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Abstract In the biomedical domain, taxonomies organize the acquisition modalities of scientific images in hierarchical structures. Such taxonomies leverage large sets of correct image labels and provide essential information about the importance of a scientific publication, which could then be used in biocuration tasks. However, the hierarchical nature of the labels, the overhead of processing images, the absence or incompleteness of labelled data and the expertise required to label this type of data impede the creation of useful datasets for biocuration. From a multi‐year collaboration with biocurators and text‐mining researchers, we derive an iterative visual analytics and active learning (AL) strategy to address these challenges. We implement this strategy in a system called BI‐LAVA—Biocuration with Hierarchical Image Labelling through Active Learning and Visual Analytics. BI‐LAVA leverages a small set of image labels, a hierarchical set of image classifiers and AL to help model builders deal with incomplete ground‐truth labels, target a hierarchical taxonomy of image modalities and classify a large pool of unlabelled images. BI‐LAVA's front end uses custom encodings to represent data distributions, taxonomies, image projections and neighbourhoods of image thumbnails, which help model builders explore an unfamiliar image dataset and taxonomy and correct and generate labels. An evaluation with machine learning practitioners shows that our mixed human–machine approach successfully supports domain experts in understanding the characteristics of classes within the taxonomy, as well as validating and improving data quality in labelled and unlabelled collections. 

September 2023 marked the 50th anniversary of the Electronic Visualization Laboratory (EVL). This paper summarizes EVL’s efforts in Visual Data Science, with a focus on the many networked, immersive, collaborative visualization and virtual-reality (VR) systems and applications the Lab has developed and deployed, as well as lessons learned and future plans. 

Biocuration is the process of analyzing biological or biomedical articles to organize biological data into data repositories using taxonomies and ontologies. Due to the expanding number of articles and the relatively small number of biocurators, automation is desired to improve the workflow of assessing articles worth curating. As figures convey essential information, automatically integrating images may improve curation. In this work, we instantiate and evaluate a first-in-kind, hybrid image+text document search system for biocuration. The system, MouseScholar, leverages an image modality taxonomy derived in collaboration with biocurators, in addition to figure segmentation, and classifiers components as a back-end and a streamlined front-end interface to search and present document results. We formally evaluated the system with ten biocurators on a mouse genome informatics biocuration dataset and collected feedback. The results demonstrate the benefits of blending text and image information when presenting scientific articles for biocuration. 

We describe the design process and the challenges we met during a rapid multi-disciplinary pandemic project related to stay-at-home orders and social media moral frames. Unlike our typical design experience, we had to handle a steeper learning curve, emerging and continually changing datasets, as well as under-specified design requirements, persistent low visual literacy, and an extremely fast turnaround for new data ingestion, prototyping, testing and deployment. We describe the lessons learned through this experience. 

Abstract MotivationFigures in biomedical papers communicate essential information with the potential to identify relevant documents in biomedical and clinical settings. However, academic search interfaces mainly search over text fields. ResultsWe describe a search system for biomedical documents that leverages image modalities and an existing index server. We integrate a problem-specific taxonomy of image modalities and image-based data into a custom search system. Our solution features a front-end interface to enhance classical document search results with image-related data, including page thumbnails, figures, captions and image-modality information. We demonstrate the system on a subset of the CORD-19 document collection. A quantitative evaluation demonstrates higher precision and recall for biomedical document retrieval. A qualitative evaluation with domain experts further highlights our solution’s benefits to biomedical search. Availability and implementationA demonstration is available at https://runachay.evl.uic.edu/scholar. Our code and image models can be accessed via github.com/uic-evl/bio-search. The dataset is continuously expanded. 

Objective: Evaluate the effectiveness of machine learning tools that incorporate spatial information such as disease location and lymph node metastatic patterns-of-spread, for prediction of survival and toxicity in HPV+ oropharyngeal cancer (OPC). Materials & methods: 675 HPV+ OPC patients that were treated at MD Anderson Cancer Center between 2005 and 2013 with curative intent IMRT were retrospectively collected under IRB approval. Risk stratifications incorporating patient radiometric data and lymph node metastasis patterns via an anatomically-adjacent representation with hierarchical clustering were identified. These clusterings were combined into a 3-level patient stratification and included along with other known clinical features in a Cox model for predicting survival outcomes, and logistic regression for toxicity, using independent subsets for training and validation. Results: Four groups were identified and combined into a 3-level stratification. The inclusion of patient stratifications in predictive models for 5-yr Overall survival (OS), 5-year recurrence free survival, (RFS) and Radiation-associated dysphagia (RAD) consistently improved model performance measured using the area under the curve (AUC). Test set AUC improvements over models with clinical covariates, was 9 % for predicting OS, and 18 % for predicting RFS, and 7 % for predicting RAD. For models with both clinical and AJCC covariates, AUC improvement was 7 %, 9 %, and 2 % for OS, RFS, and RAD, respectively. Conclusion: Including data-driven patient stratifications considerably improve prognosis for survival and toxicity outcomes over the performance achieved by clinical staging and clinical covariates alone. These stratifications generalize well to across cohorts, and sufficient information for reproducing these clusters is included. 

Patient-Reported Outcomes (PRO) are collected directly from the patients using symptom questionnaires. In the case of head and neck cancer patients, PRO surveys are recorded every week during treatment with each patient’s visit to the clinic and at different follow-up times after the treatment has concluded. PRO surveys can be very informative regarding the patient’s status and the effect of treatment on the patient’s quality of life (QoL). Processing PRO data is challenging for several reasons. First, missing data is frequent as patients might skip a question or a questionnaire altogether. Second, PROs are patient-dependent, a rating of 5 for one patient might be a rating of 10 for another patient. Finally, most patients experience severe symptoms during treatment which usually subside over time. However, for some patients, late toxicities persist negatively affecting the patient’s QoL. These long-term severe symptoms are hard to predict and are the focus of this study. In this work, we model PRO data collected from head and neck cancer patients treated at the MD Anderson Cancer Center using the MD Anderson Symptom Inventory (MDASI) questionnaire as time series. We impute missing values with a combination of K nearest neighbor (KNN) and Long Short-Term Memory (LSTM) neural networks, and finally, apply LSTM to predict late symptom severity 12 months after treatment. We compare performance against clinical and ARIMA models. We show that the LSTM model combined with KNN imputation is effective in predicting late-stage symptom ratings for occurrence and severity under the AUC and F1 score metrics.