Porcine reproductive and respiratory syndrome is an infectious disease of pigs caused by PRRS virus (PRRSV). A modified live-attenuated vaccine has been widely used to control the spread of PRRSV and the classification of field strains is a key for a successful control and prevention. Restriction fragment length polymorphism targeting the Open reading frame 5 (ORF5) genes is widely used to classify PRRSV strains but showed unstable accuracy. Phylogenetic analysis is a powerful tool for PRRSV classification with consistent accuracy but it demands large computational power as the number of sequences gets increased. Our study aimed to apply four machine learning (ML) algorithms, random forest, k-nearest neighbor, support vector machine and multilayer perceptron, to classify field PRRSV strains into four clades using amino acid scores based on ORF5 gene sequence. Our study used amino acid sequences of ORF5 gene in 1931 field PRRSV strains collected in the US from 2012 to 2020. Phylogenetic analysis was used to labels field PRRSV strains into one of four clades: Lineage 5 or three clades in Linage 1. We measured accuracy and time consumption of classification using four ML approaches by different size of gene sequences. We found that all four ML algorithms classify a large number of field strains in a very short time (<2.5 s) with very high accuracy (>0.99 Area under curve of the Receiver of operating characteristics curve). Furthermore, the random forest approach detects a total of 4 key amino acid positions for the classification of field PRRSV strains into four clades. Our finding will provide an insightful idea to develop a rapid and accurate classification model using genetic information, which also enables us to handle large genome datasets in real time or semi-real time for data-driven decision-making and more timely surveillance.
more »
« less
Trustworthy Predictive Algorithms for Complex Forest System Decision-Making
Advances in predictive algorithms are revolutionizing how we understand and design effective decision support systems in many sectors. The expanding role of predictive algorithms is part of a broader movement toward using data-driven machine learning (ML) for modalities including images, natural language, speech. This article reviews whether and to what extent predictive algorithms can assist decision-making in forest conservation and management. Although state-of-the-art ML algorithms provide new opportunities, adoption has been slow in forest decision-making. This review shows how domain-specific characteristics, such as system complexity, impose limits on using predictive algorithms in forest conservation and management. We conclude with possible directions for developing new predictive tools and approaches to support meaningful forest decisions through easily interpretable and explainable recommendations.
more »
« less
- Award ID(s):
- 1717530
- NSF-PAR ID:
- 10276335
- Date Published:
- Journal Name:
- Frontiers in Forests and Global Change
- Volume:
- 3
- ISSN:
- 2624-893X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)A quiet revolution is afoot in the field of law. Technical systems employing algorithms are shaping and displacing professional decision making, and they are disrupting and restructuring relationships between law firms, lawyers, and clients. Decision-support systems marketed to legal professionals to support e-discovery—generally referred to as “technology assisted review” (TAR)—increasingly rely on “predictive coding”: machine-learning techniques to classify and predict which of the voluminous electronic documents subject to litigation should be withheld or produced to the opposing side. These systems and the companies offering them are reshaping relationships between lawyers and clients, introducing new kinds of professionals into legal practice, altering the discovery process, and shaping how lawyers construct knowledge about their cases and professional obligations. In the midst of these shifting relationships—and the ways in which these systems are shaping the construction and presentation of knowledge—lawyers are grappling with their professional obligations, ethical duties, and what it means for the future of legal practice. Through in-depth, semi-structured interviews of experts in the e-discovery technology space—the technology company representatives who develop and sell such systems to law firms and the legal professionals who decide whether and how to use them in practice—we shed light on the organizational structures, professional rules and norms, and technical system properties that are shaping and being reshaped by predictive coding systems. Our findings show that AI-supported decision systems such as these are reconfiguring professional work practices. In particular, they highlight concerns about potential loss of professional agency and skill, limited understanding and thereby both over- and under reliance on decision-support systems, and confusion about responsibility and accountability as new kinds of technical professionals and technologies are brought into legal practice. The introduction of predictive coding systems and the new professional and organizational arrangements they are ushering into legal practice compound general concerns over the opacity of technical systems with specific concerns about encroachments on the construction of expert knowledge, liability frameworks, and the potential (mis)alignment of machine reasoning with professional logic and ethics. Based on our findings, we conclude that predictive coding tools—and likely other algorithmic systems lawyers use to construct knowledge and reason about legal practice— challenge the current model for evaluating whether and how tools are appropriate for legal practice. As tools become both more complex and more consequential, it is unreasonable to rely solely on legal professionals—judges, law firms, and lawyers—to determine which technologies are appropriate for use. The legal professionals we interviewed report relying on the evaluation and judgment of a range of new technical experts within law firms and, increasingly, third-party vendors and their technical experts. This system for choosing technical systems upon which lawyers rely to make professional decisions—e.g., whether documents are responsive, or whether the standard of proportionality has been met—is no longer sufficient. As the tools of medicine are reviewed by appropriate experts before they are put out for consideration and adoption by medical professionals, we argue that the legal profession must develop new processes for determining which algorithmic tools are fit to support lawyers’ decision making. Relatedly, because predictive coding systems are used to produce lawyers’ professional judgment, we argue they must be designed for contestability— providing greater transparency, interaction, and configurability around embedded choices to ensure decisions about how to embed core professional judgments, such as relevance and proportionality, remain salient and demand engagement from lawyers, not just their technical experts.more » « less
-
more » « less
Abstract Mitigating the adverse impacts caused by increasing flood risks in urban coastal communities requires effective flood prediction for prompt action. Typically, physics‐based 1‐D pipe/2‐D overland flow models are used to simulate urban pluvial flooding. Because these models require significant computational resources and have long run times, they are often unsuitable for real‐time flood prediction at a street scale. This study explores the potential of a machine learning method, Random Forest (RF), to serve as a surrogate model for urban flood predictions. The surrogate model was trained to relate topographic and environmental features to hourly water depths simulated by a high‐resolution 1‐D/2‐D physics‐based model at 16,914 road segments in the coastal city of Norfolk, Virginia, USA. Two training scenarios for the RF model were explored: (i) training on only the most flood‐prone street segments in the study area and (ii) training on all 16,914 street segments in the study area. The RF model yielded high predictive skill, especially for the scenario when the model was trained on only the most flood‐prone streets. The results also showed that the surrogate model reduced the computational run time of the physics‐based model by a factor of 3,000, making real‐time decision support more feasible compared to using the full physics‐based model. We concluded that machine learning surrogate models strategically trained on high‐resolution and high‐fidelity physics‐based models have the potential to significantly advance the ability to support decision making in real‐time flood management within urban communities.
-
null (Ed.)Predictions from species distribution models (SDMs) are commonly used in support of environmental decision-making to explore potential impacts of climate change on biodiversity. However, because future climates are likely to differ from current climates, there has been ongoing interest in understanding the ability of SDMs to predict species responses under novel conditions (i.e., model transferability). Here, we explore the spatial and environmental limits to extrapolation in SDMs using forest inventory data from 11 model algorithms for 108 tree species across the western United States. Algorithms performed well in predicting occurrence for plots that occurred in the same geographic region in which they were fitted. However, a substantial portion of models performed worse than random when predicting for geographic regions in which algorithms were not fitted. Our results suggest that for transfers in geographic space, no specific algorithm was better than another as there were no significant differences in predictive performance across algorithms. There were significant differences in predictive performance for algorithms transferred in environmental space with GAM performing best. However, the predictive performance of GAM declined steeply with increasing extrapolation in environmental space relative to other algorithms. The results of this study suggest that SDMs may be limited in their ability to predict species ranges beyond the environmental data used for model fitting. When predicting climate-driven range shifts, extrapolation may also not reflect important biotic and abiotic drivers of species ranges, and thus further misrepresent the realized shift in range. Future studies investigating transferability of process based SDMs or relationships between geodiversity and biodiversity may hold promise.more » « less
-
null (Ed.)Intertemporal choices involve assessing options with different reward amounts available at different time delays. The similarity approach to intertemporal choice focuses on judging how similar amounts and delays are. Yet we do not fully understand the cognitive process of how these judgments are made. Here, we use machine-learning algorithms to predict similarity judgments to (1) investigate which algorithms best predict these judgments, (2) assess which predictors are most useful in predicting participants’ judgments, and (3) determine the minimum number of judgments required to accurately predict future judgments. We applied eight algorithms to similarity judgments for reward amount and time delay made by participants in two data sets. We found that neural network, random forest, and support vector machine algorithms generated the highest out-of-sample accuracy. Though neural networks and support vector machines offer little clarity in terms of a possible process for making similarity judgments, random forest algorithms generate decision trees that can mimic the cognitive computations of human judgment making. We also found that the numerical difference between amount values or delay values was the most important predictor of these judgments, replicating previous work. Finally, the best performing algorithms such as random forest can make highly accurate predictions of judgments with relatively small sample sizes (~ 15), which will help minimize the numbers of judgments required to extrapolate to new value pairs. In summary, machine-learning algorithms provide both theoretical improvements to our understanding of the cognitive computations involved in similarity judgments and intertemporal choices as well as practical improvements in designing better ways of collecting data.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/ffgc.2020.587178
