Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately $200,000$ instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.
Text-to-image generation (TTI) refers to the usage of models that could process text input and generate high fidelity images based on text descriptions. Text-to-image generation using neural networks could be traced back to the emergence of Generative Adversial Network (GAN), followed by the autoregressive Transformer. Diffusion models are one prominent type of generative model used for the generation of images through the systematic introduction of noises with repeating steps. As an effect of the impressive results of diffusion models on image synthesis, it has been cemented as the major image decoder used by text-to-image models and brought text-to-image generation to the forefront of machine-learning (ML) research. In the era of large models, scaling up model size and the integration with large language models have further improved the performance of TTI models, resulting the generation result nearly indistinguishable from real-world images, revolutionizing the way we retrieval images. Our explorative study has incentivised us to think that there are further ways of scaling text-to-image models with the combination of innovative model architectures and prediction enhancement techniques. We have divided the work of this survey into five main sections wherein we detail the frameworks of major literature in order to delve into the different types of text-to-image generation methods. Following this we provide a detailed comparison and critique of these methods and offer possible pathways of improvement for future work. In the future work, we argue that TTI development could yield impressive productivity improvements for creation, particularly in the context of the AIGC era, and could be extended to more complex tasks such as video generation and 3D generation.
Electrocardiography (ECG) is a non-invasive tool for predicting cardiovascular diseases (CVDs). Current ECG-based diagnosis systems show promising performance owing to the rapid development of deep learning techniques. However, the label scarcity problem, the co-occurrence of multiple CVDs and the poor performance on unseen datasets greatly hinder the widespread application of deep learning-based models. Addressing them in a unified framework remains a significant challenge. To this end, we propose a multi-label semi-supervised model (ECGMatch) to recognize multiple CVDs simultaneously with limited supervision. In the ECGMatch, an ECGAugment module is developed for weak and strong ECG data augmentation, which generates diverse samples for model training. Subsequently, a hyperparameter-efficient framework with neighbor agreement modeling and knowledge distillation is designed for pseudo-label generation and refinement, which mitigates the label scarcity problem. Finally, a label correlation alignment module is proposed to capture the co-occurrence information of different CVDs within labeled samples and propagate this information to unlabeled samples. Extensive experiments on four datasets and three protocols demonstrate the effectiveness and stability of the proposed model, especially on unseen datasets. As such, this model can pave the way for diagnostic systems that achieve robust performance on multi-label CVDs prediction with limited supervision.
Hypernetworks, or hypernets in short, are neural networks that generate weights for another neural network, known as the target network. They have emerged as a powerful deep learning technique that allows for greater flexibility, adaptability, faster training, information sharing, and model compression etc. Hypernets have shown promising results in a variety of deep learning problems, including continual learning, causal inference, transfer learning, weight pruning, uncertainty quantification, zero-shot learning, natural language processing, and reinforcement learning etc. Despite their success across different problem settings, currently, there is no review available to inform the researchers about the developments and help in utilizing hypernets. To fill this gap, we review the progress in hypernets. We present an illustrative example to train deep neural networks using hypernets and propose to categorize hypernets on five criteria that affect the design of hypernets as inputs, outputs, variability of inputs and outputs, and architecture of hypernets. We also review applications of hypernets across different deep learning problem settings. Finally, we discuss the challenges and future directions that remain under-explored in the field of hypernets. We believe that hypernetworks have the potential to revolutionize the field of deep learning. They offer a new way to design and train neural networks, and they have the potential to improve the performance of deep learning models on a variety of tasks. Through this review, we aim to inspire further advancements in deep learning through hypernetworks.
Existing heterogeneous treatment effects learners, also known as conditional average treatment effects (CATE) learners, lack a general mechanism for end-to-end inter-treatment information sharing, and data have to be split among potential outcome functions to train CATE learners which can lead to biased estimates with limited observational datasets. To address this issue, we propose a novel deep learning-based framework to train CATE learners that facilitates dynamic end-to-end information sharing among treatment groups. The framework is based on \textit{soft weight sharing} of \textit{hypernetworks}, which offers advantages such as parameter efficiency, faster training, and improved results. The proposed framework complements existing CATE learners and introduces a new class of uncertainty-aware CATE learners that we refer to as \textit{HyperCATE}. We develop HyperCATE versions of commonly used CATE learners and evaluate them on IHDP, ACIC-2016, and Twins benchmarks. Our experimental results show that the proposed framework improves the CATE estimation error via counterfactual inference, with increasing effectiveness for smaller datasets.
The lack of data democratization and information leakage from trained models hinder the development and acceptance of robust deep learning-based healthcare solutions. This paper argues that irreversible data encoding can provide an effective solution to achieve data democratization without violating the privacy constraints imposed on healthcare data and clinical models. An ideal encoding framework transforms the data into a new space where it is imperceptible to a manual or computational inspection. However, encoded data should preserve the semantics of the original data such that deep learning models can be trained effectively. This paper hypothesizes the characteristics of the desired encoding framework and then exploits random projections and random quantum encoding to realize this framework for dense and longitudinal or time-series data. Experimental evaluation highlights that models trained on encoded time-series data effectively uphold the information bottleneck principle and hence, exhibit lesser information leakage from trained models.
Natural Language Generation (NLG) accepts input data in the form of images, videos, or text and generates corresponding natural language text as output. Existing NLG methods mainly adopt a supervised approach and rely heavily on coupled data-to-text pairs. However, for many targeted scenarios and for non-English languages, sufficient quantities of labeled data are often not available. To relax the dependency on labeled data of downstream tasks, we propose an intuitive and effective zero-shot learning framework, ZeroNLG, which can deal with multiple NLG tasks, including image-to-text (image captioning), video-to-text (video captioning), and text-to-text (neural machine translation), across English, Chinese, German, and French within a unified framework. ZeroNLG does not require any labeled downstream pairs for training. During training, ZeroNLG (i) projects different domains (across modalities and languages) to corresponding coordinates in a shared common latent space; (ii) bridges different domains by aligning their corresponding coordinates in this space; and (iii) builds an unsupervised multilingual auto-encoder to learn to generate text by reconstructing the input text given its coordinate in shared latent space. Consequently, during inference, based on the data-to-text pipeline, ZeroNLG can generate target sentences across different languages given the coordinate of input data in the common space. Within this unified framework, given visual (imaging or video) data as input, ZeroNLG can perform zero-shot visual captioning; given textual sentences as input, ZeroNLG can perform zero-shot machine translation. We present the results of extensive experiments on twelve NLG tasks, showing that, without using any labeled downstream pairs for training, ZeroNLG generates high-quality and believable outputs and significantly outperforms existing zero-shot methods.
Electronic Health Records (EHRs) contain sensitive patient information, which presents privacy concerns when sharing such data. Synthetic data generation is a promising solution to mitigate these risks, often relying on deep generative models such as Generative Adversarial Networks (GANs). However, recent studies have shown that diffusion models offer several advantages over GANs, such as generation of more realistic synthetic data and stable training in generating data modalities, including image, text, and sound. In this work, we investigate the potential of diffusion models for generating realistic mixed-type tabular EHRs, comparing TabDDPM model with existing methods on four datasets in terms of data quality, utility, privacy, and augmentation. Our experiments demonstrate that TabDDPM outperforms the state-of-the-art models across all evaluation metrics, except for privacy, which confirms the trade-off between privacy and utility.
Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like Knowledge Distillation (KD), it is possible to create smaller versions that perform almost as well as their larger counterparts. In this work, we specifically focus on development of compact language models for processing clinical texts (i.e. progress notes, discharge summaries etc). We developed a number of efficient lightweight clinical transformers using knowledge distillation and continual learning, with the number of parameters ranging from 15 million to 65 million. These models performed comparably to larger models such as BioBERT and ClinicalBioBERT and significantly outperformed other compact models trained on general or biomedical data. Our extensive evaluation was done across several standard datasets and covered a wide range of clinical text-mining tasks, including Natural Language Inference, Relation Extraction, Named Entity Recognition, and Sequence Classification. To our knowledge, this is the first comprehensive study specifically focused on creating efficient and compact transformers for clinical NLP tasks. The models and code used in this study can be found on our Huggingface profile at https://huggingface.co/nlpie and Github page at https://github.com/nlpie-research/Lightweight-Clinical-Transformers, respectively, promoting reproducibility of our results.
For medical image segmentation, contrastive learning is the dominant practice to improve the quality of visual representations by contrasting semantically similar and dissimilar pairs of samples. This is enabled by the observation that without accessing ground truth label, negative examples with truly dissimilar anatomical features, if sampled, can significantly improve the performance. In reality, however, these samples may come from similar anatomical features and the models may struggle to distinguish the minority tail-class samples, making the tail classes more prone to misclassification, both of which typically lead to model collapse. In this paper, we propose ARCO, a semi-supervised contrastive learning (CL) framework with stratified group sampling theory in medical image segmentation. In particular, we first propose building ARCO through the concept of variance-reduced estimation, and show that certain variance-reduction techniques are particularly beneficial in medical image segmentation tasks with extremely limited labels. Furthermore, we theoretically prove these sampling techniques are universal in variance reduction. Finally, we experimentally validate our approaches on three benchmark datasets with different label settings, and our methods consistently outperform state-of-the-art semi- and fully-supervised methods. Additionally, we augment the CL frameworks with these sampling techniques and demonstrate significant gains over previous methods. We believe our work is an important step towards semi-supervised medical image segmentation by quantifying the limitation of current self-supervision objectives for accomplishing medical image analysis tasks.