More Like this

1. A Machine Learning Model for Week-Ahead Hypoglycemia Prediction From Continuous Glucose Monitoring Data

   https://doi.org/10.1177/19322968241236208  

   Giammarino, Flavia ; Senanayake, Ransalu ; Prahalad, Priya ; Maahs, David M. ; Scheinker, David ( March 2024 , Journal of Diabetes Science and Technology)

   Remote patient monitoring (RPM) programs augment type 1 diabetes (T1D) care based on retrospective continuous glucose monitoring (CGM) data. Few methods are available to estimate the likelihood of a patient experiencing clinically significant hypoglycemia within one week.

   We developed a machine learning model to estimate the probability that a patient will experience a clinically significant hypoglycemic event, defined as CGM readings below 54 mg/dL for at least 15 consecutive minutes, within one week. The model takes as input the patient’s CGM time series over a given week, and outputs the predicted probability of a clinically significant hypoglycemic event the following week. We used 10-fold cross-validation and external validation (testing on cohorts different from the training cohort) to evaluate performance. We used CGM data from three different cohorts of patients with T1D: REPLACE-BG (226 patients), Juvenile Diabetes Research Foundation (JDRF; 355 patients) and Tidepool (120 patients).

   In 10-fold cross-validation, the average area under the receiver operating characteristic curve (ROC-AUC) was 0.77 (standard deviation [SD]: 0.0233) on the REPLACE-BG cohort, 0.74 (SD: 0.0188) on the JDRF cohort, and 0.76 (SD: 0.02) on the Tidepool cohort. In external validation, the average ROC-AUC across the three cohorts was 0.74 (SD: 0.0262).

   We developed a machine learning algorithm to estimate the probability of a clinically significant hypoglycemic event within one week. Predictive algorithms may provide diabetes care providers using RPM with additional context when prioritizing T1D patients for review.

    

   more » « less
2. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

   more » « less
3. A quantitative model to ensure capacity sufficient for timely access to care in a remote patient monitoring program

   https://doi.org/10.1002/edm2.435  

   Chang, Annie ; Gao, Michael Z. ; Ferstad, Johannes O. ; Dupenloup, Paul ; Zaharieva, Dessi P. ; Maahs, David M. ; Prahalad, Priya ; Johari, Ramesh ; Scheinker, David ( June 2023 , Endocrinology, Diabetes & Metabolism)

   Abstract Introduction Algorithm‐enabled remote patient monitoring (RPM) programs pose novel operational challenges. For clinics developing and deploying such programs, no standardized model is available to ensure capacity sufficient for timely access to care. We developed a flexible model and interactive dashboard of capacity planning for whole‐population RPM‐based care for T1D. Methods Data were gathered from a weekly RPM program for 277 paediatric patients with T1D at a paediatric academic medical centre. Through the analysis of 2 years of observational operational data and iterative interviews with the care team, we identified the primary operational, population, and workforce metrics that drive demand for care providers. Based on these metrics, an interactive model was designed to facilitate capacity planning and deployed as a dashboard. Results The primary population‐level drivers of demand are the number of patients in the program, the rate at which patients enrol and graduate from the program, and the average frequency at which patients require a review of their data. The primary modifiable clinic‐level drivers of capacity are the number of care providers, the time required to review patient data and contact a patient, and the number of hours each provider allocates to the program each week. At the institution studied, the model identified a variety of practical operational approaches to better match the demand for patient care. Conclusion We designed a generalizable, systematic model for capacity planning for a paediatric endocrinology clinic providing RPM for T1D. We deployed this model as an interactive dashboard and used it to facilitate expansion of a novel care program (4 T Study) for newly diagnosed patients with T1D. This model may facilitate the systematic design of RPM‐based care programs. 

   more » « less
4. Deep learning for deterioration prediction of COVID-19 patients based on time-series of three vital signs

   https://doi.org/10.1038/s41598-023-37013-3  

   Mehrdad, Sarmad ; Shamout, Farah E. ; Wang, Yao ; Atashzar, S. Farokh ( June 2023 , Scientific Reports)

   Unrecognized deterioration of COVID-19 patients can lead to high morbidity and mortality. Most existing deterioration prediction models require a large number of clinical information, typically collected in hospital settings, such as medical images or comprehensive laboratory tests. This is infeasible for telehealth solutions and highlights a gap in deterioration prediction models based on minimal data, which can be recorded at a large scale in any clinic, nursing home, or even at the patient’s home. In this study, we develop and compare two prognostic models that predict if a patient will experience deterioration in the forthcoming 3 to 24 h. The models sequentially process routine triadic vital signs: (a) oxygen saturation, (b) heart rate, and (c) temperature. These models are also provided with basic patient information, including sex, age, vaccination status, vaccination date, and status of obesity, hypertension, or diabetes. The difference between the two models is the way that the temporal dynamics of the vital signs are processed. Model #1 utilizes a temporally-dilated version of the Long-Short Term Memory model (LSTM) for temporal processes, and Model #2 utilizes a residual temporal convolutional network (TCN) for this purpose. We train and evaluate the models using data collected from 37,006 COVID-19 patients at NYU Langone Health in New York, USA. The convolution-based model outperforms the LSTM based model, achieving a high AUROC of 0.8844–0.9336 for 3 to 24 h deterioration prediction on a held-out test set. We also conduct occlusion experiments to evaluate the importance of each input feature, which reveals the significance of continuously monitoring the variation of the vital signs. Our results show the prospect for accurate deterioration forecast using a minimum feature set that can be relatively easily obtained using wearable devices and self-reported patient information.

    

   more » « less
5. Multi-step ahead predictive model for blood glucose concentrations of type-1 diabetic patients

   https://doi.org/10.1038/s41598-021-03341-5  

   Zaidi, Syed Mohammed Arshad ; Chandola, Varun ; Ibrahim, Muhanned ; Romanski, Bianca ; Mastrandrea, Lucy D. ; Singh, Tarunraj ( December 2021 , Scientific Reports)

   Continuous monitoring of blood glucose (BG) levels is a key aspect of diabetes management. Patients with Type-1 diabetes (T1D) require an effective tool to monitor these levels in order to make appropriate decisions regarding insulin administration and food intake to keep BG levels in target range. Effectively and accurately predicting future BG levels at multi-time steps ahead benefits a patient with diabetes by helping them decrease the risks of extremes in BG including hypo- and hyperglycemia. In this study, we present a novel multi-component deep learning model that predicts the BG levels in a multi-step look ahead fashion. The model is evaluated both quantitatively and qualitatively on actual blood glucose data for 97 patients. For the prediction horizon (PH) of 30 mins, the average values forroot mean squared error(RMSE),mean absolute error(MAE),mean absolute percentage error(MAPE), andnormalized mean squared error(NRMSE) are$$23.22 \pm 6.39$$$23.22\pm 6.39$mg/dL, 16.77 ± 4.87 mg/dL,$$12.84 \pm 3.68$$$12.84\pm 3.68$and$$0.08 \pm 0.01$$$0.08\pm 0.01$respectively. When Clarke and Parkes error grid analyses were performed comparing predicted BG with actual BG, the results showed average percentage of points in Zone A of$$80.17 \pm 9.20$$$80.17\pm 9.20$and$$84.81 \pm 6.11,$$$84.81\pm 6.11,$respectively. We offer this tool as a mechanism to enhance the predictive capabilities of algorithms for patients with T1D.

    

   more » « less