The following interaction is named entity recognition, which is looking through the element possibility to refer to in the document. Multiple pages, names, and instructive pages pseudonyms additionally considered to get the equivalent words. Applications of named entity recognition assist you with recognizing the vital components in text, similar to monetary values, brands, places, names of people, and many more.
Separating the primary elements in text aids sort unstructured data and recognize significant data, which is pivotal if you need to manage a huge NER dataset. A publication site or online journal holds a huge number of scholarly articles and research papers.
There can be many papers on a solitary subject with slight adjustments. Coordinating this information in an all-around organized way can get fiddly. There are a few different ways to make the cycle of customer feedback taking care of smooth, and Named Entity Recognition could be one of them. Numerous advanced applications, like YouTube and Netflix, depend on recommendation frameworks to make ideal user experiences.
A ton of these frameworks depend on Named Entity Recognition which can make ideas dependent on user search history. With this methodology, a search term will be coordinated with just the little entities of substances examined in each article, prompting quicker hunt execution.
Enrolment specialists spend numerous hours of their day experiencing resumes, searching for the right candidate. When we read a text, we naturally recognize named entities like people, values, locations, and so on. For computers, however, we need to help them recognize entities first so that they can categorize them.
NLP studies the structure and rules of language and creates intelligent systems capable of deriving meaning from text and speech, while machine learning helps machines learn and improve over time. To learn what an entity is, an NER model needs to be able to detect a word, or string of words that form an entity e. New York City , and know which entity category it belongs to.
So first, we need to create entity categories, like Name, Location, Event, Organization , etc. Try out our pre-trained named entity extractor , to see how it works:. Named entity recognition NER helps you easily identify the key elements in a text, like names of people, places, brands, monetary values, and more. Extracting the main entities in a text helps sort unstructured data and detect important information, which is crucial if you have to deal with large datasets. You can also use entity extraction to pull relevant pieces of data, like product names or serial numbers, making it easier to route tickets to the most suitable agent or team for handling that issue.
Online reviews are a great source of customer feedback : they can provide rich insights about what clients like and dislike about your products, and the aspects of your business that need improving. NER systems can be used to organize all this customer feedback and pinpoint recurring problems. NER has various applications in multiple industries such as news and media, search engines, and content recommendations. An NER System is capable of discovering entity elements from raw data and determines the category the element belongs to.
The system reads the sentence and highlights the important entity elements in the text. NER might be given separate sensitive entities depending on the project. This means that NER systems designed for one project may not be reused for another task. Figure: NER Workflow. For a general entity such as name, location, organization, date and pre-trained library, Stanford NER and Spacy can be used.
But for a domain specific entity, an NER model can be trained with custom training data requires lots of human efforts and time. For various applications, custom models can be trained with labeled data sets. Figure 6. If we consider the hidden layer h n in Figure 6 , first, the embedding layer embeds the word gene into a vector X n.
The combined output resulting from the backward and the forward LSTMs is then passed through an activation function tanh that results in the output Y n.
Consequently, in this example, Y n is tagged as I-gene , i. Semi-supervised methods: Semi-supervised learning is usually used when a small amount of labeled data and a larger amount of unlabeled data are available, which is often the case when it comes to Biomedical collections. If labeled data is expressed as X x 1 , x 2 , The pipeline runs the labeled and unlabeled data in two parallel lines wherein one line labeled data is processed through NLP techniques to extract rich features such as word and character n-grams, lemma, and orthographic information as in BANNER.
In the second line, the unlabeled data corpus is cleaned, tokenized, and run through brown hierarchical clustering and word2vec algorithms to extract word representation vectors, and clustered using k-means.
All of the extracted features from labeled and unlabeled data are then used to train a BioNER model using conditional random fields. The authors of this system emphasize that the system does not use lexical features or dictionaries.
Unsupervised methods: While unsupervised machine learning has potent in organizing new high throughput data without previous processing and improving the ability of the existing system to process previously unseen information, it is not very often the first choice for developing BioNER systems. However, Zhang and Elhadad introduced a system, which uses an unsupervised approach to BioNER with the concepts of seed knowledge and signature similarities between entities.
Second, the candidate corpora are processed using a noun phrase chunker and an inverse document frequency filter, which formulates word sense disambiguation vectors for a given named entity using a clustering approach. The next step generates the signature vectors for each entity class with the intuition that the same class tends to have contextually similar words.
The final step compares the candidate named entity signatures and entity class signatures by calculating similarities. As a result, they found the highest F-score of Sabbir et al. These unsupervised methods tend to work well when dealing with ambiguous Biomedical entities. Currently, there are several state-of-the-art applications of BioNER, that combine the best aspects of all the above three methods.
Since machine learning approaches have shown to result in better recall values, whereas both dictionary-based and rule-based approaches tend to have better precision values, the former method shows improved F-scores. For instance, OrganismTagger Naderi et al. Furthermore, state of the art tools such as Gimli Campos et al. On the other hand, some systems have been able to combine statistical machine-learning approaches with rule-based models to achieve higher results, as described in this more recent work Soomro et al.
This study uses the probability analysis of orthographic, POS, n-gram, affixes, and contextual features with Bayesian, Naive-Bayesian, and partial decision tree models to formulate rules of classification.
While not all systems require or use post-processing, it can improve the quality and accuracy of the output by resolving abbreviation ambiguities, disambiguation of classes and terms, as well as parenthesis mismatching instances Bhasuran et al. For example, if a certain BioNE is only tagged in one place of the text, yet the same or a co-referring term exist elsewhere in the text, untagged, then the post-processing would make sure these missed NEs are tagged with their respective class.
Also, in the case of a partial entity being tagged in a multi-word BioNE, this step would enable the complete NE to be annotated. In the case where some of the abbreviations are wrongly classified or failed to be tagged, some systems use tools such as the BioC abbreviation resolver Intxaurrondo et al.
Furthermore, failure to tag NE also stems from unbalanced parenthesis in isolated entities, which also can be addressed during pre-processing. Interestingly, Wei et al. Another important sub-task that is essential at this point, is to resolve coreferences. This may be also important for extracting stronger associations between entities, discussed in the next section. Coreferences are those terms that refer to a named entity without using its proper name, but by using some form of anaphora, cataphora, split-reference or compound noun-phrase Sukthanker et al.
When it comes to biomedical coreference resolution, it is important to note that generalized methods may not be very effective, given that there are fewer usages of common personal pronouns. Some approaches that have been used in the biomedical text mining literature are heuristic rule sets, statistical approaches and machine learning-based methods.
Most of the earlier systems commonly used mention-pair based binary classification and rule-sets to filter coreferences such that only domain significant ones are tagged Zheng et al. While the rule set methods have provided state-of-the-art precision they often do not have a high recall. Hence, a sieve-based architecture Bell et al.
Recently, deep learning methods have been used for coreference resolution in general domain successfully without using syntactic parsers, for example in Lee et al.
The same system has been applied to biomedical coreference resolution in Trieu et al. Here, it is worth mentioning that the CRAFT corpus, earlier mentioned in Table 1 , has an improved version that can be used for coreference resolution for biomedical texts Cohen et al. In the biomedical literature coreference resolution is sometimes conducted e.
A reason for this could be that biomedical articles are differently written in the sense that, e. However, if this is indeed the reason or if there is an omission in the biomedical NER pipeline requires further investigations. After BioNER, the identification of associations between the named entities follows.
For establishing such associations, the majority of studies use one of the following techniques Yang et al. The simplest of these methods, co-occurrence based approaches, consider entities to be associated if they occur together in target sentences.
The hypothesis is that the more frequent two entities occur together, the higher the probability that they are associated with each other. In an extension of this approach, a relationship is deemed to exist between two or more entities if they share an association with a third entity acting as a reciprocal link Percha et al.
In a rule-based approach, the relationship extraction depends highly on the syntactic and semantic analysis of sentences. As such, these methods rely on part-of-speech POS tagging tools to identify associations, e. For instance, in Fundel et al. In this approach, many systems additionally incorporate a list of verbs that are considered to show implications between nouns, i.
In Figure 7 , an example of a syntactic sentence parse tree created by POS tagging, is shown. In this figure, nodes signify syntax abbreviations, i. The method first fragments a sentence into noun phrases and verb phrases, and each of these phrases is further segmented to adjectives, nouns, prepositions, and conjunctions for clarity of analysis.
More details of the strength of associations will include in section 4. Figure 7. The most commonly used machine learning approaches use an annotated corpus with pre-identified relations as training data to learn a model supervised learning. Previously, the biggest obstacle for using such machine learning approaches for relation detection was acquiring the labeled training and testing data.
However, data sets generated through biomedical text mining competitions such as BioCreative and BioNLP have moderated this problem significantly. Specifically, in Table 2 , we list a few of the main gold-standard corpora available in the literature for this task.
Historically, SVMs have been the first choice for this task due to their excellent performance in text data classification with a low tendency for overfitting. Furthermore, they have also proven to be good with sentence polarity analyzing for extracting positive, negative, and neutral relationships as described by Yang et al. Of course, in SVM based approaches, feature selection acts as the strength-indicator for accuracy and, therefore, is considered a crucial step in relationship mining using this approach.
This study used a combination of methods for evaluating an appropriate kernel function for predicting gene-disease associations. Specifically, the kernel function used a similarity measure incorporating a normalized edit-distances between the paths of two genes, as extracted from a dependency parse tree.
In contrast to this, the study by Yang et al. This method also included a word2vec representation in combination with rich semantic and syntactic features. As a result, they improved F-scores for identifying disease-gene associations. Although SVMs appear to take predominance in this task, other machine learning methods have been used as well. For instance, in Jensen et al. Due to the state of the art performance and less need for complicated feature processing, deep learning DL methods are becoming increasingly popular for relation extraction in the last five years.
The feature inputs to DL models may include sentence-level, word-level, and lexical-level features represented as vectors Zeng et al. The vectors are looked up from pre-trained word and positional vector space on either a single corpus or multiple corpora Quan et al.
Significantly, the majority of deep learning methods use sentence dependency graphs mentioned in the rule-based approach Figure 8 to extract the shortest path between entities and relations as features for training Hua and Quan, a , b ; Zhang et al. Other studies have used POS tagging, and chunk tagging features in combination with position and dependency paths to improve performance Peng and Lu, The models are trained to either distinguish between sentences with relations or to output the type of relation.
Figure 8. Since CNN's require every training example to be of similar size, instances are padded with zeros as required Liu et al. After several layers of convolutional operations and pooling, these methods are followed by a fully connected feed-forward neural layer with soft-max activation funct ion Hua and Quan, b.
These RNN based models perform well with relating entities that lie far apart from each other in sentences.
Whereas, CNNs requires restrictive sized inputs, the RNNs have no such restrains and are useful when long sentences are available, since the input is sequentially processed.
These models have been used to extract drug-drug and protein-protein interactions Hsieh et al. Extending this further, Zhang et al. Here the hierarchical bi-LSTM has shown a better performance. In recent years, there have also been studies that use a novel approach, i. Graph convolutional networks use the same concept of CNN, but with the advantage of using graphs as inputs and outputs. By using dependency paths to represent text as graphs, GCNs can be applied to relation extraction tasks.
In Zhao et al. Furthermore, for identifying drug-drug interactions, a syntax convolutional neural network has been evaluated for the DDIExtraction corpus Herrero-Zazo et al. In extension, Zheng et al. The method has been used to extract chemical-disease relations, and have been trained and evaluated on CDR corpus Li et al. Whereas, authors of Zhang et al. These hybrid methods aim to combine the CNN's efficiency in learning local lexical and syntactic features short sentences with RNN's ability to learn dependency features over long and complicated sequences of words long sentences.
Both of the above models have been found to perform well with their respective corpora. While complex sentence structures may lead to nested relations, this method facilitates identifying common syntactic patterns indicating significant associations Luo et al. Once the named entities are tagged, the next steps involve splitting sentences, annotating them with POS, and processing other feature extractions as required. Graph extraction is usually performed at this point as a part of the feature extracting process.
For example, in Liu et al. A similar approach has been used in MacKinlay et al. The paper by Luo et al. Also, the combination of machine learning and graph-based approaches have been studied with great success. For instance, in Kim et al. In order to enrich the information captured by kernels, Peng et al. Furthermore, in Panyam et al. As a result, they found that the all-path-graph kernel performs significantly better in this task.
In this section, we discuss methods that do not fit in either of the above categories but provide interesting approaches. In Zhou and Fu , an extended variant of the frequency approach is studied, which combines co-occurrence frequency and Inverse Document Frequency IDF for relations extraction.
The study sets the first precedence to entity co-occurrence in MeSH terms and second to those in the article title, and third to the ones in the article abstract by assigning weights to each precedence level. A vector representation for each document sample is created using these weights for calculating the score of each key-term-association by multiplying IDF with PWK penalty weight for the keyword, depending on the distance from MeSH root.
The authors then evaluate the system by comparing precision, recall, and cosine similarity. In contrast, the study by Percha and Altman introduces an entirely novel algorithm to mine relations between entities called Ensemble Clustering for Classification EBC. This algorithm extract drug-gene associations by combining an unsupervised learning step and a lightly supervised step that uses a small seed data set. The supervised step follows by comparing how often the seed set pairs and test set pairs co-cluster together using a scoring function, and relationships are ranked accordingly.
The same authors have extended this method further in Percha and Altman , by applying hierarchical clustering after EBC to extract four types of association between gene-gene, chemical-gene, gene-disease, and chemical-disease. Incidentally, this hierarchical step has enabled additional classification of these relationships into themes such as ten different types of chemical-gene relations or seven distinct types of chemical-disease associations. A further refinement following a relation detection is an analysis of the polarity and the strength of the identified associations, providing additional information about the relations and, hence, enhances extracted domain-specific knowledge.
A polarity analysis of relations is similar to a sentiment analysis Swaminathan et al. For inferring the polarity of relations, similar machine learning approaches can be used, as discussed in section 3. However, a crucial difference is that for the supervised methods, appropriate training data need to be available, providing information about the different polarity classes.
For instance, one could have three polarity classes, namely, positive associations e. In general, a polarity analysis opens new ways to study research questions of how entities interact with each other in a network. For example, the influence of a given food metabolite on certain diseases can be identified, which may open new courses of food-based treatment regiments Miao et al.
A strength analysis comes after identifying associations between entities in a text since all extracted events might not be considered significant associations. Especially in simple co-occurrences based method to identify relationships, strength analysis can be vital, since just a simple mention of two entities in a sentence with no explicit reciprocity, may result in them wrongly defined as associations.
Some of the most common methods employed in the literature include distance analysis and dependency path analysis, or an extension of those methods. An example of a method that implements a word distance analysis is Polysearch Liu et al. Polysearch is essentially a biomedical web crawler focusing on entity associations.
This tool first estimates co-occurrence frequencies and the association verbs to locate content that is predicted to have entity associations. Next, using the word-distances between entity-pairs in the selected text, content relevancy i. Incidentally, this system is currently able to search in several text corpora and databases, using the above method, to find relevant content for over associative combinations of named entity classes. In Coulet et al. Each tree then converts into a directed and labeled dependency graph, whereas nodes are words, and edges are dependency labels.
Next, by extracting shortest paths between node pairs in the graph, they transform associations into the form Verb Entity 1 , Entity 2 , such that Entity 1 and Entity 2 are connected by Verb.
This approach, which is an extension of the association-identifying method described in section 3. Other studies that use a dependency analysis of sentences to determine the strength of the associations include Quan and Ren, ; Kuhn et al. After individual relations between biomedical entities have been inferred, it is convenient to assemble these in the form of networks Skusa et al.
In such networks, nodes also called vertices correspond to entities and edges also called links to relations between entities. The resulting networks can be either weighted or unweighted. If polarity or strength of relations has been obtained, one can use this information to define the weights of edges as the strength of the relations, leading to weighted networks. Polarity information and relation type classifications can further be used to label edges.
For example, these labels could be positive regulation, negative regulation , or transcription. In this case, edges tend to be directed indicating which entity is influenced by which. The visualization of interaction networks often provides a useful first summary of the results extracted from the relation extraction task.
The networks are either built from scratch or automatically by using software tools. Two such commonly used tools for the network visualization are Cytoscape Franz et al.
Cytoscape can also be used interactively via a web-interface, while Gephi can be used for 3D rendering of graphs and networks. There are also several libraries specifically developed for network visualization in different languages. For instance, NetbioV Tripathi et al. Measures frequently used for biomedical network analysis include node centrality measures, shortest paths, network clustering, and network density Sarangdhar et al. The measures selected to analyze a graph predominantly depend on the task at hand; for example, shortest path analysis is vital for discovering signaling pathways, while clustering analysis helps identify functional subnetwork units.
Further commonly used metrics are centrality measures and network density methods, e. Whereas graph density compares the number of existing relations between the nodes vs. There are four main centrality measures, namely, degree, betweenness, closeness, and eigenvector centrality Emmert-Streib et al.
Degree centrality, the simplest of the above measures, corresponds just to the number of connections of a node. Closeness centrality is given by the reciprocal of the sum of all shortest path lengths between a node and all other nodes in the network, as such it measures the spread of information. Also betweenness centrality utilizes shortest paths by taking into account the information flow of the network.
This is realized by counting shortest paths through pairs of nodes. Finally, eigenvector centrality is a measure of influence where each node is assigned a score based on how many other influential nodes are connected to it. For instance, consider Figure 9 , a disease-gene network. Here blue nodes correspond to genes and pink nodes represent diseases.
For instance, blue nodes with a higher degree centrality correspond to those genes associated with a higher number of diseases. Similarly, pink nodes with a high degree centrality correspond to diseases that are associated with more genes.
Furthermore, the genes with a high closeness centrality are important because they have a direct or indirect association to the largest number of other genes and diseases. Further, if a gene X that is connected to a large number of diseases, and is furthermore connected to gene Y with a high eigenvector centrality, it may be worth exploring if there are diseases in the neighborhood of gene X, that are possibly also associated to gene Y and vice versa. Hence, based on centrality measures, one may be able to find previously undiscovered relations between certain diseases and genes.
Figure 9. Genes are shown as blue nodes and diseases as pink nodes. In this section, we will discuss some of the main benchmark tools and resources available for Named-Entity Recognition and Relation Extraction used in the biomedical domain. While the training corpora for machine learning methods in BioNER and BioRD both have been discussed extensively in the sections above, here we mention some of the databases with entities and relation mappings.
These are crucial for dictionary-based methods and in post-processing, and as such, are often used for biomedical text mining research. Some of the Named-Entity specific databases that have comprehensive collections of jargon include Gene Ontology Consortium, , Chemical Entities of Biological Interest Shardlow et al.
The majority of these has been used by Liu et al. These databases have been used by various authors to evaluate relation extraction systems.
In Table 3 , we provide an overview of BioNER tools that are available for different programming languages. While there are several other tools, our selection criterion was to cover the earliest successful implementations, benchmark tools as well as the most recent tools using novel approaches. The improvement of resources and techniques for biomedical annotation has also brought about an abundance of open source tools that have simplified the information extraction for relation mining in biomedical texts.
Many of these are general-purpose text mining tools that can be easily configured to process biomedical texts.
For instance, Xing et al. Other useful tools that can be application adaptable and have higher F-score measures are; DeepDive Niu et al. One of the most important applications of BioNER and BioRD is narrowing down the search space when exploring millions of online biomedical journal articles.
Often, one needs to find articles that do not merely include a search term but also include contextual information. That would only be possible if the search method knows how to locate genes as well as classify them as chromosome 9 related.
Another application is for disease diagnosis and treatment, where mining prior treatment data and research work could assist in narrowing down the diagnosis and possibly effective treatment regiments for a given complicated set of symptoms presented by a patient Zhu et al.
In recent years, there has been much attention to designing automated healthcare chatbot systems that are configured to respond to user queries and provide advice or support.
Healthcare chatbots use various biomedical text mining techniques to process queries, match them to answers in their knowledge base to either provide medical advice or to refer them Chawla and Anuradha, ; Ghosh et al. Such systems require the ability to process entities and relations such as diseases, drugs, symptoms, body parts, diagnosis, treatments, or adverse effects Ghiasvand and Kate, ; Wang et al.
Another notable application of relation detection is for generating biological interaction networks Azam et al. Once such associations are established, they can be summarized as a network representing prostate cancer gene interactions or drug-to-drug interactions with side effects.
These networks not only provide a summation of thousands of research articles and a visualization but also allow us to derive novel hypotheses. As such, creating a network with known interactions extracted from research would allow us to explore other possible interactions between drugs and adverse effects Luo et al.
That means an optimal combination of data and methods is required for achieving the best results. Regarding the data, most current studies are based on information from abstracts of scientific articles as provided, e. However, such articles contain much more information, which is only accessible if one would have access to full-text publications.
However, many articles are still hidden behind a paywall, e. A related problem refers to capturing information from tables or Supplementary Files. Especially the latter possess new challenges because most publishers do not provide formatting guidelines for Supplementary Files rendering such texts as unstructured. Importantly, information extracted from such full-text publications or Supplementary Files could not only lead to additional information but to redundant information that could be utilized for correcting errors obtained from using journal abstracts solely.
Hence, one could expect to improve the quality of the analysis performance by using additional input texts as provided by full-text publications or Supplementary Files. Another problem relates to the extraction of italicized or quoted text which may not be captured. A common question asked is what is the performance of a method and how does it compare to other related methods? Since the papers reviewed in this article have all been published in either scientific journals or conferences or preprint servers all of them have been studied numerically, at least to some extend.
However, for any serious application the information required is the generalization error GenErr Emmert-Streib and Dehmer b and the dependence of the GenErr on variations of the data.
The statistical estimation of the GenErr is in general challenging and not straight forward. This implies that this error may be considerably different to the numerical results provided in the reviewed papers and, hence, a case-by-case analysis is required to select the proper method for a given application domain.
For this reason, as a warning, we would like to remark that despite the fact that we provided throughout the paper information about obtained F-scores or recall values, such information needs to be considered cautiously. Hence, such values should not be seen as an absolute indicator of performance but as guideline for your own dedicated context-specific performance analysis.
From a methodological point of view, deep learning approaches are still relatively new, leaving plenty of room for improvement Yadav and Bethard, Certainly, this characteristic is not entirely domain and data-independent Smolander et al.
Interestingly, recent results for patient phenotyping from electronic health records eHRs show that this might be the case Yang et al. Regarding methods, unsupervised and semi-supervised methods have the most significant potential for improvement because annotated benchmark corpora are still relatively small; see Table 1 and the information about the available sample sizes.
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