# A novel language model for predicting serious adverse event results in clinical trials from their prospective registrations

arXiv: https://arxiv.org/abs/2507.22919 · HTML: https://mlsanity.com/paper/2507.22919/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 43 references that are in the map.
- First posted on arXiv 21 Jul 2025.

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [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)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Large Language Models Are Zero-Shot Time Series Forecasters](https://mlsanity.com/paper/2310.07820/) (2023)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [Table Meets LLM: Can Large Language Models Understand Structured Table Data? A Benchmark and Empirical Study](https://mlsanity.com/paper/2305.13062/) (2023)
- [Found in the Middle: How Language Models Use Long Contexts Better via Plug-and-Play Positional Encoding](https://mlsanity.com/paper/2403.04797/) (2024)
- [On the consistency of supervised learning with missing values](https://mlsanity.com/paper/1902.06931/) (2019)
- [The first step is the hardest: Pitfalls of Representing and Tokenizing Temporal Data for Large Language Models](https://mlsanity.com/paper/2309.06236/) (2023)
- [Hierarchical Context Merging: Better Long Context Understanding for Pre-trained LLMs](https://mlsanity.com/paper/2404.10308/) (2024)
- [Benchmarking missing-values approaches for predictive models on health databases](https://mlsanity.com/paper/2202.10580/) (2022)
- [Transfer Learning with Clinical Concept Embeddings from Large Language Models](https://mlsanity.com/paper/2409.13893/) (2024)
- [Comparing representations of long clinical texts for the task of patient note-identification](https://mlsanity.com/paper/2503.24006/) (2025)

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

- [CT Open: An Open-Access, Uncontaminated, Live Platform for the Open Challenge of Clinical Trial Outcome Prediction](https://mlsanity.com/paper/2604.16742/) (2026)

## Abstract (arXiv)

Objectives: With accurate estimates of expected safety results, clinical trials could be better designed and monitored. We evaluated methods for predicting serious adverse event (SAE) results in clinical trials using information only from their registrations prior to the trial. Material and Methods: We analyzed 22,107 two-arm parallel interventional clinical trials from ClinicalTrials.gov with structured summary results. Two prediction models were developed: a classifier predicting whether a greater proportion of participants in an experimental arm would have SAEs (area under the receiver operating characteristic curve; AUC) compared to the control arm, and a regression model to predict the proportion of participants with SAEs in the control arms (root mean squared error; RMSE). A transfer learning approach using pretrained language models (e.g., ClinicalT5, BioBERT) was used for feature extraction, combined with a downstream model for prediction. To maintain semantic representation in long trial texts exceeding localized language model input limits, a sliding window method was developed for embedding extraction. Results: The best model (ClinicalT5+Transformer+MLP) had 77.6% AUC when predicting which trial arm had a higher proportion of SAEs. When predicting SAE proportion in the control arm, the same model achieved RMSE of 18.6%. The sliding window approach consistently outperformed direct comparisons. Across 12 classifiers, the average absolute AUC increase was 2.00%, and absolute RMSE reduction was 1.58% across 12 regressors. Discussion: Summary results data from ClinicalTrials.gov remains underutilized. Predicted results of publicly reported trials provides an opportunity to identify discrepancies between expected and reported safety results.