Safe Training with Sensitive In-domain Data: Leveraging Data Fragmentation To Mitigate Linkage Attacks

Current text generation models are trained using real data which can potentially contain sensitive information, such as confidential patient information and the like. Under certain conditions output of the training data which they have memorised can be triggered, exposing sensitive data. To mitigate against this risk we propose a safer alternative which sees fragmented data in the form of domain-specific short phrases randomly grouped together shared instead of full texts. Thus, text fragments that could re-identify an individual cannot be reproduced by the model in one sequence, giving significant protection against linkage attacks. We fine-tune several state-of-the-art LLMs using meaningful syntactic chunks to explore their utility. In particular, we fine-tune BERT-based models to predict two cardiovascular diagnoses. Our results demonstrate the capacity of LLMs to benefit from the pre-trained knowledge and deliver classification results when fine-tuned with fragmented data comparable to fine-tuning with full training data.

Clinically meaningful timeline summarisation in social media for mental health monitoring

We introduce the new task of clinically meaningful summarisation of social media user timelines, appropriate for mental health monitoring. We develop a novel approach for unsupervised abstractive summarisation that produces a two-layer summary consisting of both high-level information, covering aspects useful to clinical experts, as well as accompanying time sensitive evidence from a user's social media timeline. A key methodological novelty comes from the timeline summarisation component based on a version of hierarchical variational autoencoder (VAE) adapted to represent long texts and guided by LLM-annotated key phrases. The resulting timeline summary is input into a LLM (LLaMA-2) to produce the final summary containing both the high level information, obtained through instruction prompting, as well as corresponding evidence from the user's timeline. We assess the summaries generated by our novel architecture via automatic evaluation against expert written summaries and via human evaluation with clinical experts, showing that timeline summarisation by TH-VAE results in logically coherent summaries rich in clinical utility and superior to LLM-only approaches in capturing changes over time.

Source Code is a Graph, Not a Sequence: A Cross-Lingual Perspective on Code Clone Detection

Source code clone detection is the task of finding code fragments that have the same or similar functionality, but may differ in syntax or structure. This task is important for software maintenance, reuse, and quality assurance (Roy et al. 2009). However, code clone detection is challenging, as source code can be written in different languages, domains, and styles. In this paper, we argue that source code is inherently a graph, not a sequence, and that graph-based methods are more suitable for code clone detection than sequence-based methods. We compare the performance of two state-of-the-art models: CodeBERT (Feng et al. 2020), a sequence-based model, and CodeGraph (Yu et al. 2023), a graph-based model, on two benchmark data-sets: BCB (Svajlenko et al. 2014) and PoolC (PoolC no date). We show that CodeGraph outperforms CodeBERT on both data-sets, especially on cross-lingual code clones. To the best of our knowledge, this is the first work to demonstrate the superiority of graph-based methods over sequence-based methods on cross-lingual code clone detection.

Controlled Text Generation using T5 based Encoder-Decoder Soft Prompt Tuning and Analysis of the Utility of Generated Text in AI

Controlled text generation is a very important task in the arena of natural language processing due to its promising applications. In order to achieve this task we mainly introduce the novel soft prompt tuning method of using soft prompts at both encoder and decoder levels together in a T5 model and investigate the performance as the behaviour of an additional soft prompt related to the decoder of a T5 model in controlled text generation remained unexplored. Then we also investigate the feasibility of steering the output of this extended soft prompted T5 model at decoder level and finally analyse the utility of generated text to be used in AI related tasks such as training AI models with an interpretability analysis of the classifier trained with synthetic text, as there is a lack of proper analysis of methodologies in generating properly labelled data to be utilized in AI tasks. Through the performed in-depth intrinsic and extrinsic evaluations of this generation model along with the artificially generated data, we found that this model produced better results compared to the T5 model with a single soft prompt at encoder level and the sentiment classifier trained using this artificially generated data can produce comparable classification results to the results of a classifier trained with real labelled data and also the classifier decision is interpretable with respect to the input text content.

Modeling Disagreement in Automatic Data Labelling for Semi-Supervised Learning in Clinical Natural Language Processing

Computational models providing accurate estimates of their uncertainty are crucial for risk management associated with decision making in healthcare contexts. This is especially true since many state-of-the-art systems are trained using the data which has been labelled automatically (self-supervised mode) and tend to overfit. In this work, we investigate the quality of uncertainty estimates from a range of current state-of-the-art predictive models applied to the problem of observation detection in radiology reports. This problem remains understudied for Natural Language Processing in the healthcare domain. We demonstrate that Gaussian Processes (GPs) provide superior performance in quantifying the risks of 3 uncertainty labels based on the negative log predictive probability (NLPP) evaluation metric and mean maximum predicted confidence levels (MMPCL), whilst retaining strong predictive performance.

Medical Scientific Table-to-Text Generation with Human-in-the-Loop under the Data Sparsity Constraint

Structured (tabular) data in the preclinical and clinical domains contains valuable information about individuals and an efficient table-to-text summarization system can drastically reduce manual efforts to condense this data into reports. However, in practice, the problem is heavily impeded by the data paucity, data sparsity and inability of the state-of-the-art natural language generation models (including T5, PEGASUS and GPT-Neo) to produce accurate and reliable outputs. In this paper, we propose a novel table-to-text approach and tackle these problems with a novel two-step architecture which is enhanced by auto-correction, copy mechanism and synthetic data augmentation. The study shows that the proposed approach selects salient biomedical entities and values from structured data with improved precision (up to 0.13 absolute increase) of copying the tabular values to generate coherent and accurate text for assay validation reports and toxicology reports. Moreover, we also demonstrate a light-weight adaptation of the proposed system to new datasets by fine-tuning with as little as 40\% training examples. The outputs of our model are validated by human experts in the Human-in-the-Loop scenario.

Unsupervised Numerical Reasoning to Extract Phenotypes from Clinical Text by Leveraging External Knowledge

Extracting phenotypes from clinical text has been shown to be useful for a variety of clinical use cases such as identifying patients with rare diseases. However, reasoning with numerical values remains challenging for phenotyping in clinical text, for example, temperature 102F representing Fever. Current state-of-the-art phenotyping models are able to detect general phenotypes, but perform poorly when they detect phenotypes requiring numerical reasoning. We present a novel unsupervised methodology leveraging external knowledge and contextualized word embeddings from ClinicalBERT for numerical reasoning in a variety of phenotypic contexts. Comparing against unsupervised benchmarks, it shows a substantial performance improvement with absolute gains on generalized Recall and F1 scores up to 79% and 71%, respectively. In the supervised setting, it also surpasses the performance of alternative approaches with absolute gains on generalized Recall and F1 scores up to 70% and 44%, respectively.

Revisiting Contextual Toxicity Detection in Conversations

Understanding toxicity in user conversations is undoubtedly an important problem. As it has been argued in previous work, addressing "covert" or implicit cases of toxicity is particularly hard and requires context. Very few previous studies have analysed the influence of conversational context in human perception or in automated detection models. We dive deeper into both these directions. We start by analysing existing contextual datasets and come to the conclusion that toxicity labelling by humans is in general influenced by the conversational structure, polarity and topic of the context. We then propose to bring these findings into computational detection models by introducing (a) neural architectures for contextual toxicity detection that are aware of the conversational structure, and (b) data augmentation strategies that can help model contextual toxicity detection. Our results have shown the encouraging potential of neural architectures that are aware of the conversation structure. We have also demonstrated that such models can benefit from synthetic data, especially in the social media domain.

Self-Supervised Detection of Contextual Synonyms in a Multi-Class Setting: Phenotype Annotation Use Case

Contextualised word embeddings is a powerful tool to detect contextual synonyms. However, most of the current state-of-the-art (SOTA) deep learning concept extraction methods remain supervised and underexploit the potential of the context. In this paper, we propose a self-supervised pre-training approach which is able to detect contextual synonyms of concepts being training on the data created by shallow matching. We apply our methodology in the sparse multi-class setting (over 15,000 concepts) to extract phenotype information from electronic health records. We further investigate data augmentation techniques to address the problem of the class sparsity. Our approach achieves a new SOTA for the unsupervised phenotype concept annotation on clinical text on F1 and Recall outperforming the previous SOTA with a gain of up to 4.5 and 4.0 absolute points, respectively. After fine-tuning with as little as 20\% of the labelled data, we also outperform BioBERT and ClinicalBERT. The extrinsic evaluation on three ICU benchmarks also shows the benefit of using the phenotypes annotated by our model as features.

Clinical Utility of the Automatic Phenotype Annotation in Unstructured Clinical Notes: ICU Use Cases

Clinical notes contain information not present elsewhere, including drug response and symptoms, all of which are highly important when predicting key outcomes in acute care patients. We propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information to predict outcomes in the Intensive Care Unit (ICU). This information is complementary to typically used vital signs and laboratory test results. We demonstrate and validate our approach conducting experiments on the prediction of in-hospital mortality, physiological decompensation and length of stay in the ICU setting for over 24,000 patients. The prediction models incorporating phenotypic information consistently outperform the baseline models leveraging only vital signs and laboratory test results. Moreover, we conduct a thorough interpretability study, showing that phenotypes provide valuable insights at the patient and cohort levels. Our approach illustrates the viability of using phenotypes to determine outcomes in the ICU.