Question: What is the meaning of events in Biomedical Event Extraction?
Evidence: Event Extraction in the Biomedical domain is a task that has gained more importance recently. Event Extraction goes beyond Relation Extraction. In Biomedical Event Extraction, events generally refer to a change in the state of biological molecules such as proteins and DNA. Generally, it includes detection of targeted event types such as gene expression, regulation, localisation and transcription. Each event type in addition can have multiple arguments that need to be detected. An additional layer of complexity comes from the fact that events can also be arguments of other events, giving rise to a nested structure. This helps to capture the underlying biology better BIBREF1 . Detecting the event type often involves recognising and classifying trigger words. Often, these words are verbs such as “activates”, “inhibits”, “phosphorylation” that may indicate a single, or sometimes multiple event types. In this section, we will discuss some of the successful models for Event Extraction in some detail.
Event Extraction gained a lot of interest with the availability of an annotated corpus with the BioNLP'09 Shared Task on Event Extraction BIBREF34 . The task involves prediction of trigger words over nine event types such as expression, transcription, catabolism, binding, etc. given only annotation of named entities (proteins, genes, etc.). For each event, its class, trigger expression and arguments need to be extracted. Since the events can be arguments to other events, the final output in general is a graph representation with events and named entities as nodes, and edges that correspond to event arguments. BIBREF33 present a pipeline based method that is heavily dependent on dependency parsing. Their pipeline approach consists of three steps: trigger detection, argument detection and semantic post-processing. While the first two components are learning based systems, the last component is a rule based system. For the BioNLP'09 corpus, only 5% of the events span multiple sentences. Hence the approach does not get affected severely by considering only single sentences. It is important to note that trigger words cannot simply be reduced to a dictionary lookup. This is because a specific word may belong to multiple classes, or may not always be a trigger word for an event. For example, “activate” is found to not be a trigger word in over 70% of the cases. A multi-class SVM is trained for trigger detection on each token, using a large feature set consisting of semantic and syntactic features. It is interesting to note that the hyperparameters of this classifier are optimised based on the performance of the entire end-to-end system.
For the second component to detect arguments, labels for edges between entities must be predicted. For the BioNLP'09 Shared Task, each directed edge from one event node to another event node, or from an event node to a named entity node are classified as “theme”, “cause”, or None. The second component of the pipeline makes these predictions independently. This is also trained using a multi-class SVM which involves heavy use of syntactic features, including the shortest dependency path between the nodes. The authors note that the precision-recall choice of the first component affects the performance of the second component: since the second component is only trained on Gold examples, any error by the first component will lead to a cascading of errors. The final component, which is a semantic post-processing step, consists of rules and heuristics to correct the output of the second component. Since the edge predictions are made independently, it is possible that some event nodes do not have any edges, or have an improper combination of edges. The rule based component corrects these and applies rules to break directed cycles in the graph, and some specific heuristics for different types of events. The final model gives a cumulative F-Score of 52% on the test set, and was the best model on the task.
 BIBREF35 note that previous approaches on the task suffer due to the pipeline nature and the propagation of errors. To counter this, they adopt a joint inference method based on Markov Logic Networks BIBREF36 for the same task on BioNLP'09. The Markov Logic Network jointly predicts whether each token is a trigger word, and if yes, the class it belongs to; for each dependency edge, whether it is an argument path leading to a “theme” or a “cause”. By formulating the Event Extraction problem using an MLN, the approach becomes computationally feasible and only linear in the length of the sentence. They incorporate hard constraints to encode rules such as “an argument path must have an event”, “a cause path must start with a regulation event”, etc. In addition, they also include some domain specific soft constraints as well as some linguistically-motivated context-specific soft constraints. In order to train the MLN, stochastic gradient descent was used. Certain heuristic methods are implemented in order to deal with errors due to syntactic parsing, especially ambiguities in PP-attachment and coordination. Their final system is competitive and comes very close to the system by BIBREF33 with an average F-Score of 50%. To further improve the system, they suggest leveraging additional joint-inference opportunities and integrating the syntactic parser better. Some other more recent models for Biomedical Event Extraction include BIBREF37 , BIBREF38 .
In Biomedical Event Extraction, events generally refer to a change in the state of biological molecules such as proteins and DNA.
Answer: In Biomedical Event Extraction, events generally refer to a change in the state of biological molecules such as proteins and DNA.