We investigate how semantic relations between concepts extracted from medical documents, and linked to a reference knowledge base, can be employed to improve the retrieval of medical literature. Semantic relations explicitly represent relatedness between concepts and carry high informative power that can be leveraged to improve the e ectiveness of the retrieval. We present preliminary results and show how relations are able to provide a sizable increase of the precision for several topics, albeit having no impact on others. We then discuss some future directions to minimize the impact of negative results while maximizing the impact of good results.
The volume of medical literature published every year keeps growing at a very
fast pace. The time required by clinicians to retrieve relevant information from
such an amount of literature using standard systems is often prohibitive.
Therefore, there has been a strong interest in Clinical Decision Support (CDS)
systems [
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A key characteristic of the medical literature is the large use of synonyms and context-speci c expressions. To address this term heterogeneity, Knowledge Bases (KBs) have often been exploited by Information Retrieval (IR) systems. The current availability of medical KBs o ers us the opportunity to develop techniques that better capture the semantics of medical documents, leading to the following research question:
How can we employ the rich semantic information within medical case reports and related literature to boost retrieval performances and ease the clinical decision process?
Semantic relations are a key aspect within the semantics of a document. They have been mainly used to nd relevant concepts to expand a user query, but not as semantic elements to be indexed and retrieved. We hypothesize semantic relations can provide a higher semantic representation of medical cases and literature.
In this work, we present an initial study on the e ectiveness of the use of semantic relations for the retrieval of medical literature. We de ne an approach comprising two methods: a rule-based method and a learning method. In the rule-based method, we assign a relation to a pair of concepts { contained within the same sentence { when it holds within a reference KB. In the learning method, we train a sentence-level relation extractor that is able to infer relation between a pair of concepts given the sentence context.
We evaluated our approach by using the publicly shared OHSUMED
collection [
Concept-based IR aims at making use of external sources (like thesauri and
ontologies) to provide additional knowledge and context that may not be explicit
in a document collection and users' queries. Concept-based methods can be
categorized in two types: (i) methods that use concepts in both indexing and
retrieval stages [
In the biomedical domain { where there are authoritative and curated ontologies { concept-based approaches demonstrate consistent improvements over classic keyword-based systems. In [10], `is-a' relationships between concepts are used to weight documents containing concepts subsumed by the query concepts. [12] proposes a method to represent medical records and queries by focusing only on medical concepts essential for the information need of a medical search task. In [11], queries are expanded by inferring additional conceptual relationships from domain-speci c resources as well as by extracting informative concepts from the top-ranked medical records.
The eld of Biomedical Information Extraction (BioIE) is highly relevant for
CDS. [13] reviews the recent advances in learning-based approaches for BioIE
tasks. BioIE tasks comprise entity linking [23], event identi cation [
Regarding relations in IR, [19] studies the problem of nding human readable descriptions of a given relationship in a knowledge graph. [17] applies supervised relation extraction to documents that are relevant for an information need Q and studies how many of the extracted relations are indeed relevant for Q. [9] explores current state of the art in unsupervised relation extraction (OpenIE) for the task of nding support passages to complement an entity ranking with human-readable explanations of how those retrieved entities are connected to the information need. Conversely, our approach applies supervised relation extraction to extract semantic relations that are used in both the indexing and the retrieval stages. Hence, relations play a pivotal role in the actual retrieval of documents. 3
We present a new approach that uses semantic relations for medical case-based retrieval. The methodology is composed of the information extraction step, that is applied both at the indexing and the retrieval stages (Subsection 3.1), and the speci c information retrieval stage (Subsection 3.2). 3.1
The information extraction step is divided into an entity linking component and a relation extraction component.
The entity linking component extracts entity mentions within the text and links them to a reference KB; this reduces the high number of synonyms, abbreviations and context speci c expressions that are present in the medical literature. For entity linking we adopt MetaMap,1 an authoritative tool to detect medical entity mentions in free-text. MetaMap analyses biomedical free-text and identi es concepts belonging to the Uni ed Medical Language System (UMLS),2
associating each mention with a number of concepts from the UMLS Metathesaurus3 | which comprises more than 3 million distinct concepts. Within UMLS, a substantial understanding of the medical domain is included, comprising medical concepts, relations, de nitions and so on.
The relation extraction component detects semantic relations between pairs of concepts within a sentence. To be consistent with concepts extracted with MetaMap, we consider semantic relations from UMLS Metathesaurus as well. Furthermore, since our task requires a high coverage of the medical domain, considering UMLS Metathesaurus relations { which are coarse-grained relationships that span to a high number of concepts { allows us to increase the recall of extracted relations.
We de ne two methods for the extraction of relations from documents and queries: a rule-based method and a learning method.
Rule-based: a relation is assigned to a pair of concepts if it relates them within UMLS. We assume that a UMLS relation between two concepts always occurs, even when it is not explicitly mentioned in the sentence containing the two concepts.
Learning: we train a distantly supervised [14] sentence-level Bidirectional Long
Short-Term Memory (BiLSTM) neural network to detect if a relation exists
between two concepts based on the context of the sentence. The network
architecture is composed of an input (word embedding) layer of concatenated word
features and positional features. Words are rst converted into pre-trained word
embeddings trained on 26 million abstracts and citations in PubMed | released
by [15]. Then these word features are concatenated with two sets of positional
features | to explicitly account for the pairs of words to which we expect to
assign relations [21]. We apply a max-pooling layer right after the bidirectional
recurrent layer and before the output layer | in order to combine segment-level
features that, although not very strong in representing the entire sentence,
represent local patterns well [22]. In this way, we try to overcome the tendency of
recurrent connections to forget long-term information too quickly, leading the
supervision at the end of the sentence to be hardly propagated to early steps in
model training (due to gradient vanishing [
Before to be in the condition to retrieve documents, it is necessary to index the documents, so the documents are indexed by considering all terms as in the Bagof-Words (BoW) representation, but we also extend the BoW representation to both concepts (BoC) and relations (BoR) by considering for the indexing all the extracted concepts and relations respectively. Afterwards the ranking is obtained using Okapi BM25 ranking function [16].
Since relations are extracted at sentence level, we also index passages { i.e. groups of consecutive sentences { by considering all the relations occurring within each group of sentences (passage-level BoR). Relevant passages should contain 3 https://www.nlm.nih.gov/research/umls/knowledge sources/metathesaurus/ a higher number of relations related to the information need when compared to non relevant passages | being more similar in their semantic contents to the query. Therefore, documents that contain more relevant passages can be considered more relevant to the query.
We de ne a weighting scheme such that a document score is computed as the weighted sum of its passages scores, where scores are computed using BM25 as above. The passage-level weighting scheme is as follows: score(q; d) = p2d X jRp \ Rqj BM 25(p; q) jRqj (1) where d is the document, q is the query, p is a passage belonging to document d, Rq is the set of relations extracted from query q and Rp is the set of relations extracted from passage p. 4
We employed the OHSUMED test collection which contains 348,566 references from the on-line medical information database MEDLINE,4 consisting of titles and/or abstracts from 270 medical journals over a ve-year period (1987-1991). The available elds are: title, abstract, MeSH5 indexing terms, author, source, and publication type. There are 106 queries in the collection. Each query is composed of two sentences: title + description. Title is the brief summary of the medical case at hand, description is the information need required to answer a speci c question for the case.
Experimental Setup: We performed two experiments: i) One using the rule-based method to extract relations out of documents and queries. ii) The other using the learning method to extract relations out of documents and queries. We compared the results obtained applying BM25 to the three representations (i.e. BoW, BoC and BoR) and we evaluated the results using the nDCG measure.
Results: i) The rule-based method was able to extract relations from a subset of 44 queries. Therefore, to investigate the e ectiveness of relations, we restrict the experiments to this subset only | since the remaining queries lead to no results when considering relations. Of these 44 queries, only 39 have relations matching with some documents. Regarding the relations, we obtained the best results with the passage-level approach. We set the passage length to 2, in order to be compliant with query length. Document score was computed using the formula shown above (1). The nDCG results on these 39 queries are variable { ranging from 0 (18 cases) to 1 (5 cases), as can be seen in Figure 1. Such a variance
gives us some hints about the informative power of relations. When properly extracted, relations can be highly e ective, indeed; we compared the average nDCG values of concepts and relations on only those topics where relations give a result di erent than 0 and we found a statistically signi cant average improvement of 20%. A t-test was performed to validate the improvement. Regarding the comparison between relations and terms, the behavior of relations is similar to the one of terms (baseline approach), and there is no statistically signi cant di erence between the two.
ii) The learning method was able to extract relations from a subset of 25 queries. Of these 25 queries, only 12 have relations matching with some documents. The results on these 12 queries are comparable to those presented for the rule-base method, with nDCG values ranging from 0 (in 7 cases) to 1 (in 1 case). The reason for this is two-fold: (a) the shortness of queries that limits the relations that can be extracted; and, (b) the highly di erent syntactic structure of queries if compared to the sentences within the medical abstracts leading to a mismatch between the query-relations and abstract-relations. 5
In this work, we proposed and evaluated the e ectiveness of semantic relations as basic constituents for a CDS system. We de ned two methods for extracting relations from queries and documents: a rule-based method and a learning method. We found that relations { when pertinent to the initial information need { are highly valuable, outperforming concepts. The challenge lies in how to limit those cases where relations provide no relevant results for the information need. To this end, considering collections where queries present a long and narrative structure (e.g. TREC CDS tracks6) might be a possible direction to balance such issue.
Furthermore, de ning more IR-oriented relation extraction approaches that are capable of overcoming the high precision-low recall nature of state-of-the-art methods is a direction that can be investigated.
Finally, we could compare the relation extraction approaches in terms of quality of the results to verify if the extracted relations are semantically correct. This can further clarify whether relations' limited e ectiveness in IR tasks lies in current state-of-the-art relation extraction approaches or in the poor representativeness of relations themselves for IR tasks.
An initial version of this paper has been presented at the ACM 12th
International Workshop on Data and Text Mining in Biomedical Informatics (DTMBio),
held in conjunction with ACM 27th Conference on Information and Knowledge
Management (CIKM) [
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