Active querying approach to epidemic source detection on contact networks.

The problem of identifying the source of an epidemic (also called patient zero) given a network of contacts and a set of infected individuals has attracted interest from a broad range of research communities. The successful and timely identification of the source can prevent a lot of harm as the number of possible infection routes can be narrowed down and potentially infected individuals can be isolated. Previous research on this topic often assumes that it is possible to observe the state of a substantial fraction of individuals in the network before attempting to identify the source. We, on the contrary, assume that observing the state of individuals in the network is costly or difficult and, hence, only the state of one or few individuals is initially observed. Moreover, we presume that not only the source is unknown, but also the duration for which the epidemic has evolved. From this more general problem setting a need to query the state of other (so far unobserved) individuals arises. In analogy with active learning, this leads us to formulate the active querying problem. In the active querying problem, we alternate between a source inference step and a querying step. For the source inference step, we rely on existing work but take a Bayesian perspective by putting a prior on the duration of the epidemic. In the querying step, we aim to query the states of individuals that provide the most information about the source of the epidemic, and to this end, we propose strategies inspired by the active learning literature. Our results are strongly in favor of a querying strategy that selects individuals for whom the disagreement between individual predictions, made by all possible sources separately, and a consensus prediction is maximal. Our approach is flexible and, in particular, can be applied to static as well as temporal networks. To demonstrate our approach's practical importance, we experiment with three empirical (temporal) contact networks: a network of pig movements, a network of sexual contacts, and a network of face-to-face contacts between residents of a village in Malawi. The results show that active querying strategies can lead to substantially improved source inference results as compared to baseline heuristics. In fact, querying only a small fraction of nodes in a network is often enough to achieve a source inference performance comparable to a situation where the infection states of all nodes are known.

Towards risk-based surveillance of African Swine Fever in Switzerland.

African Swine Fever (ASF) has emerged as a disease of great concern to swine producers and government disease control agencies because of its severe consequences to animal health and the pig industry. Early detection of an ASF introduction is considered essential for reducing the impact of the disease. Risk-based surveillance approaches have been used as enhancements to early disease epidemic detection systems in livestock populations. Such approaches may consider the role wildlife plays in hosting and transmitting a disease. In this study, a method is presented to estimate and map the risk of introducing ASF into the domestic pig population through wild boar intermediate hosts. It makes use of data about hunted wild boar, rest areas along motorways connecting ASF affected countries to Switzerland, outdoor piggeries, and forest cover. These data were used to compute relative wild boar abundance as well as to estimate the risk of both disease introduction into the wild boar population and disease transmission to domestic pigs. The way relative wild boar abundance was calculated adds to the current state of the art by considering the effect of beech mast on hunting success and the probability of wild boar occurrence when distributing relative abundance values among individual grid cells. The risk of ASF introduction into the domestic pig population by wild boar was highest near the borders of France, Germany, and Italy. On the north side of the Alps, areas of high risk were located on the unshielded side of the main motorway crossing the Central Plateau, which acts as a barrier for wild boar. Estimating the risk of disease introduction into the domestic pig population without the intermediary of wild boar suggested that dispersing wild boar may play a key role in spreading the risk to areas remote from motorways. The results of this study can be used to focus surveillance efforts for early disease detection on high risk areas. The developed method may also inform policies to control other diseases that are transmitted by a direct contact from wild boar to domestic pigs.

Toward a systematic conflict resolution framework for ontologies.

BACKGROUND: The ontology authoring step in ontology development involves having to make choices about what subject domain knowledge to include. This may concern sorting out ontological differences and making choices between conflicting axioms due to limitations in the logic or the subject domain semantics. Examples are dealing with different foundational ontologies in ontology alignment and OWL 2 DL's transitive object property versus a qualified cardinality constraint. Such conflicts have to be resolved somehow. However, only isolated and fragmented guidance for doing so is available, which therefore results in ad hoc decision-making that may not be the best choice or forgotten about later. RESULTS: This work aims to address this by taking steps towards a framework to deal with the various types of modeling conflicts through meaning negotiation and conflict resolution in a systematic way. It proposes an initial library of common conflicts, a conflict set, typical steps toward resolution, and the software availability and requirements needed for it. The approach was evaluated with an actual case of domain knowledge usage in the context of epizootic disease outbreak, being avian influenza, and running examples with COVID-19 ontologies. CONCLUSIONS: The evaluation demonstrated the potential and feasibility of a conflict resolution framework for ontologies.

Outbreak detection for temporal contact data.

Epidemic spreading is a widely studied process due to its importance and possibly grave consequences for society. While the classical context of epidemic spreading refers to pathogens transmitted among humans or animals, it is straightforward to apply similar ideas to the spread of information (e.g., a rumor) or the spread of computer viruses. This paper addresses the question of how to optimally select nodes for monitoring in a network of timestamped contact events between individuals. We consider three optimization objectives: the detection likelihood, the time until detection, and the population that is affected by an outbreak. The optimization approach we use is based on a simple greedy approach and has been proposed in a seminal paper focusing on information spreading and water contamination. We extend this work to the setting of disease spreading and present its application with two example networks: a timestamped network of sexual contacts and a network of animal transports between farms. We apply the optimization procedure to a large set of outbreak scenarios that we generate with a susceptible-infectious-recovered model. We find that simple heuristic methods that select nodes with high degree or many contacts compare well in terms of outbreak detection performance with the (greedily) optimal set of nodes. Furthermore, we observe that nodes optimized on past periods may not be optimal for outbreak detection in future periods. However, seasonal effects may help in determining which past period generalizes well to some future period. Finally, we demonstrate that the detection performance depends on the simulation settings. In general, if we force the simulator to generate larger outbreaks, the detection performance will improve, as larger outbreaks tend to occur in the more connected part of the network where the top monitoring nodes are typically located. A natural progression of this work is to analyze how a representative set of outbreak scenarios can be generated, possibly taking into account more realistic propagation models.

The pig transport network in Switzerland: Structure, patterns, and implications for the transmission of infectious diseases between animal holdings.

The topology of animal transport networks contributes substantially to how fast and to what extent a disease can transmit between animal holdings. Therefore, public authorities in many countries mandate livestock holdings to report all movements of animals. However, the reported data often does not contain information about the exact sequence of transports, making it impossible to assess the effect of truck sharing and truck contamination on disease transmission. The aim of this study was to analyze the topology of the Swiss pig transport network by means of social network analysis and to assess the implications for disease transmission between animal holdings. In particular, we studied how additional information about transport sequences changes the topology of the contact network. The study is based on the official animal movement database in Switzerland and a sample of transport data from one transport company. The results show that the Swiss pig transport network is highly fragmented, which mitigates the risk of a large-scale disease outbreak. By considering the time sequence of transports, we found that even in the worst case, only 0.34% of all farm-pairs were connected within one month. However, both network connectivity and individual connectedness of farms increased if truck sharing and especially truck contamination were considered. Therefore, the extent to which a disease may be transmitted between animal holdings may be underestimated if we only consider data from the official animal movement database. Our results highlight the need for a comprehensive analysis of contacts between farms that includes indirect contacts due to truck sharing and contamination. As the nature of animal transport networks is inherently temporal, we strongly suggest the use of temporal network measures in order to evaluate individual and overall risk of disease transmission through animal transportation.

A Transdisciplinary Approach Supporting the Implementation of a Big Data Project in Livestock Production: An Example From the Swiss Pig Production Industry.

Big Data approaches offer potential benefits for improving animal health, but they have not been broadly implemented in livestock production systems. Privacy issues, the large number of stakeholders, and the competitive environment all make data sharing, and integration a challenge in livestock production systems. The Swiss pig production industry illustrates these and other Big Data issues. It is a highly decentralized and fragmented complex network made up of a large number of small independent actors collecting a large amount of heterogeneous data. Transdisciplinary approaches hold promise for overcoming some of the barriers to implementing Big Data approaches in livestock production systems. The purpose of our paper is to describe the use of a transdisciplinary approach in a Big Data research project in the Swiss pig industry. We provide a brief overview of the research project named "Pig Data," describing the structure of the project, the tools developed for collaboration and knowledge transfer, the data received, and some of the challenges. Our experience provides insight and direction for researchers looking to use similar approaches in livestock production system research.