Question: What framework does the paper develop?
Evidence: Medical search engines are an essential component for many online medical applications, such as online diagnosis systems and medical document databases. A typical online diagnosis system, for instance, relies on a medical search engine. The search engine takes as input a user query that describes some symptoms and then outputs clinical concept entries that provide relevant information to assist in diagnosing the problem. One challenge medical search engines face is the segmentation of individual clinical entities. When a user query consists of multiple clinical entities, a search engine would often fail to recognize them as separate entities. For example, the user query “fever joint pain weight loss headache” contains four separate clinical entities: “fever”, “joint pain”, “weight loss”, and “headache”. But when the search engine does not recognize them as separate entities and proceeds to retrieve results for each word in the query, it may find "pain" in body locations other than "joint pain", or it may miss "headache" altogether, for example. Some search engines allow the users to enter a single clinical concept by selecting from an auto-completion pick list. But this could also result in retrieving inaccurate or partial results and lead to poor user experience.
We want to improve the medical search engine so that it can accurately retrieve all the relevant clinical concepts mentioned in a user query, where relevant clinical concepts are defined with respect to the terminologies the search engine uses. The problem of extracting clinical concept mentions from a user query can be seen as a variant of the Concept Extraction (CE) task in the frequently-cited NLP challenges in healthcare, such as 2010 i2b2/VA BIBREF0 and 2013 ShARe/CLEF Task 1 BIBREF1. Both CE tasks in 2010 i2b2/VA and 2013 ShARe/CLEF Task 1 ask the participants to design an algorithm to tag a set of predefined entities of interest in clinical notes. These entity tagging tasks are also known as clinical Named Entity Recognition (NER). For example, the CE task in 2010 i2b2/VA defines three types of entities: “problem”, “treatment”, and “test”. The CE task in 2013 ShARe/CLEF defines various types of disorder such as “injury or poisoning”, "disease or syndrome”, etc. In addition to tagging, the CE task in 2013 ShARe/CLEF has an encoding component which requires selecting one and only one Concept Unique Identifier (CUI) from Systematized Nomenclature Of Medicine Clinical Terms (SNOMED-CT) for each disorder entity tagged. Our problem, similar to the CE task in 2013 ShARe/CLEF, also contains two sub-problems: tagging mentions of entities of interest (entity tagging), and selecting appropriate terms from a glossary to match the mentions (term matching). However, several major differences exist. First, compared to clinical notes, the user queries are much shorter, less technical, and often less coherent. Second, instead of encoding, we are dealing with term matching where we rank a few best terms that match an entity, instead of selecting only one. This is because the users who type the queries may not have a clear idea about what they are looking for, or could be laymen who know little terminology, it may be more helpful to provide a set of likely results and let the users choose. Third, the types of entities are different. Each medical search engine may have its own types of entities to tag. There is also one minor difference in the tagging scheme between our problem and the CE task in 2013 ShARe/CLEF - We limit our scope to dealing with entities of consecutive words and not disjoint entities . We use only Beginning, Inside, Outside (BIO) tags. Given the differences listed above, we need to customize a framework consisting of an entity tagging and term matching component for our CE problem.
Medical search engines are an essential component for many online medical applications, such as online diagnosis systems and medical document databases. A typical online diagnosis system, for instance, relies on a medical search engine. The search engine takes as input a user query that describes some symptoms and then outputs clinical concept entries that provide relevant information to assist in diagnosing the problem. One challenge medical search engines face is the segmentation of individual clinical entities. When a user query consists of multiple clinical entities, a search engine would often fail to recognize them as separate entities. For example, the user query “fever joint pain weight loss headache” contains four separate clinical entities: “fever”, “joint pain”, “weight loss”, and “headache”. But when the search engine does not recognize them as separate entities and proceeds to retrieve results for each word in the query, it may find "pain" in body locations other than "joint pain", or it may miss "headache" altogether, for example. Some search engines allow the users to enter a single clinical concept by selecting from an auto-completion pick list. But this could also result in retrieving inaccurate or partial results and lead to poor user experience.
We want to improve the medical search engine so that it can accurately retrieve all the relevant clinical concepts mentioned in a user query, where relevant clinical concepts are defined with respect to the terminologies the search engine uses. The problem of extracting clinical concept mentions from a user query can be seen as a variant of the Concept Extraction (CE) task in the frequently-cited NLP challenges in healthcare, such as 2010 i2b2/VA BIBREF0 and 2013 ShARe/CLEF Task 1 BIBREF1. Both CE tasks in 2010 i2b2/VA and 2013 ShARe/CLEF Task 1 ask the participants to design an algorithm to tag a set of predefined entities of interest in clinical notes. These entity tagging tasks are also known as clinical Named Entity Recognition (NER). For example, the CE task in 2010 i2b2/VA defines three types of entities: “problem”, “treatment”, and “test”. The CE task in 2013 ShARe/CLEF defines various types of disorder such as “injury or poisoning”, "disease or syndrome”, etc. In addition to tagging, the CE task in 2013 ShARe/CLEF has an encoding component which requires selecting one and only one Concept Unique Identifier (CUI) from Systematized Nomenclature Of Medicine Clinical Terms (SNOMED-CT) for each disorder entity tagged. Our problem, similar to the CE task in 2013 ShARe/CLEF, also contains two sub-problems: tagging mentions of entities of interest (entity tagging), and selecting appropriate terms from a glossary to match the mentions (term matching). However, several major differences exist. First, compared to clinical notes, the user queries are much shorter, less technical, and often less coherent. Second, instead of encoding, we are dealing with term matching where we rank a few best terms that match an entity, instead of selecting only one. This is because the users who type the queries may not have a clear idea about what they are looking for, or could be laymen who know little terminology, it may be more helpful to provide a set of likely results and let the users choose. Third, the types of entities are different. Each medical search engine may have its own types of entities to tag. There is also one minor difference in the tagging scheme between our problem and the CE task in 2013 ShARe/CLEF - We limit our scope to dealing with entities of consecutive words and not disjoint entities . We use only Beginning, Inside, Outside (BIO) tags. Given the differences listed above, we need to customize a framework consisting of an entity tagging and term matching component for our CE problem.
We want to improve the medical search engine so that it can accurately retrieve all the relevant clinical concepts mentioned in a user query, where relevant clinical concepts are defined with respect to the terminologies the search engine uses.**** Given the differences listed above, we need to customize a framework consisting of an entity tagging and term matching component for our CE problem.
Answer: A framework for the entity tagging and term matching problem in a medical search engine.