Toward assessing clinical trial publications for reporting transparency.

OBJECTIVE: To annotate a corpus of randomized controlled trial (RCT) publications with the checklist items of CONSORT reporting guidelines and using the corpus to develop text mining methods for RCT appraisal. METHODS: We annotated a corpus of 50 RCT articles at the sentence level using 37 fine-grained CONSORT checklist items. A subset (31 articles) was double-annotated and adjudicated, while 19 were annotated by a single annotator and reconciled by another. We calculated inter-annotator agreement at the article and section level using MASI (Measuring Agreement on Set-Valued Items) and at the CONSORT item level using Krippendorff's α. We experimented with two rule-based methods (phrase-based and section header-based) and two supervised learning approaches (support vector machine and BioBERT-based neural network classifiers), for recognizing 17 methodology-related items in the RCT Methods sections. RESULTS: We created CONSORT-TM consisting of 10,709 sentences, 4,845 (45%) of which were annotated with 5,246 labels. A median of 28 CONSORT items (out of possible 37) were annotated per article. Agreement was moderate at the article and section levels (average MASI: 0.60 and 0.64, respectively). Agreement varied considerably among individual checklist items (Krippendorff's α= 0.06-0.96). The model based on BioBERT performed best overall for recognizing methodology-related items (micro-precision: 0.82, micro-recall: 0.63, micro-F1: 0.71). Combining models using majority vote and label aggregation further improved precision and recall, respectively. CONCLUSION: Our annotated corpus, CONSORT-TM, contains more fine-grained information than earlier RCT corpora. Low frequency of some CONSORT items made it difficult to train effective text mining models to recognize them. For the items commonly reported, CONSORT-TM can serve as a testbed for text mining methods that assess RCT transparency, rigor, and reliability, and support methods for peer review and authoring assistance. Minor modifications to the annotation scheme and a larger corpus could facilitate improved text mining models. CONSORT-TM is publicly available at https://github.com/kilicogluh/CONSORT-TM.

Evaluating the Readability of Force Directed Graph Layouts: A Deep Learning Approach.

Existing graph layout algorithms are usually not able to optimize all the aesthetic properties desired in a graph layout. To evaluate how well the desired visual features are reflected in a graph layout, many readability metrics have been proposed in the past decades. However, the calculation of these readability metrics often requires access to the node and edge coordinates and is usually computationally inefficient, especially for dense graphs. Importantly, when the node and edge coordinates are not accessible, it becomes impossible to evaluate the graph layouts quantitatively. In this paper, we present a novel deep learning-based approach to evaluate the readability of graph layouts by directly using graph images. A convolutional neural network architecture is proposed and trained on a benchmark dataset of graph images, which is composed of synthetically generated graphs and graphs created by sampling from real large networks. Multiple representative readability metrics (including edge crossing, node spread, and group overlap) are considered in the proposed approach. We quantitatively compare our approach to traditional methods and qualitatively evaluate our approach by showing usage scenarios and visualizing convolutional layers. This paper is a first step towards using deep learning based methods to quantitatively evaluate images from the visualization field.