PathologyBERT -- Pre-trained Vs. A New Transformer Language Model for Pathology Domain

Pathology text mining is a challenging task given the reporting variability and constant new findings in cancer sub-type definitions. However, successful text mining of a large pathology database can play a critical role to advance 'big data' cancer research like similarity-based treatment selection, case identification, prognostication, surveillance, clinical trial screening, risk stratification, and many others. While there is a growing interest in developing language models for more specific clinical domains, no pathology-specific language space exist to support the rapid data-mining development in pathology space. In literature, a few approaches fine-tuned general transformer models on specialized corpora while maintaining the original tokenizer, but in fields requiring specialized terminology, these models often fail to perform adequately. We propose PathologyBERT - a pre-trained masked language model which was trained on 347,173 histopathology specimen reports and publicly released in the Huggingface repository. Our comprehensive experiments demonstrate that pre-training of transformer model on pathology corpora yields performance improvements on Natural Language Understanding (NLU) and Breast Cancer Diagnose Classification when compared to nonspecific language models.

Multimodal spatiotemporal graph neural networks for improved prediction of 30-day all-cause hospital readmission

Measures to predict 30-day readmission are considered an important quality factor for hospitals as accurate predictions can reduce the overall cost of care by identifying high risk patients before they are discharged. While recent deep learning-based studies have shown promising empirical results on readmission prediction, several limitations exist that may hinder widespread clinical utility, such as (a) only patients with certain conditions are considered, (b) existing approaches do not leverage data temporality, (c) individual admissions are assumed independent of each other, which is unrealistic, (d) prior studies are usually limited to single source of data and single center data. To address these limitations, we propose a multimodal, modality-agnostic spatiotemporal graph neural network (MM-STGNN) for prediction of 30-day all-cause hospital readmission that fuses multimodal in-patient longitudinal data. By training and evaluating our methods using longitudinal chest radiographs and electronic health records from two independent centers, we demonstrate that MM-STGNN achieves AUROC of 0.79 on both primary and external datasets. Furthermore, MM-STGNN significantly outperforms the current clinical reference standard, LACE+ score (AUROC=0.61), on the primary dataset. For subset populations of patients with heart and vascular disease, our model also outperforms baselines on predicting 30-day readmission (e.g., 3.7 point improvement in AUROC in patients with heart disease). Lastly, qualitative model interpretability analysis indicates that while patients' primary diagnoses were not explicitly used to train the model, node features crucial for model prediction directly reflect patients' primary diagnoses. Importantly, our MM-STGNN is agnostic to node feature modalities and could be utilized to integrate multimodal data for triaging patients in various downstream resource allocation tasks.

Generalization of Deep Convolutional Neural Networks -- A Case-study on Open-source Chest Radiographs

Deep Convolutional Neural Networks (DCNNs) have attracted extensive attention and been applied in many areas, including medical image analysis and clinical diagnosis. One major challenge is to conceive a DCNN model with remarkable performance on both internal and external data. We demonstrate that DCNNs may not generalize to new data, but increasing the quality and heterogeneity of the training data helps to improve the generalizibility factor. We use InceptionResNetV2 and DenseNet121 architectures to predict the risk of 5 common chest pathologies. The experiments were conducted on three publicly available databases: CheXpert, ChestX-ray14, and MIMIC Chest Xray JPG. The results show the internal performance of each of the 5 pathologies outperformed external performance on both of the models. Moreover, our strategy of exposing the models to a mix of different datasets during the training phase helps to improve model performance on the external dataset.

Was there COVID-19 back in 2012? Challenge for AI in Diagnosis with Similar Indications

Purpose: Since the recent COVID-19 outbreak, there has been an avalanche of research papers applying deep learning based image processing to chest radiographs for detection of the disease. To test the performance of the two top models for CXR COVID-19 diagnosis on external datasets to assess model generalizability. Methods: In this paper, we present our argument regarding the efficiency and applicability of existing deep learning models for COVID-19 diagnosis. We provide results from two popular models - COVID-Net and CoroNet evaluated on three publicly available datasets and an additional institutional dataset collected from EMORY Hospital between January and May 2020, containing patients tested for COVID-19 infection using RT-PCR. Results: There is a large false positive rate (FPR) for COVID-Net on both ChexPert (55.3%) and MIMIC-CXR (23.4%) dataset. On the EMORY Dataset, COVID-Net has 61.4% sensitivity, 0.54 F1-score and 0.49 precision value. The FPR of the CoroNet model is significantly lower across all the datasets as compared to COVID-Net - EMORY(9.1%), ChexPert (1.3%), ChestX-ray14 (0.02%), MIMIC-CXR (0.06%). Conclusion: The models reported good to excellent performance on their internal datasets, however we observed from our testing that their performance dramatically worsened on external data. This is likely from several causes including overfitting models due to lack of appropriate control patients and ground truth labels. The fourth institutional dataset was labeled using RT-PCR, which could be positive without radiographic findings and vice versa. Therefore, a fusion model of both clinical and radiographic data may have better performance and generalization.

Learning Semantics for Image Annotation

Image search and retrieval engines rely heavily on textual annotation in order to match word queries to a set of candidate images. A system that can automatically annotate images with meaningful text can be highly beneficial for such engines. Currently, the approaches to develop such systems try to establish relationships between keywords and visual features of images. In this paper, We make three main contributions to this area: (i) We transform this problem from the low-level keyword space to the high-level semantics space that we refer to as the "{\em image theme}", (ii) Instead of treating each possible keyword independently, we use latent Dirichlet allocation to learn image themes from the associated texts in a training phase. Images are then annotated with image themes rather than keywords, using a modified continuous relevance model, which takes into account the spatial coherence and the visual continuity among images of common theme. (iii) To achieve more coherent annotations among images of common theme, we have integrated ConceptNet in learning the semantics of images, and hence augment image descriptions beyond annotations provided by humans. Images are thus further annotated by a few most significant words of the prominent image theme. Our extensive experiments show that a coherent theme-based image annotation using high-level semantics results in improved precision and recall as compared with equivalent classical keyword annotation systems.

Image Annotation using Multi-Layer Sparse Coding

Automatic annotation of images with descriptive words is a challenging problem with vast applications in the areas of image search and retrieval. This problem can be viewed as a label-assignment problem by a classifier dealing with a very large set of labels, i.e., the vocabulary set. We propose a novel annotation method that employs two layers of sparse coding and performs coarse-to-fine labeling. Themes extracted from the training data are treated as coarse labels. Each theme is a set of training images that share a common subject in their visual and textual contents. Our system extracts coarse labels for training and test images without requiring any prior knowledge. Vocabulary words are the fine labels to be associated with images. Most of the annotation methods achieve low recall due to the large number of available fine labels, i.e., vocabulary words. These systems also tend to achieve high precision for highly frequent words only while relatively rare words are more important for search and retrieval purposes. Our system not only outperforms various previously proposed annotation systems, but also achieves symmetric response in terms of precision and recall. Our system scores and maintains high precision for words with a wide range of frequencies. Such behavior is achieved by intelligently reducing the number of available fine labels or words for each image based on coarse labels assigned to it.