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Doctor Penguin Weekly

Welcome to the sixth week for the Doctor Penguin newsletter! 

Over the past week, these AI papers caught our attention: 
Hegde et al. develop a histopathology similar image search tool (Similar Medical Images Like Yours, SMILY) without using labeled histopathology images, using embeddings of query images and comparing the embedding with those in the database in a computationally efficient manner. Weinstein et al. develop a novel form of microscopy, called DNA microscopy, which uses ML to reconstruct the positions of molecules from the stochastic output of a stand-alone chemical reaction. Chan et al. demonstrate that a support vector machine (SVM) can classify agonal breathing instances (evident in approximately half of cardiac arrest cases reported to 911) in real-time within a bedroom environment. Balkenhol et al. study the effect of automated hotpot selection on manual mitotic counting compared with conventional glass slide assessment.
-- Eric Topol & Pranav Rajpurkar  

Quick Links:

  1. Similar image search for histopathology: SMILY
  2. DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction
  3. Contactless cardiac arrest detection using smart devices
  4. Deep learning assisted mitotic counting for breast cancer
In NPJ Digital Medicine

The increasing availability of large institutional and public histopathology image datasets is enabling the searching of these datasets for diagnosis, research, and education. Although these datasets typically have associated metadata such as diagnosis or clinical notes, even carefully curated datasets rarely contain annotations of the location of regions of interest on each image. As pathology images are extremely large (up to 100,000 pixels in each dimension), further laborious visual search of each image may be needed to find the feature of interest. In this paper, we introduce a deep-learning-based reverse image search tool for histopathology images: Similar Medical Images Like Yours (SMILY). We assessed SMILY’s ability to retrieve search results in two ways: using pathologist-provided annotations, and via prospective studies where pathologists evaluated the quality of SMILY search results. As a negative control in the second evaluation, pathologists were blinded to whether search results were retrieved by SMILY or randomly. In both types of assessments, SMILY was able to retrieve search results with similar histologic features, organ site, and prostate cancer Gleason grade compared with the original query. SMILY may be a useful general-purpose tool in the pathologist’s arsenal, to improve the efficiency of searching large archives of histopathology images, without the need to develop and implement specific tools for each application.

Narayan Hegde, Jason D. Hipp, Yun Liu, Michael Emmert-Buck, Emily Reif, Daniel Smilkov, Michael Terry, Carrie J. Cai, Mahul B. Amin, Craig H. Mermel, Phil Q. Nelson, Lily H. Peng, Greg S. Corrado & Martin C. Stumpe

In Cell

Analyzing the spatial organization of molecules in cells and tissues is a cornerstone of biological research and clinical practice. However, despite enormous progress in molecular profiling of cellular constituents, spatially mapping them remains a disjointed and specialized machinery-intensive process, relying on either light microscopy or direct physical registration. Here, we demonstrate DNA microscopy, a distinct imaging modality for scalable, optics-free mapping of relative biomolecule positions. In DNA microscopy of transcripts, transcript molecules are tagged in situ with randomized nucleotides, labeling each molecule uniquely. A second in situreaction then amplifies the tagged molecules, concatenates the resulting copies, and adds new randomized nucleotides to uniquely label each concatenation event. An algorithm decodes molecular proximities from these concatenated sequences and infers physical images of the original transcripts at cellular resolution with precise sequence information. Because its imaging power derives entirely from diffusive molecular dynamics, DNA microscopy constitutes a chemically encoded microscopy system.
Figure thumbnail fx1

Joshua A. Weinstein, Aviv Regev, Feng Zhang


In NPJ Digital Medicine

Out-of-hospital cardiac arrest is a leading cause of death worldwide. Rapid diagnosis and initiation of cardiopulmonary resuscitation (CPR) is the cornerstone of therapy for victims of cardiac arrest. Yet a significant fraction of cardiac arrest victims have no chance of survival because they experience an unwitnessed event, often in the privacy of their own homes. An under-appreciated diagnostic element of cardiac arrest is the presence of agonal breathing, an audible biomarker and brainstem reflex that arises in the setting of severe hypoxia. Here, we demonstrate that a support vector machine (SVM) can classify agonal breathing instances in real-time within a bedroom environment. Using real-world labeled 9-1-1 audio of cardiac arrests, we train the SVM to accurately classify agonal breathing instances. We obtain an area under the curve (AUC) of 0.9993 ± 0.0003 and an operating point with an overall sensitivity and specificity of 97.24% (95% CI: 96.86–97.61%) and 99.51% (95% CI: 99.35–99.67%). We achieve a false positive rate between 0 and 0.14% over 82 h (117,985 audio segments) of polysomnographic sleep lab data that includes snoring, hypopnea, central, and obstructive sleep apnea events. We also evaluate our classifier in home sleep environments: the false positive rate was 0–0.22% over 164 h (236,666 audio segments) of sleep data collected across 35 different bedroom environments. We prototype our proof-of-concept contactless system using commodity smart devices (Amazon Echo and Apple iPhone) and demonstrate its effectiveness in identifying cardiac arrest-associated agonal breathing instances played over the air.

Justin Chan, Thomas Rea, Shyamnath Gollakota & Jacob E. Sunshine



In Laboratory investigation; a journal of technical methods and pathology

As part of routine histological grading, for every invasive breast cancer the mitotic count is assessed by counting mitoses in the (visually selected) region with the highest proliferative activity. Because this procedure is prone to subjectivity, the present study compares visual mitotic counting with deep learning based automated mitotic counting and fully automated hotspot selection. Two cohorts were used in this study. Cohort A comprised 90 prospectively included tumors which were selected based on the mitotic frequency scores given during routine glass slide diagnostics. This pathologist additionally assessed the mitotic count in these tumors in whole slide images (WSI) within a preselected hotspot. A second observer performed the same procedures on this cohort. The preselected hotspot was generated by a convolutional neural network (CNN) trained to detect all mitotic figures in digitized hematoxylin and eosin (H&E) sections. The second cohort comprised a multicenter, retrospective TNBC cohort (n = 298), of which the mitotic count was assessed by three independent observers on glass slides. The same CNN was applied on this cohort and the absolute number of mitotic figures in the hotspot was compared to the averaged mitotic count of the observers. Baseline interobserver agreement for glass slide assessment in cohort A was good (kappa 0.689; 95% CI 0.580-0.799). Using the CNN generated hotspot in WSI, the agreement score increased to 0.814 (95% CI 0.719-0.909). Automated counting by the CNN in comparison with observers counting in the predefined hotspot region yielded an average kappa of 0.724. We conclude that manual mitotic counting is not affected by assessment modality (glass slides, WSI) and that counting mitotic figures in WSI is feasible. Using a predefined hotspot area considerably improves reproducibility. Also, fully automated assessment of mitotic score appears to be feasible without introducing additional bias or variability.

Balkenhol Maschenka C A, Tellez David, Vreuls Willem, Clahsen Pieter C, Pinckaers Hans, Ciompi Francesco, Bult Peter, van der Laak Jeroen A W M


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