Clinical trials are essential for drug development but are extremely expensive and time-consuming to conduct. It is beneficial to study similar historical trials when designing a clinical trial. However, lengthy trial documents and lack of labeled data make trial similarity search difficult. We propose a zero-shotclinical trial retrieval method, called Trial2Vec, which learns through self-supervision without the need for annotating similar clinical trials. Specifically, the meta-structure of trial documents (e.g., title, eligibility criteria, target disease) along with clinical knowledge (e.g., UMLS knowledge base) are leveraged to automatically generate contrastive samples. Besides, encodes trial documents considering meta-structure thus producing compact embeddings aggregating multi-aspect information from the whole document. We show that our method yields medically interpretable embeddings by visualization and it gets 15% average improvement over the best baselines on precision/recall for trial retrieval, which is evaluated on our labeled 1600 trial pairs. In addition, we prove the pretrained embeddings benefit the downstream trial outcome prediction task over 240k trials. Software is available at https://github.com/RyanWangZf/Trial2Vec.
Accessing longitudinal multimodal Electronic Healthcare Records (EHRs) is challenging due to privacy concerns, which hinders the use of ML for healthcare applications. Synthetic EHRs generation bypasses the need to share sensitive real patient records. However, existing methods generate single-modal EHRs by unconditional generation or by longitudinal inference, which falls short of low flexibility and makes unrealistic EHRs. In this work, we propose to formulate EHRs generation as a text-to-text translation task by language models (LMs), which suffices to highly flexible event imputation during generation. We also design prompt learning to control the generation conditioned by numerical and categorical demographic features. We evaluate synthetic EHRs quality by two perplexity measures accounting for their longitudinal pattern (longitudinal imputation perplexity, lpl) and the connections cross modalities (cross-modality imputation perplexity, mpl). Moreover, we utilize two adversaries: membership and attribute inference attacks for privacy-preserving evaluation. Experiments on MIMIC-III data demonstrate the superiority of our methods on realistic EHRs generation (53.1% decrease of lpl and 45.3% decrease of mpl on average compared to the best baselines) with low privacy risks. Software is available at https://github.com/RyanWangZf/PromptEHR.
Existing vision-text contrastive learning like CLIP aims to match the paired image and caption embeddings while pushing others apart, which improves representation transferability and supports zero-shot prediction. However, medical image-text datasets are orders of magnitude below the general images and captions from the internet. Moreover, previous methods encounter many false negatives, i.e., images and reports from separate patients probably carry the same semantics but are wrongly treated as negatives. In this paper, we decouple images and texts for multimodal contrastive learning, thus scaling the usable training data in a combinatorial magnitude with low cost. We also propose to replace the InfoNCE loss with semantic matching loss based on medical knowledge to eliminate false negatives in contrastive learning. We prove that MedCLIP is a simple yet effective framework: it outperforms state-of-the-art methods on zero-shot prediction, supervised classification, and image-text retrieval. Surprisingly, we observe that with only 20K pre-training data, MedCLIP wins over the state-of-the-art method (using 200K data). The code is available at https://github.com/RyanWangZf/MedCLIP.
Distant supervision (DS) is a strong way to expand the datasets for enhancing relation extraction (RE) models but often suffers from high label noise. Current works based on attention, reinforcement learning, or GAN are black-box models so they neither provide meaningful interpretation of sample selection in DS nor stability on different domains. On the contrary, this work proposes a novel model-agnostic instance sampling method for DS by influence function (IF), namely REIF. Our method identifies favorable/unfavorable instances in the bag based on IF, then does dynamic instance sampling. We design a fast influence sampling algorithm that reduces the computational complexity from 𝒪(mn) to 𝒪(1), with analyzing its robustness on the selected sampling function. Experiments show that by simply sampling the favorable instances during training, REIF is able to win over a series of baselines which have complicated architectures. We also demonstrate that REIF can support interpretable instance selection.