arXiv subjects

Ashish Anand

Publications and source records attributed to Ashish Anand.

28 records · Page 2Linked to original sources

arXiv2017

Investigating how well contextual features are captured by bi-directional recurrent neural network models

Learning algorithms for natural language processing (NLP) tasks traditionally rely on manually defined relevant contextual features. On the other hand, neural network models using an only distributional representation of words have been successfully applied for several NLP tasks. Such models learn features automatically and avoid explicit feature engineering. Across several domains, neural models become a natural choice specifically when limited characteristics of data are known. However, this flexibility comes at the cost of interpretability. In this paper, we define three different methods to investigate ability of bi-directional recurrent neural networks (RNNs) in capturing contextual features. In particular, we analyze RNNs for sequence tagging tasks. We perform a comprehensive analysis on general as well as biomedical domain datasets. Our experiments focus on important contextual words as features, which can easily be extended to analyze various other feature types. We also investigate positional effects of context words and show how the developed methods can be used for error analysis.

cs.CL↗

arXiv2017

What matters in a transferable neural network model for relation classification in the biomedical domain?

Lack of sufficient labeled data often limits the applicability of advanced machine learning algorithms to real life problems. However efficient use of Transfer Learning (TL) has been shown to be very useful across domains. TL utilizes valuable knowledge learned in one task (source task), where sufficient data is available, to the task of interest (target task). In biomedical and clinical domain, it is quite common that lack of sufficient training data do not allow to fully exploit machine learning models. In this work, we present two unified recurrent neural models leading to three transfer learning frameworks for relation classification tasks. We systematically investigate effectiveness of the proposed frameworks in transferring the knowledge under multiple aspects related to source and target tasks, such as, similarity or relatedness between source and target tasks, and size of training data for source task. Our empirical results show that the proposed frameworks in general improve the model performance, however these improvements do depend on aspects related to source and target tasks. This dependence then finally determine the choice of a particular TL framework.

cs.CL↗

arXiv2017

Drug-Drug Interaction Extraction from Biomedical Text Using Long Short Term Memory Network

Simultaneous administration of multiple drugs can have synergistic or antagonistic effects as one drug can affect activities of other drugs. Synergistic effects lead to improved therapeutic outcomes, whereas, antagonistic effects can be life-threatening, may lead to increased healthcare cost, or may even cause death. Thus identification of unknown drug-drug interaction (DDI) is an important concern for efficient and effective healthcare. Although multiple resources for DDI exist, they are often unable to keep pace with rich amount of information available in fast growing biomedical texts. Most existing methods model DDI extraction from text as a classification problem and mainly rely on handcrafted features. Some of these features further depend on domain specific tools. Recently neural network models using latent features have been shown to give similar or better performance than the other existing models dependent on handcrafted features. In this paper, we present three models namely, {\it B-LSTM}, {\it AB-LSTM} and {\it Joint AB-LSTM} based on long short-term memory (LSTM) network. All three models utilize word and position embedding as latent features and thus do not rely on explicit feature engineering. Further use of bidirectional long short-term memory (Bi-LSTM) networks allow implicit feature extraction from the whole sentence. The two models, {\it AB-LSTM} and {\it Joint AB-LSTM} also use attentive pooling in the output of Bi-LSTM layer to assign weights to features. Our experimental results on the SemEval-2013 DDI extraction dataset show that the {\it Joint AB-LSTM} model outperforms all the existing methods, including those relying on handcrafted features. The other two proposed LSTM models also perform competitively with state-of-the-art methods.

cs.CL↗

arXiv2017

Unified Neural Architecture for Drug, Disease and Clinical Entity Recognition

Most existing methods for biomedical entity recognition task rely on explicit feature engineering where many features either are specific to a particular task or depends on output of other existing NLP tools. Neural architectures have been shown across various domains that efforts for explicit feature design can be reduced. In this work we propose an unified framework using bi-directional long short term memory network (BLSTM) for named entity recognition (NER) tasks in biomedical and clinical domains. Three important characteristics of the framework are as follows - (1) model learns contextual as well as morphological features using two different BLSTM in hierarchy, (2) model uses first order linear conditional random field (CRF) in its output layer in cascade of BLSTM to infer label or tag sequence, (3) model does not use any domain specific features or dictionary, i.e., in another words, same set of features are used in the three NER tasks, namely, disease name recognition (Disease NER), drug name recognition (Drug NER) and clinical entity recognition (Clinical NER). We compare performance of the proposed model with existing state-of-the-art models on the standard benchmark datasets of the three tasks. We show empirically that the proposed framework outperforms all existing models. Further our analysis of CRF layer and word-embedding obtained using character based embedding show their importance.

cs.CL↗

arXiv2017

Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models

Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all event extraction methods. However many of the current approaches either rely on complex hand-crafted features or consider features only within a window. In this paper we propose a method that takes the advantage of recurrent neural network (RNN) to extract higher level features present across the sentence. Thus hidden state representation of RNN along with word and entity type embedding as features avoid relying on the complex hand-crafted features generated using various NLP toolkits. Our experiments have shown to achieve state-of-art F1-score on Multi Level Event Extraction (MLEE) corpus. We have also performed category-wise analysis of the result and discussed the importance of various features in trigger identification task.

cs.CL↗

arXiv2017

Representation learning of drug and disease terms for drug repositioning

Drug repositioning (DR) refers to identification of novel indications for the approved drugs. The requirement of huge investment of time as well as money and risk of failure in clinical trials have led to surge in interest in drug repositioning. DR exploits two major aspects associated with drugs and diseases: existence of similarity among drugs and among diseases due to their shared involved genes or pathways or common biological effects. Existing methods of identifying drug-disease association majorly rely on the information available in the structured databases only. On the other hand, abundant information available in form of free texts in biomedical research articles are not being fully exploited. Word-embedding or obtaining vector representation of words from a large corpora of free texts using neural network methods have been shown to give significant performance for several natural language processing tasks. In this work we propose a novel way of representation learning to obtain features of drugs and diseases by combining complementary information available in unstructured texts and structured datasets. Next we use matrix completion approach on these feature vectors to learn projection matrix between drug and disease vector spaces. The proposed method has shown competitive performance with state-of-the-art methods. Further, the case studies on Alzheimer's and Hypertension diseases have shown that the predicted associations are matching with the existing knowledge.

cs.CL↗

arXiv2017

Fine-Grained Entity Type Classification by Jointly Learning Representations and Label Embeddings

Fine-grained entity type classification (FETC) is the task of classifying an entity mention to a broad set of types. Distant supervision paradigm is extensively used to generate training data for this task. However, generated training data assigns same set of labels to every mention of an entity without considering its local context. Existing FETC systems have two major drawbacks: assuming training data to be noise free and use of hand crafted features. Our work overcomes both drawbacks. We propose a neural network model that jointly learns entity mentions and their context representation to eliminate use of hand crafted features. Our model treats training data as noisy and uses non-parametric variant of hinge loss function. Experiments show that the proposed model outperforms previous state-of-the-art methods on two publicly available datasets, namely FIGER (GOLD) and BBN with an average relative improvement of 2.69% in micro-F1 score. Knowledge learnt by our model on one dataset can be transferred to other datasets while using same model or other FETC systems. These approaches of transferring knowledge further improve the performance of respective models.

cs.CL↗

arXiv2016

Relation extraction from clinical texts using domain invariant convolutional neural network

In recent years extracting relevant information from biomedical and clinical texts such as research articles, discharge summaries, or electronic health records have been a subject of many research efforts and shared challenges. Relation extraction is the process of detecting and classifying the semantic relation among entities in a given piece of texts. Existing models for this task in biomedical domain use either manually engineered features or kernel methods to create feature vector. These features are then fed to classifier for the prediction of the correct class. It turns out that the results of these methods are highly dependent on quality of user designed features and also suffer from curse of dimensionality. In this work we focus on extracting relations from clinical discharge summaries. Our main objective is to exploit the power of convolution neural network (CNN) to learn features automatically and thus reduce the dependency on manual feature engineering. We evaluate performance of the proposed model on i2b2-2010 clinical relation extraction challenge dataset. Our results indicate that convolution neural network can be a good model for relation exaction in clinical text without being dependent on expert's knowledge on defining quality features.

cs.CL↗

arXiv2016

Recurrent neural network models for disease name recognition using domain invariant features

Hand-crafted features based on linguistic and domain-knowledge play crucial role in determining the performance of disease name recognition systems. Such methods are further limited by the scope of these features or in other words, their ability to cover the contexts or word dependencies within a sentence. In this work, we focus on reducing such dependencies and propose a domain-invariant framework for the disease name recognition task. In particular, we propose various end-to-end recurrent neural network (RNN) models for the tasks of disease name recognition and their classification into four pre-defined categories. We also utilize convolution neural network (CNN) in cascade of RNN to get character-based embedded features and employ it with word-embedded features in our model. We compare our models with the state-of-the-art results for the two tasks on NCBI disease dataset. Our results for the disease mention recognition task indicate that state-of-the-art performance can be obtained without relying on feature engineering. Further the proposed models obtained improved performance on the classification task of disease names.

cs.CL↗

arXiv2015

Inferring disease correlation from healthcare data

Electronic Health Records maintained in health care settings are a potential source of substantial clinical knowledge. The massive volume of data, unstructured nature of records and obligatory requirement of domain acquaintance together pose a challenge in knowledge extraction from it. The aim of this study is to overcome this challenge with a methodical analysis, abstraction and summarization of such data. This is an attempt to explain clinical observations through bio-medical and genomic data. Discharge summaries of obesity patients were processed to extract coherent patterns. This was supported by Machine Learning and Natural Language Processing based technologies and concept mapping tool along with biomedical, clinical and genomic knowledge bases. Semantic relations between diseases were extracted and filtered through Chi square test to remove spurious relations. The remaining relations were validated against biomedical literature and gene interaction networks. A collection of binary relations of diseases was derived from the data. One set implied co-morbidity while the other set contained diseases which are risk factors of others. Validation against bio-medical literature increased the prospect of correlation between diseases. Gene interaction network revealed that the diseases are related and their corresponding genes are in close proximity. Conclusion: This study focuses on deducing meaningful relations between diseases from discharge summaries. For analytical purpose, the scope has been limited to a few common, well-researched diseases. It can be extended to incorporate relatively unknown, complex diseases and discover new traits to help in clinical assessments.

cs.IR↗