Machine learning for syndromic surveillance using veterinary necropsy reports

Animal disease surveillance: How to represent textual data for classifying epidemiological information

The value of informal sources in increasing the timeliness of disease outbreak detection and providing detailed epidemiological information in the early warning and preparedness context is recognized. This study evaluates machine learning methods for classifying information from animal disease-related news at a fine-grained level (i.e., epidemiological topic). We compare two textual representations, the bag-of-words method and a distributional approach, i.e., word embeddings. Both representations performed well for binary relevance classification (F-measure of 0.839 and 0.871, respectively). Bag-of-words representation was outperformed by word embedding representation for classifying sentences into fine-grained epidemiological topics (F-measure of 0.745). Our results suggest that the word embedding approach is of interest in the context of low-frequency classes in a specialized domain. However, this representation did not bring significant performance improvements for binary relevance classification, indicating that the textual representation should be adapted to each classification task.

Classification Performance of Machine Learning Methods for Identifying Resistance, Resilience, and Susceptibility to Haemonchus contortus Infections in Sheep

This study investigated the feasibility of using easy-to-measure phenotypic traits to predict sheep resistant, resilient, and susceptible to gastrointestinal nematodes, compared the classification performance of multinomial logistic regression (MLR), linear discriminant analysis (LDA), random forest (RF), and artificial neural network (ANN) methods, and evaluated the applicability of the best classification model on each farm. The database comprised 3654 records of 1250 Santa Inês sheep from 6 farms. The animals were classified into resistant (2605 records), resilient (939 records), and susceptible (110 records) according to fecal egg count and packed cell volume. A random oversampling method was performed to balance the dataset. The classification methods were fitted using the information of age class, the month of record, farm, sex, Famacha© degree, body weight, and body condition score as predictors, and the resistance, resilience, and susceptibility to gastrointestinal nematodes as the target classes to be predicted considering data from all farms randomly. An additional leave-one-farm-out cross-validation technique was used to assess prediction quality across farms. The MLR and LDA models presented good performances in predicting susceptible and resistant animals. The results suggest that the use of readily available records and easily measurable traits may provide useful information for supporting management decisions at the farm level.

Artificial intelligence in veterinary diagnostic imaging: A literature review

Artificial intelligence in veterinary medicine is an emerging field. Machine learning, a subfield of artificial intelligence, allows computer programs to analyze large imaging datasets and learn to perform tasks relevant to veterinary diagnostic imaging. This review summarizes the small, yet growing body of artificial intelligence literature in veterinary imaging, provides necessary background to understand these papers, and provides author commentary on the state of the field. To date, less than 40 peer-reviewed publications have utilized machine learning to perform imaging-associated tasks across multiple anatomic regions in veterinary clinical and biomedical research. Major challenges in this field include collection and cleaning of sufficient image data, selection of high-quality ground truth labels, formation of relationships between veterinary and machine learning professionals, and closure of the gap between academic uses of artificial intelligence and currently available commercial products. Further development of artificial intelligence has the potential to help meet the growing need for radiological services through applications in workflow, quality control, and image interpretation for both general practitioners and radiologists.

Day-1 Competencies for Veterinarians Specific to Health Informatics

In 2015, the American Association of Veterinary Medical Colleges (AAVMC) developed the Competency-Based Veterinary Education (CBVE) framework to prepare practice-ready veterinarians through competency-based education, which is an outcomes-based approach to equipping students with the skills, knowledge, attitudes, values, and abilities to do their jobs. With increasing use of health informatics (HI: the use of information technology to deliver healthcare) by veterinarians, competencies in HI need to be developed. To reach consensus on a HI competency framework in this study, the Competency Framework Development (CFD) process was conducted using an online adaptation of Developing-A-Curriculum, an established methodology in veterinary medicine for reaching consensus among experts. The objectives of this study were to (1) create an HI competency framework for new veterinarians; (2) group the competency statements into common themes; (3) map the HI competency statements to the AAVMC competencies as illustrative sub-competencies; (4) provide insight into specific technologies that are currently relevant to new veterinary graduates; and (5) measure panelist satisfaction with the CFD process. The primary emphasis of the final HI competency framework was that veterinarians must be able to assess, select, and implement technology to optimize the client-patient experience, delivery of healthcare, and work-life balance for the veterinary team. Veterinarians must also continue their own education regarding technology by engaging relevant experts and opinion leaders.

Association between case signalment and disease diagnosis in urinary bladder disease in Australian cats and dogs

Urinary bladder diseases are common in dogs and cats; however, there is little published work on urinary bladder disease in Australian pets. We identified pathology records of Australian dogs and cats with urinary bladder tissue submitted to the University of Queensland Veterinary Laboratory Service during 1994-2016 (n = 320). We described the proportion of bladder diseases in dogs and cats, and applied the less-commonly used logistic regression procedure to quantify associations between signalment variables and disease diagnosis that were evident using descriptive statistics alone. After preliminary analysis, both species were combined because of similar results. Spayed/castrated animals were 74% less likely to be diagnosed with cystitis compared with intact animals. Animals 4-11 y old were also at lower risk of being diagnosed with cystitis compared with younger or older animals. Male animals were at increased risk of neoplasia compared to females, which contrasts with reports from North America and Europe. There was increased risk for developing neoplasia with progressive age, with up to 20 times higher odds in the > 11-y age group. Logistic regression modeling provided unique insight into proportionate morbidity of urinary bladder diseases in Australian dogs and cats.

Research perspectives on animal health in the era of artificial intelligence

Leveraging artificial intelligence (AI) approaches in animal health (AH) makes it possible to address highly complex issues such as those encountered in quantitative and predictive epidemiology, animal/human precision-based medicine, or to study host × pathogen interactions. AI may contribute (i) to diagnosis and disease case detection, (ii) to more reliable predictions and reduced errors, (iii) to representing more realistically complex biological systems and rendering computing codes more readable to non-computer scientists, (iv) to speeding-up decisions and improving accuracy in risk analyses, and (v) to better targeted interventions and anticipated negative effects. In turn, challenges in AH may stimulate AI research due to specificity of AH systems, data, constraints, and analytical objectives. Based on a literature review of scientific papers at the interface between AI and AH covering the period 2009-2019, and interviews with French researchers positioned at this interface, the present study explains the main AH areas where various AI approaches are currently mobilised, how it may contribute to renew AH research issues and remove methodological or conceptual barriers. After presenting the possible obstacles and levers, we propose several recommendations to better grasp the challenge represented by the AH/AI interface. With the development of several recent concepts promoting a global and multisectoral perspective in the field of health, AI should contribute to defract the different disciplines in AH towards more transversal and integrative research.

Autoregressive Models Applied to Time-Series Data in Veterinary Science

A time-series is any set of N time-ordered observations of a process. In veterinary epidemiology, our focus is generally on disease occurrence (the “process”) over time, but animal production, welfare or other traits might also be of interest. A common source of time-series datasets are animal disease monitoring and surveillance systems. Here, we scan the application of methods to analyse time-series data in the peer-reviewed, published literature. Based on this literature scan we focus on autocorrelation and illustrate the recommended steps using ARIMA (Autoregressive Integrated Moving Average Models) methods via analysis of a time-series of canine parvovirus (CPV) events in a pet dog population in Australia, 2009 to 2015. We conclude by identifying the barriers to the application of ARIMA methods in veterinary epidemiology and suggest some possible solutions. In the literature scan the selected 37 studies focused mostly on infectious and parasitic diseases, predominantly for analytical, rather than descriptive or predictive, purposes. Trends and seasonality were investigated, and autocorrelation analyzed, in most studies, most commonly using R software. An approach to analyzing autocorrelation using ARIMA methods was then illustrated using a time-series (week and month units) of CPV events in a pet dog population in Australia, reported to a national companion animal disease surveillance system. This time-series was derived by summing veterinarian reports of confirmed CPV diagnoses. We present data analysis output generated via the R statistical environment, and make this code available for the reader to apply to this or other time-series datasets. We also illustrate prediction of CPV events by rainfall as a covariate. Time-series analysis using ARIMA methods to understand and explore autocorrelation appears to be relatively uncommon in veterinary epidemiology. Some of the reasons might include limited availability of data of sufficient time unit length, lack of familiarity with analytical methods and available software, and how to best use the information generated. We recommend that wherever feasible, such time-series data be made available both for analysis and for methods development.