abstracting the majority of the childhood cancer pathology reports accurately and reliably.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Deep active learning for classifying cancer pathology reports

Abstract Background Automated text classification has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often difficult and expensive. Active learning techniques may mitigate this challenge by reducing the amount of labelled data required to effectively train a model. In this study, we analyze the effectiveness of 11 active learning algorithms on classifying subsite and histology from cancer pathology reports using a Convolutional Neural Network as the text classification model. Results We compare the performance of each active learning strategy using two differently sized datasets and two different classification tasks. Our results show that on all tasks and dataset sizes, all active learning strategies except diversity-sampling strategies outperformed random sampling, i.e., no active learning. On our large dataset (15K initial labelled samples, adding 15K additional labelled samples each iteration of active learning), there was no clear winner between the different active learning strategies. On our small dataset (1K initial labelled samples, adding 1K additional labelled samples each iteration of active learning), marginal and ratio uncertainty sampling performed better than all other active learning techniques. We found that compared to random sampling, active learning strongly helps performance on rare classes by focusing on underrepresented classes. Conclusions Active learning can save annotation cost by helping human annotators efficiently and intelligently select which samples to label. Our results show that a dataset constructed using effective active learning techniques requires less than half the amount of labelled data to achieve the same performance as a dataset constructed using random sampling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Privacy-Preserving Knowledge Transfer with Bootstrap Aggregation of Teacher Ensembles

There is a need to transfer knowledge among institutions and organizations to save effort in annotation and labeling or in enhancing task performance. However, knowledge transfer is difficult because of restrictions that are in place to ensure data security and privacy. Institutions are not allowed to exchange data or perform any activity that may expose personal information. With the leverage of a differential privacy algorithm in a high-performance computing environment, we propose a new training protocol, Bootstrap Aggregation of Teacher Ensembles (BATE), which is applicable to various types of machine learning models. The BATE algorithm is based on and provides enhancements to the PATE algorithm, maintaining competitive task performance scores on complex datasets with underrepresented class labels.We conducted a proof-of-the-concept study of the information extraction from cancer pathology report data from four cancer registries and performed comparisons between four scenarios: no collaboration, no privacy-preserving collaboration, the PATE algorithm, and the proposed BATE algorithm. The results showed that the BATE algorithm maintained competitive macro-averaged F1 scores, demonstrating that the suggested algorithm is an effective yet privacy-preserving method for machine learning and deep learning solutions.

Yoon, Hong-Jun↗
DOE OSTI2020

Multimodal Data Representation with Deep Learning for Extracting Cancer Characteristics from Clinical Text

This paper presents a multimodal data representation to improve the performance of deep learning models for extracting cancer key characteristics from unstructured text in pathology reports. Specifically, in addition to using the text as the input to deep learning models, we use concept unique identifiers (CUIs) as another source of information to the models. We analyze the performance of different text and CUI data representations, including word embeddings and bag of embeddings (BOE), with a convolutional neural network (CNN) and a fully connected multilayer perceptron neural network (MLP-NN). The high level document embeddings from text and CUI inputs are combined by concatenating them and then applying a classifier. The model is used for extracting cancer subsite and histology from pathology reports. These two classification tasks have a large number of labels, i.e. 317 for subsite and 556 for histology, with extreme class imbalance. We compare the performance of the developed DL models across the two tasks based on micro- and macro-F1 scores. The evaluation shows that a multi-channel DL model that utilizes text represented by word embeddings and CUIs represented by BOE outperforms other DL models. Also, this approach significantly improves the model performance on low prevalence classes.

Alawad, Mohammed↗
DOE OSTI2020

Using case-level context to classify cancer pathology reports

Individual electronic health records (EHRs) and clinical reports are often part of a larger sequence—for example, a single patient may generate multiple reports over the trajectory of a disease. In applications such as cancer pathology reports, it is necessary not only to extract information from individual reports, but also to capture aggregate information regarding the entire cancer case based off case-level context from all reports in the sequence. In this paper, we introduce a simple modular add-on for capturing case-level context that is designed to be compatible with most existing deep learning architectures for text classification on individual reports. We test our approach on a corpus of 431,433 cancer pathology reports, and we show that incorporating case-level context significantly boosts classification accuracy across six classification tasks—site, subsite, laterality, histology, behavior, and grade. We expect that with minimal modifications, our add-on can be applied towards a wide range of other clinical text-based tasks.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Adversarial Training for Privacy-Preserving Deep Learning Model Distribution

Collaboration among cancer registries is essential to develop accurate, robust, and generalizable deep learning models for automated information extraction from cancer pathology reports. Sharing data presents a serious privacy issue, especially in biomedical research and healthcare delivery domains. Distributing pretrained deep learning (DL) models has been proposed to avoid critical data sharing. However, there is growing recognition that collaboration among clinical institutes through DL model distribution exposes new security and privacy vulnerabilities. These vulnerabilities increase in natural language processing (NLP) applications, in which the dataset vocabulary with word vector representations needs to be associated with the other model parameters. In this paper, we propose a novel privacy-preserving DL model distribution across cancer registries for information extraction from cancer pathology reports with privacy and confidentiality considerations. The proposed approach exploits the adversarial training framework to distinguish private features from shared features among different datasets. It only shares registry-invariant model parameters, without sharing raw data nor registry-specific model parameters among cancer registries. Thus, it protects both the data and the trained model simultaneously. We compare our proposed approach to single-registry models, and a model trained on centrally hosted data from different cancer registries. The results show that the proposed approach significantly outperforms the single-registry models and achieves statistically indistinguishable micro and macro F1-score as compared to the centralized model.

Alawad, Mohammed↗
DOE OSTI2019

Automatic extraction of cancer registry reportable information from free-text pathology reports using multitask convolutional neural networks

Objective: In this work we implement 2 different multitask learning (MTL) techniques, hard parameter sharing and cross-stitch, to train a word-level convolutional neural network (CNN) specifically designed for automatic extraction of cancer data from unstructured text in pathology reports. We show the importance of learning related information extraction (IE) tasks leveraging shared representations across the tasks to achieve state-of-the-art performance in classification accuracy and computational efficiency. Materials and Methods: Multitask CNN (MTCNN) attempts to tackle document information extraction by learning to extract multiple key cancer characteristics simultaneously. We trained our MTCNN to perform 5 information extraction tasks: (1) primary cancer site (65 classes), (2) laterality (4 classes), (3) behavior (3 classes), (4) histological type (63 classes), and (5) histological grade (5 classes). We evaluated the performance on a corpus of 95 231 pathology documents (71 223 unique tumors) obtained from the Louisiana Tumor Registry. We compared the performance of the MTCNN models against single-task CNN models and 2 traditional machine learning approaches, namely support vector machine (SVM) and random forest classifier (RFC). Results: MTCNNs offered superior performance across all 5 tasks in terms of classification accuracy as compared with the other machine learning models. Based on retrospective evaluation, the hard parameter sharing and cross-stitch MTCNN models correctly classified 59.04% and 57.93% of the pathology reports respectively across all 5 tasks. The baseline models achieved 53.68% (CNN), 46.37% (RFC), and 36.75% (SVM). Based on prospective evaluation, the percentages of correctly classified cases across the 5 tasks were 60.11% (hard parameter sharing), 58.13% (cross-stitch), 51.30% (single-task CNN), 42.07% (RFC), and 35.16% (SVM). Moreover, hard parameter sharing MTCNNs outperformed the other models in computational efficiency by using about the same number of trainable parameters as a single-task CNN. Conclusions: The hard parameter sharing MTCNN offers superior classification accuracy for automated coding support of pathology documents across a wide range of cancers and multiple information extraction tasks while maintaining similar training and inference time as those of a single task–specific model.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2019

Classifying Cancer Pathology Reports with Hierarchical Self-Attention Networks

We introduce a deep learning architecture, hierarchical self-attention networks (HiSANs), designed for classifying pathology reports and show how its unique architecture leads to a new state-of-the-art in accuracy, faster training, and clear interpretability. We evaluate performance on a corpus of 374,899 pathology reports obtained from the National Cancer Institute's (NCI) Surveillance, Epidemiology, and End Results (SEER) program. Each pathology report is associated with five clinical classification tasks – site, laterality, behavior, histology, and grade. We compare the performance of the HiSAN against other machine learning and deep learning approaches commonly used on medical text data – Naive Bayes, logistic regression, convolutional neural networks, and hierarchical attention networks (the previous state-of-the-art). We show that HiSANs are superior to other machine learning and deep learning text classifiers in both accuracy and macro F-score across all five classification tasks. Compared to the previous state-of-the-art, hierarchical attention networks, HiSANs not only are an order of magnitude faster to train, but also achieve about 1% better relative accuracy and 5% better relative macro F-score.

60 APPLIED LIFE SCIENCES↗