# Classification of hierarchical text using geometric deep learning: the case of clinical trials corpus

arXiv: https://arxiv.org/abs/2110.15710 · HTML: https://mlsanity.com/paper/2110.15710/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 47 references that are in the map.
- First posted on arXiv 4 Oct 2021.

## Builds on (most cited first, 27 of 27)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [Reformer: The Efficient Transformer](https://mlsanity.com/paper/2001.04451/) (2020)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [Convolutional Neural Networks for Sentence Classification](https://mlsanity.com/paper/1408.5882/) (2014)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [Bag of Tricks for Efficient Text Classification](https://mlsanity.com/paper/1607.01759/) (2016)
- [Long Range Arena: A Benchmark for Efficient Transformers](https://mlsanity.com/paper/2011.04006/) (2020)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [Efficient Attention: Attention with Linear Complexities](https://mlsanity.com/paper/1812.01243/) (2018)
- [Graph Convolutional Networks for Text Classification](https://mlsanity.com/paper/1809.05679/) (2018)
- [Improved Semantic Representations From Tree-Structured Long Short-Term Memory Networks](https://mlsanity.com/paper/1503.00075/) (2015)
- [GRAM: Graph-based Attention Model for Healthcare Representation Learning](https://mlsanity.com/paper/1611.07012/) (2016)
- [Pre-training of Graph Augmented Transformers for Medication Recommendation](https://mlsanity.com/paper/1906.00346/) (2019)
- [GAMENet: Graph Augmented MEmory Networks for Recommending Medication Combination](https://mlsanity.com/paper/1809.01852/) (2018)
- [Be More with Less: Hypergraph Attention Networks for Inductive Text Classification](https://mlsanity.com/paper/2011.00387/) (2020)

## Built on by (most cited first, 1 of 1)

- [Early Risk Stratification of Dosing Errors in Clinical Trials Using Machine Learning](https://mlsanity.com/paper/2602.22285/) (2026)

## Abstract (arXiv)

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 the 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-scores around 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.