3,276 research outputs found
Unsupervised Biomedical Named Entity Recognition
Named entity recognition (NER) from text is an important task for several applications, including in the biomedical domain. Supervised machine learning based systems have been the most successful on NER task, however, they require correct annotations in large quantities for training. Annotating text manually is very labor intensive and also needs domain expertise. The purpose of this research is to reduce human annotation effort and to decrease cost of annotation for building NER systems in the biomedical domain. The method developed in this work is based on leveraging the availability of resources like UMLS (Unified Medical Language System), that contain a list of biomedical entities and a large unannotated corpus to build an unsupervised NER system that does not require any manual annotations.
The method that we developed in this research has two phases. In the first phase, a biomedical corpus is automatically annotated with some named entities using UMLS through unambiguous exact matching which we call weakly-labeled data. In this data, positive examples are the entities in the text that exactly match in UMLS and have only one semantic type which belongs to the desired entity class to be extracted (for example, diseases and disorders). Negative examples are the entities in the text that exactly match in UMLS but are of semantic types other than those that belong to the desired entity class. These examples are then used to train a machine learning classifier using features that represent the contexts in which they appeared in the text. The trained classifier is applied back to the text to gather more examples iteratively through the process of self-training. The trained classifier is then capable of classifying mentions in an unseen text as of the desired entity class or not from the contexts in which they appear.
Although the trained named entity detector is good at detecting the presence of entities of the desired class in text, it cannot determine their correct boundaries. In the second phase of our method, called “Boundary Expansion”, the correct boundaries of the entities are determined. This method is based on a novel idea that utilizes machine learning and UMLS. Training examples for boundary expansion are gathered directly from UMLS and do not require any manual annotations. We also developed a new WordNet based approach for boundary expansion.
Our developed method was evaluated on three datasets - SemEval 2014 Task 7 dataset that has diseases and disorders as the desired entity class, GENIA dataset that has proteins, DNAs, RNAs, cell types, and cell lines as the desired entity classes, and i2b2 dataset that has problems, tests, and treatments as the desired entity classes. Our method performed well and obtained performance close to supervised methods on the SemEval dataset. On the other datasets, it outperformed an existing unsupervised method on most entity classes. Availability of a list of entity names with their semantic types and a large unannotated corpus are the only requirements of our method to work well. Given these, our method generalizes across different types of entities and different types of biomedical text. Being unsupervised, the method can be easily applied to new NER tasks without needing costly annotations
Multiple Instance Learning: A Survey of Problem Characteristics and Applications
Multiple instance learning (MIL) is a form of weakly supervised learning
where training instances are arranged in sets, called bags, and a label is
provided for the entire bag. This formulation is gaining interest because it
naturally fits various problems and allows to leverage weakly labeled data.
Consequently, it has been used in diverse application fields such as computer
vision and document classification. However, learning from bags raises
important challenges that are unique to MIL. This paper provides a
comprehensive survey of the characteristics which define and differentiate the
types of MIL problems. Until now, these problem characteristics have not been
formally identified and described. As a result, the variations in performance
of MIL algorithms from one data set to another are difficult to explain. In
this paper, MIL problem characteristics are grouped into four broad categories:
the composition of the bags, the types of data distribution, the ambiguity of
instance labels, and the task to be performed. Methods specialized to address
each category are reviewed. Then, the extent to which these characteristics
manifest themselves in key MIL application areas are described. Finally,
experiments are conducted to compare the performance of 16 state-of-the-art MIL
methods on selected problem characteristics. This paper provides insight on how
the problem characteristics affect MIL algorithms, recommendations for future
benchmarking and promising avenues for research
On Classification with Bags, Groups and Sets
Many classification problems can be difficult to formulate directly in terms
of the traditional supervised setting, where both training and test samples are
individual feature vectors. There are cases in which samples are better
described by sets of feature vectors, that labels are only available for sets
rather than individual samples, or, if individual labels are available, that
these are not independent. To better deal with such problems, several
extensions of supervised learning have been proposed, where either training
and/or test objects are sets of feature vectors. However, having been proposed
rather independently of each other, their mutual similarities and differences
have hitherto not been mapped out. In this work, we provide an overview of such
learning scenarios, propose a taxonomy to illustrate the relationships between
them, and discuss directions for further research in these areas
Mining Entity Synonyms with Efficient Neural Set Generation
Mining entity synonym sets (i.e., sets of terms referring to the same entity)
is an important task for many entity-leveraging applications. Previous work
either rank terms based on their similarity to a given query term, or treats
the problem as a two-phase task (i.e., detecting synonymy pairs, followed by
organizing these pairs into synonym sets). However, these approaches fail to
model the holistic semantics of a set and suffer from the error propagation
issue. Here we propose a new framework, named SynSetMine, that efficiently
generates entity synonym sets from a given vocabulary, using example sets from
external knowledge bases as distant supervision. SynSetMine consists of two
novel modules: (1) a set-instance classifier that jointly learns how to
represent a permutation invariant synonym set and whether to include a new
instance (i.e., a term) into the set, and (2) a set generation algorithm that
enumerates the vocabulary only once and applies the learned set-instance
classifier to detect all entity synonym sets in it. Experiments on three real
datasets from different domains demonstrate both effectiveness and efficiency
of SynSetMine for mining entity synonym sets.Comment: AAAI 2019 camera-ready versio
Beyond MeSH: Fine-Grained Semantic Indexing of Biomedical Literature based on Weak Supervision
In this work, we propose a method for the automated refinement of subject
annotations in biomedical literature at the level of concepts. Semantic
indexing and search of biomedical articles in MEDLINE/PubMed are based on
semantic subject annotations with MeSH descriptors that may correspond to
several related but distinct biomedical concepts. Such semantic annotations do
not adhere to the level of detail available in the domain knowledge and may not
be sufficient to fulfil the information needs of experts in the domain. To this
end, we propose a new method that uses weak supervision to train a concept
annotator on the literature available for a particular disease. We test this
method on the MeSH descriptors for two diseases: Alzheimer's Disease and
Duchenne Muscular Dystrophy. The results indicate that concept-occurrence is a
strong heuristic for automated subject annotation refinement and its use as
weak supervision can lead to improved concept-level annotations. The
fine-grained semantic annotations can enable more precise literature retrieval,
sustain the semantic integration of subject annotations with other domain
resources and ease the maintenance of consistent subject annotations, as new
more detailed entries are added in the MeSH thesaurus over time.Comment: 36 pages, 8 figures; Dictionary-based baselines added and conclusions
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