# ctELM: Decoding and Manipulating Embeddings of Clinical Trials with Embedding Language Models

arXiv: https://arxiv.org/abs/2601.18796 · HTML: https://mlsanity.com/paper/2601.18796/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 27 of its 40 references that are in the map.
- First posted on arXiv 26 Jan 2026.

## 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)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [G-Eval: NLG Evaluation using GPT-4 with Better Human Alignment](https://mlsanity.com/paper/2303.16634/) (2023)
- [SimCSE: Simple Contrastive Learning of Sentence Embeddings](https://mlsanity.com/paper/2104.08821/) (2021)
- [Interpretability Beyond Feature Attribution: Quantitative Testing with Concept Activation Vectors (TCAV)](https://mlsanity.com/paper/1711.11279/) (2017)
- [Man is to Computer Programmer as Woman is to Homemaker? Debiasing Word Embeddings](https://mlsanity.com/paper/1607.06520/) (2016)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Vision-Language Models for Vision Tasks: A Survey](https://mlsanity.com/paper/2304.00685/) (2023)
- [BERTopic: Neural topic modeling with a class-based TF-IDF procedure](https://mlsanity.com/paper/2203.05794/) (2022)
- [CTRL: A Conditional Transformer Language Model for Controllable Generation](https://mlsanity.com/paper/1909.05858/) (2019)
- [Towards General Text Embeddings with Multi-stage Contrastive Learning](https://mlsanity.com/paper/2308.03281/) (2023)
- [LLM Evaluators Recognize and Favor Their Own Generations](https://mlsanity.com/paper/2404.13076/) (2024)
- [C-Pack: Packed Resources For General Chinese Embeddings](https://mlsanity.com/paper/2309.07597/) (2023)
- [LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders](https://mlsanity.com/paper/2404.05961/) (2024)
- [Topic Modeling in Embedding Spaces](https://mlsanity.com/paper/1907.04907/) (2019)
- [Information Leakage in Embedding Models](https://mlsanity.com/paper/2004.00053/) (2020)
- [Text Embeddings Reveal (Almost) As Much As Text](https://mlsanity.com/paper/2310.06816/) (2023)
- [PubMed 200k RCT: a Dataset for Sequential Sentence Classification in Medical Abstracts](https://mlsanity.com/paper/1710.06071/) (2017)
- [Pride and Prejudice: LLM Amplifies Self-Bias in Self-Refinement](https://mlsanity.com/paper/2402.11436/) (2024)
- [Sentence Embedding Leaks More Information than You Expect: Generative Embedding Inversion Attack to Recover the Whole Sentence](https://mlsanity.com/paper/2305.03010/) (2023)
- [InvBERT: Reconstructing Text from Contextualized Word Embeddings by inverting the BERT pipeline](https://mlsanity.com/paper/2109.10104/) (2021)
- [Exploring Empty Spaces: Human-in-the-Loop Data Augmentation](https://mlsanity.com/paper/2410.01088/) (2024)
- [Rethinking the Privacy of Text Embeddings: A Reproducibility Study of "Text Embeddings Reveal (Almost) As Much As Text"](https://mlsanity.com/paper/2507.07700/) (2025)
- [MapExplorer: New Content Generation from Low-Dimensional Visualizations](https://mlsanity.com/paper/2412.18673/) (2024)

## Abstract (arXiv)

Text embeddings have become an essential part of a variety of language applications. However, methods for interpreting, exploring and reversing embedding spaces are limited, reducing transparency and precluding potentially valuable generative use cases. In this work, we align Large Language Models to embeddings of clinical trials using the recently reported Embedding Language Model (ELM) method. We develop an open-source, domain-agnostic ELM architecture and training framework, design training tasks for clinical trials, and introduce an expert-validated synthetic dataset. We then train a series of ELMs exploring the impact of tasks and training regimes. Our final model, ctELM, can accurately describe and compare unseen clinical trials from embeddings alone and produce plausible clinical trials from novel vectors. We further show that generated trial abstracts are responsive to moving embeddings along concept vectors for age and sex of study subjects. Our public ELM implementation and experimental results will aid the alignment of Large Language Models to embedding spaces in the biomedical domain and beyond.