Do you want to publish a course? Click here

EnSidNet: Enhanced Hybrid Siamese-Deep Network for grouping clinical trials into drug-development pathways

Ensidnet: شبكة Siamese الهجينة المحسنة للتجميع التجارب السريرية لتجميع مسارات تطوير المخدرات

211   0   0   0.0 ( 0 )
 Publication date 2021
and research's language is English
 Created by Shamra Editor




Ask ChatGPT about the research

Siamese Neural Networks have been widely used to perform similarity classification in multi-class settings. Their architecture can be used to group the clinical trials belonging to the same drug-development pathway along the several clinical trial phases. Here we present an approach for the unmet need of drug-development pathway reconstruction, based on an Enhanced hybrid Siamese-Deep Neural Network (EnSidNet). The proposed model demonstrates significant improvement above baselines in a 1-shot evaluation setting and in a classical similarity setting. EnSidNet can be an essential tool in a semi-supervised learning environment: by selecting clinical trials highly likely to belong to the same drug-development pathway it is possible to speed up the labelling process of human experts, allowing the check of a consistent volume of data, further used in the model's training dataset.

References used
https://aclanthology.org/
rate research

Read More

We consider the hierarchical representation of documents as graphs and use geometric deep learning to classify them into different categories. While graph neural networks can efficiently handle the variable structure of hierarchical documents using t he permutation invariant message passing operations, we show that we can gain extra performance improvements using our proposed selective graph pooling operation that arises from the fact that some parts of the hierarchy are invariable across different documents. We applied our model to classify clinical trial (CT) protocols into completed and terminated categories. We use bag-of-words based, as well as pre-trained transformer-based embeddings to featurize the graph nodes, achieving f1-scoresaround 0.85 on a publicly available large scale CT registry of around 360K protocols. We further demonstrate how the selective pooling can add insights into the CT termination status prediction. We make the source code and dataset splits accessible.
Multi-label document classification (MLDC) problems can be challenging, especially for long documents with a large label set and a long-tail distribution over labels. In this paper, we present an effective convolutional attention network for the MLDC problem with a focus on medical code prediction from clinical documents. Our innovations are three-fold: (1) we utilize a deep convolution-based encoder with the squeeze-and-excitation networks and residual networks to aggregate the information across the document and learn meaningful document representations that cover different ranges of texts; (2) we explore multi-layer and sum-pooling attention to extract the most informative features from these multi-scale representations; (3) we combine binary cross entropy loss and focal loss to improve performance for rare labels. We focus our evaluation study on MIMIC-III, a widely used dataset in the medical domain. Our models outperform prior work on medical coding and achieve new state-of-the-art results on multiple metrics. We also demonstrate the language independent nature of our approach by applying it to two non-English datasets. Our model outperforms prior best model and a multilingual Transformer model by a substantial margin.
Recently, impressive performance on various natural language understanding tasks has been achieved by explicitly incorporating syntax and semantic information into pre-trained models, such as BERT and RoBERTa. However, this approach depends on proble m-specific fine-tuning, and as widely noted, BERT-like models exhibit weak performance, and are inefficient, when applied to unsupervised similarity comparison tasks. Sentence-BERT (SBERT) has been proposed as a general-purpose sentence embedding method, suited to both similarity comparison and downstream tasks. In this work, we show that by incorporating structural information into SBERT, the resulting model outperforms SBERT and previous general sentence encoders on unsupervised semantic textual similarity (STS) datasets and transfer classification tasks.
Vast amounts of data in healthcare are available in unstructured text format, usually in the local language of the countries. These documents contain valuable information. Secondary use of clinical narratives and information extraction of key facts a nd relations from them about the patient disease history can foster preventive medicine and improve healthcare. In this paper, we propose a hybrid method for the automatic transformation of clinical text into a structured format. The documents are automatically sectioned into the following parts: diagnosis, patient history, patient status, lab results. For the Diagnosis'' section a deep learning text-based encoding into ICD-10 codes is applied using MBG-ClinicalBERT - a fine-tuned ClinicalBERT model for Bulgarian medical text. From the Patient History'' section, we identify patient symptoms using a rule-based approach enhanced with similarity search based on MBG-ClinicalBERT word embeddings. We also identify symptom relations like negation. For the Patient Status'' description, binary classification is used to determine the status of each anatomic organ. In this paper, we demonstrate different methods for adapting NLP tools for English and other languages to a low resource language like Bulgarian.
Math word problem solving has attracted considerable research interest in recent years. Previous works have shown the effectiveness of utilizing graph neural networks to capture the relationships in the problem. However, these works did not carefully take the edge label information and the long-range word relationship across sentences into consideration. In addition, during generation, they focus on the most relevant areas of the currently generated word, while neglecting the rest of the problem. In this paper, we propose a novel Edge-Enhanced Hierarchical Graph-to-Tree model (EEH-G2T), in which the math word problems are represented as edge-labeled graphs. Specifically, an edge-enhanced hierarchical graph encoder is used to incorporate edge label information. This encoder updates the graph nodes hierarchically in two steps: sentence-level aggregation and problem-level aggregation. Furthermore, a tree-structured decoder with a split attention mechanism is applied to guide the model to pay attention to different parts of the input problem. Experimental results on the MAWPS and Math23K dataset showed that our EEH-G2T can effectively improve performance compared with state-of-the-art methods.

suggested questions

comments
Fetching comments Fetching comments
Sign in to be able to follow your search criteria
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا