Self-Verification Improves Few-Shot Clinical Information Extraction

Extracting patient information from unstructured text is a critical task in health decision-support and clinical research. Large language models (LLMs) have shown the potential to accelerate clinical curation via few-shot in-context learning, in contrast to supervised learning which requires much more costly human annotations. However, despite drastic advances in modern LLMs such as GPT-4, they still struggle with issues regarding accuracy and interpretability, especially in mission-critical domains such as health. Here, we explore a general mitigation framework using self-verification, which leverages the LLM to provide provenance for its own extraction and check its own outputs. This is made possible by the asymmetry between verification and generation, where the latter is often much easier than the former. Experimental results show that our method consistently improves accuracy for various LLMs in standard clinical information extraction tasks. Additionally, self-verification yields interpretations in the form of a short text span corresponding to each output, which makes it very efficient for human experts to audit the results, paving the way towards trustworthy extraction of clinical information in resource-constrained scenarios. To facilitate future research in this direction, we release our code and prompts.

Compositional Zero-Shot Domain Transfer with Text-to-Text Models

Label scarcity is a bottleneck for improving task performance in specialised domains. We propose a novel compositional transfer learning framework (DoT5 - domain compositional zero-shot T5) for zero-shot domain transfer. Without access to in-domain labels, DoT5 jointly learns domain knowledge (from MLM of unlabelled in-domain free text) and task knowledge (from task training on more readily available general-domain data) in a multi-task manner. To improve the transferability of task training, we design a strategy named NLGU: we simultaneously train NLG for in-domain label-to-data generation which enables data augmentation for self-finetuning and NLU for label prediction. We evaluate DoT5 on the biomedical domain and the resource-lean subdomain of radiology, focusing on NLI, text summarisation and embedding learning. DoT5 demonstrates the effectiveness of compositional transfer learning through multi-task learning. In particular, DoT5 outperforms the current SOTA in zero-shot transfer by over 7 absolute points in accuracy on RadNLI. We validate DoT5 with ablations and a case study demonstrating its ability to solve challenging NLI examples requiring in-domain expertise.

Context-faithful Prompting for Large Language Models

Large language models (LLMs) encode parametric knowledge about world facts and have shown remarkable performance in knowledge-driven NLP tasks. However, their reliance on parametric knowledge may cause them to overlook contextual cues, leading to incorrect predictions in context-sensitive NLP tasks (e.g., knowledge acquisition tasks). In this paper, we seek to assess and enhance LLMs' contextual faithfulness in two aspects: knowledge conflict and prediction with abstention. We demonstrate that LLMs' faithfulness can be significantly improved using carefully designed prompting strategies. In particular, we identify opinion-based prompts and counterfactual demonstrations as the most effective methods. Opinion-based prompts reframe the context as a narrator's statement and inquire about the narrator's opinions, while counterfactual demonstrations use instances containing false facts to improve faithfulness in knowledge conflict situations. Neither technique requires additional training. We conduct experiments on three datasets of two standard NLP tasks, machine reading comprehension and relation extraction, and the results demonstrate significant improvement in faithfulness to contexts.

Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing

Contrastive pretraining on parallel image-text data has attained great success in vision-language processing (VLP), as exemplified by CLIP and related methods. However, prior explorations tend to focus on general domains in the web. Biomedical images and text are rather different, but publicly available datasets are small and skew toward chest X-ray, thus severely limiting progress. In this paper, we conducted by far the largest study on biomedical VLP, using 15 million figure-caption pairs extracted from biomedical research articles in PubMed Central. Our dataset (PMC-15M) is two orders of magnitude larger than existing biomedical image-text datasets such as MIMIC-CXR, and spans a diverse range of biomedical images. The standard CLIP method is suboptimal for the biomedical domain. We propose BiomedCLIP with domain-specific adaptations tailored to biomedical VLP. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP established new state of the art in a wide range of standard datasets, substantially outperformed prior VLP approaches. Surprisingly, BiomedCLIP even outperformed radiology-specific state-of-the-art models such as BioViL on radiology-specific tasks such as RSNA pneumonia detection, thus highlighting the utility in large-scale pretraining across all biomedical image types. We will release our models at https://aka.ms/biomedclip to facilitate future research in biomedical VLP.

BLIAM: Literature-based Data Synthesis for Synergistic Drug Combination Prediction

Language models pre-trained on scientific literature corpora have substantially advanced scientific discovery by offering high-quality feature representations for downstream applications. However, these features are often not interpretable, and thus can reveal limited insights to domain experts. Instead of obtaining features from language models, we propose BLIAM, a literature-based data synthesis approach to directly generate training data points that are interpretable and model-agnostic to downstream applications. The key idea of BLIAM is to create prompts using existing training data and then use these prompts to synthesize new data points. BLIAM performs these two steps iteratively as new data points will define more informative prompts and new prompts will in turn synthesize more accurate data points. Notably, literature-based data augmentation might introduce data leakage since labels of test data points in downstream applications might have already been mentioned in the language model corpus. To prevent such leakage, we introduce GDSC-combo, a large-scale drug combination discovery dataset that was published after the biomedical language model was trained. We found that BLIAM substantially outperforms a non-augmented approach and manual prompting in this rigorous data split setting. BLIAM can be further used to synthesize data points for novel drugs and cell lines that were not even measured in biomedical experiments. In addition to the promising prediction performance, the data points synthesized by BLIAM are interpretable and model-agnostic, enabling in silico augmentation for in vitro experiments.

Continual Contrastive Finetuning Improves Low-Resource Relation Extraction

Relation extraction (RE), which has relied on structurally annotated corpora for model training, has been particularly challenging in low-resource scenarios and domains. Recent literature has tackled low-resource RE by self-supervised learning, where the solution involves pretraining the relation embedding by RE-based objective and finetuning on labeled data by classification-based objective. However, a critical challenge to this approach is the gap in objectives, which prevents the RE model from fully utilizing the knowledge in pretrained representations. In this paper, we aim at bridging the gap and propose to pretrain and finetune the RE model using consistent objectives of contrastive learning. Since in this kind of representation learning paradigm, one relation may easily form multiple clusters in the representation space, we further propose a multi-center contrastive loss that allows one relation to form multiple clusters to better align with pretraining. Experiments on two document-level RE datasets, BioRED and Re-DocRED, demonstrate the effectiveness of our method. Particularly, when using 1% end-task training data, our method outperforms PLM-based RE classifier by 10.5% and 5.8% on the two datasets, respectively.

BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

Optimizing Bi-Encoder for Named Entity Recognition via Contrastive Learning

We present an efficient bi-encoder framework for named entity recognition (NER), which applies contrastive learning to map candidate text spans and entity types into the same vector representation space. Prior work predominantly approaches NER as sequence labeling or span classification. We instead frame NER as a metric learning problem that maximizes the similarity between the vector representations of an entity mention and its type. This makes it easy to handle nested and flat NER alike, and can better leverage noisy self-supervision signals. A major challenge to this bi-encoder formulation for NER lies in separating non-entity spans from entity mentions. Instead of explicitly labeling all non-entity spans as the same class Outside (O) as in most prior methods, we introduce a novel dynamic thresholding loss, which is learned in conjunction with the standard contrastive loss. Experiments show that our method performs well in both supervised and distantly supervised settings, for nested and flat NER alike, establishing new state of the art across standard datasets in the general domain (e.g., ACE2004, ACE2005) and high-value verticals such as biomedicine (e.g., GENIA, NCBI, BC5CDR, JNLPBA).

Making the Most of Text Semantics to Improve Biomedical Vision--Language Processing

Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses additional challenges in vision-language modelling compared to the general domain, and previous work has used insufficiently adapted models that lack domain-specific language understanding. In this paper, we show that principled textual semantic modelling can substantially improve contrastive learning in self-supervised vision--language processing. We release a language model that achieves state-of-the-art results in radiology natural language inference through its improved vocabulary and novel language pretraining objective leveraging semantics and discourse characteristics in radiology reports. Further, we propose a self-supervised joint vision--language approach with a focus on better text modelling. It establishes new state of the art results on a wide range of publicly available benchmarks, in part by leveraging our new domain-specific language model. We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing. A broad evaluation, including on this new dataset, shows that our contrastive learning approach, aided by textual-semantic modelling, outperforms prior methods in segmentation tasks, despite only using a global-alignment objective.

Towards Structuring Real-World Data at Scale: Deep Learning for Extracting Key Oncology Information from Clinical Text with Patient-Level Supervision

Objective: The majority of detailed patient information in real-world data (RWD) is only consistently available in free-text clinical documents. Manual curation is expensive and time-consuming. Developing natural language processing (NLP) methods for structuring RWD is thus essential for scaling real-world evidence generation. Materials and Methods: Traditional rule-based systems are vulnerable to the prevalent linguistic variations and ambiguities in clinical text, and prior applications of machine-learning methods typically require sentence-level or report-level labeled examples that are hard to produce at scale. We propose leveraging patient-level supervision from medical registries, which are often readily available and capture key patient information, for general RWD applications. To combat the lack of sentence-level or report-level annotations, we explore advanced deep-learning methods by combining domain-specific pretraining, recurrent neural networks, and hierarchical attention. Results: We conduct an extensive study on 135,107 patients from the cancer registry of a large integrated delivery network (IDN) comprising healthcare systems in five western US states. Our deep learning methods attain test AUROC of 94-99% for key tumor attributes and comparable performance on held-out data from separate health systems and states. Discussion and Conclusion: Ablation results demonstrate clear superiority of these advanced deep-learning methods over prior approaches. Error analysis shows that our NLP system sometimes even corrects errors in registrar labels. We also conduct a preliminary investigation in accelerating registry curation and general RWD structuring via assisted curation for over 1.2 million cancer patients in this healthcare network.