YPFS Lessons Learned Oral History Project: An Interview with Matthew A. Feldman

Suggested Citation Form: Feldman, Matthew A., 2019. “Lessons Learned Interview. Interview by Mary Anne Chute Lynch and Alexander Nye. Yale Program on Financial Stability Lessons Learned Oral History Project. October 25, 2019. Transcript. https://ypfs.som.yale.edu/library/ypfs-lesson-learned-oral-history-project-interview-matthew-feldma

The Levo

The Levo is a performance tracking barbell attachment that will enhance and aid an athlete\u27s ability to understand their performance in the weight room. By tracking the movement of the barbell, several useful performance measurements can be extracted, analyzed and communicated to the athlete in a meaningful way. This document will state all requirements, their explanations, and expectations for the product at the alpha phase proof of concept, and beta phase prototype. Furthermore, it will also include the test plan, sustainability, safety, and engineering standards used to create the Levo

CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison

Large, labeled datasets have driven deep learning methods to achieve expert-level performance on a variety of medical imaging tasks. We present CheXpert, a large dataset that contains 224,316 chest radiographs of 65,240 patients. We design a labeler to automatically detect the presence of 14 observations in radiology reports, capturing uncertainties inherent in radiograph interpretation. We investigate different approaches to using the uncertainty labels for training convolutional neural networks that output the probability of these observations given the available frontal and lateral radiographs. On a validation set of 200 chest radiographic studies which were manually annotated by 3 board-certified radiologists, we find that different uncertainty approaches are useful for different pathologies. We then evaluate our best model on a test set composed of 500 chest radiographic studies annotated by a consensus of 5 board-certified radiologists, and compare the performance of our model to that of 3 additional radiologists in the detection of 5 selected pathologies. On Cardiomegaly, Edema, and Pleural Effusion, the model ROC and PR curves lie above all 3 radiologist operating points. We release the dataset to the public as a standard benchmark to evaluate performance of chest radiograph interpretation models. The dataset is freely available at https://stanfordmlgroup.github.io/competitions/chexpert .Comment: Published in AAAI 201

A Simple Standard for Sharing Ontological Mappings (SSSOM).

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

Development and Experimental Validation of a 20K Atlantic Cod (Gadus morhua) Oligonucleotide Microarray Based on a Collection of over 150,000 ESTs

The collapse of Atlantic cod (Gadus morhua) wild populations strongly impacted the Atlantic cod fishery and led to the development of cod aquaculture. In order to improve aquaculture and broodstock quality, we need to gain knowledge of genes and pathways involved in Atlantic cod responses to pathogens and other stressors. The Atlantic Cod Genomics and Broodstock Development Project has generated over 150,000 expressed sequence tags from 42 cDNA libraries representing various tissues, developmental stages, and stimuli. We used this resource to develop an Atlantic cod oligonucleotide microarray containing 20,000 unique probes. Selection of sequences from the full range of cDNA libraries enables application of the microarray for a broad spectrum of Atlantic cod functional genomics studies. We included sequences that were highly abundant in suppression subtractive hybridization (SSH) libraries, which were enriched for transcripts responsive to pathogens or other stressors. These sequences represent genes that potentially play an important role in stress and/or immune responses, making the microarray particularly useful for studies of Atlantic cod gene expression responses to immune stimuli and other stressors. To demonstrate its value, we used the microarray to analyze the Atlantic cod spleen response to stimulation with formalin-killed, atypical Aeromonas salmonicida, resulting in a gene expression profile that indicates a strong innate immune response. These results were further validated by quantitative PCR analysis and comparison to results from previous analysis of an SSH library. This study shows that the Atlantic cod 20K oligonucleotide microarray is a valuable new tool for Atlantic cod functional genomics research

Navigating frailty: how can digital tools support holistic assessments and integrate care across sectors?

Summary Using a design-led methodology and cross-organisational partnership, we worked with people living with frailty, unpaid carers, and professionals to explore the challenges of navigating care and develop new digital tools. Abstract With an increasingly frail population (1) and stretched health and social care services, the third sector has become essential for supporting people living with frailty (PLWF) and unpaid carers in navigating complex and fragmented care systems (2). Through an innovative partnership between Midlothian Health and Social Care Partnership (MHSCP), the British Red Cross (BRC), VOCAL (Voices of Carers Across Lothian) and Scotland's Digital Health and Care Innovation Centre (DHI), funded by the Scottish Government, we are developing new digitally enabled approaches which can help PLWF and carers to navigate care. Using a design-led methodology, we began with a multidisciplinary professional workshop which explored how IT systems and risk-averse information governance policies siloes information and requires individuals to tell their story many times. Next, interviews with PLWF and carers identified that many people struggled with navigating the system, coordinating care, and tracking who was involved. Application forms for services and benefits were overly complex, requiring information to be inputted multiple times. Professionals such as BRC and VOCAL advisors who helped people navigate these processes were highly valued. With this in mind, we focused on the BRC "What Matters to You?" assessment. This person-centred conversation builds a holistic picture of the person, helps them navigate options, and sets goals for living independently. BRC then agrees actions with the individual to take forward. However, BRC staff found that the paper form used for the assessment interfered with their ability to build rapport and follow the natural flow of conversation. Through participatory workshops, we unpicked the knowledge embedded within the current process and co-designed ideas with staff. We identified moments in the conversation where the tool should 'disappear', and moments when the tool could be used to support improved communication. From this, we developed digital prototypes for a new assessment tool which records information about the individual in a more holistic way, shows the people involved in someone’s care, and makes it simple to record and track actions. The information can also be shared with other professionals or used to complete applications using a transparent consent process. The prototypes were validated in workshops with BRC staff, VOCAL staff, PLWF, and unpaid carers. Their feedback showed that the tool was considered extremely valuable in helping citizens understand what information was being recorded about them and taking charge of their care. The learning gained in the project offers insight into the potential for digital tools to support person-centred frailty assessments, and the design-led process for collaboratively developing innovative tools that meet the needs of citizens and professionals. In the next phase, we plan to develop a working proof of concept, which can be trialled in Midlothian. (1) Reeves D, Pye S, Ashcroft DM, Clegg A, Kontopantelis E, Blakeman T, et al. The challenge of ageing populations and patient frailty: Can primary care adapt? BMJ (Online). 2018;362. (2) Xie Y, Hamilton M, Peisah C, Anstey KJ, Sinclair C. Navigating Community-Based Aged Care Services From the Consumer Perspective: A Scoping Review. Gerontologist. 2023;(April):1–14