The increasing size of language models raises great research interests in parameter-efficient fine-tuning (e.g. Adapter, LoRA and prompt tuning) that freezes the pre-trained model, and injects small-scale trainable parameters for multiple downstream tasks. To further enhance the efficiency of fine-tuning, we propose a framework that integrates LoRA and structured layer pruning. In addition, based on MIMIC-IV-Note, we create two deidentified medical report summarization datasets. Further, We validate the integrated framework on the proposed two datasets and two medical dialogue datasets. By tuning 0.6% parameters of the original model and pruning over 30% Transformer-layers, the framework can speed up 100% of the training phase and reduce 50% of GPU memory usage, while preserving over 92% generation qualities on free-text sequence-to-sequence tasks.
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Recent work has demonstrated that using parameter efficient tuning techniques such as prefix tuning (or P-tuning) on pretrained language models can yield performance that is comparable or superior to fine-tuning while dramatically reducing trainable parameters. Nevertheless, the effectiveness of such methods under the context of data augmentation, a common strategy to improve learning under low data regimes, has not been fully explored. In this paper, we examine the effectiveness of several popular task-agnostic data augmentation techniques, i.e., EDA, Back Translation, and Mixup, when using two general parameter efficient tuning methods, P-tuning v2 and LoRA, under data scarcity. We show that data augmentation can be used to boost the performance of P-tuning and LoRA models, but the effectiveness of each technique varies and certain methods can lead to a notable degradation in performance, particularly when using larger models and on harder tasks. We further analyze the sentence representations of P-tuning compared to fine-tuning to help understand the above behaviour, and reveal how P-tuning generally presents a more limited ability to separate the sentence embeddings from different classes of augmented data. In addition, it displays poorer performance on heavily altered data. However, we demonstrate that by adding a simple contrastive loss function it can help mitigate such issues for prefix tuning, resulting in sizable improvements to augmented data performance.
Convolutional neural networks (CNNs) and Transformer-based models are being widely applied in medical image segmentation thanks to their ability to extract high-level features and capture important aspects of the image. However, there is often a trade-off between the need for high accuracy and the desire for low computational cost. A model with higher parameters can theoretically achieve better performance but also result in more computational complexity and higher memory usage, and thus is not practical to implement. In this paper, we look for a lightweight U-Net-based model which can remain the same or even achieve better performance, namely U-Lite. We design U-Lite based on the principle of Depthwise Separable Convolution so that the model can both leverage the strength of CNNs and reduce a remarkable number of computing parameters. Specifically, we propose Axial Depthwise Convolutions with kernels 7x7 in both the encoder and decoder to enlarge the model receptive field. To further improve the performance, we use several Axial Dilated Depthwise Convolutions with filters 3x3 for the bottleneck as one of our branches. Overall, U-Lite contains only 878K parameters, 35 times less than the traditional U-Net, and much more times less than other modern Transformer-based models. The proposed model cuts down a large amount of computational complexity while attaining an impressive performance on medical segmentation tasks compared to other state-of-the-art architectures. The code will be available at: //github.com/duong-db/U-Lite.
Multi-label classification (MLC) suffers from the inevitable label noise in training data due to the difficulty in annotating various semantic labels in each image. To mitigate the influence of noisy labels, existing methods mainly devote to identifying and correcting the label mistakes via a trained MLC model. However, these methods still involve annoying noisy labels in training, which can result in imprecise recognition of noisy labels and weaken the performance. In this paper, considering that the negative labels are substantially more than positive labels, and most noisy labels are from the negative labels, we directly discard all the negative labels in the dataset, and propose a new method dubbed positive and unlabeled multi-label classification (PU-MLC). By extending positive-unlabeled learning into MLC task, our method trains model with only positive labels and unlabeled data, and introduces adaptive re-balance factor and adaptive temperature coefficient in the loss function to alleviate the catastrophic imbalance in label distribution and over-smoothing of probabilities in training. Our PU-MLC is simple and effective, and it is applicable to both MLC and MLC with partial labels (MLC-PL) tasks. Extensive experiments on MS-COCO and PASCAL VOC datasets demonstrate that our PU-MLC achieves significantly improvements on both MLC and MLC-PL settings with even fewer annotations. Code will be released.
Hybrid volumetric medical image segmentation models, combining the advantages of local convolution and global attention, have recently received considerable attention. While mainly focusing on architectural modifications, most existing hybrid approaches still use conventional data-independent weight initialization schemes which restrict their performance due to ignoring the inherent volumetric nature of the medical data. To address this issue, we propose a learnable weight initialization approach that utilizes the available medical training data to effectively learn the contextual and structural cues via the proposed self-supervised objectives. Our approach is easy to integrate into any hybrid model and requires no external training data. Experiments on multi-organ and lung cancer segmentation tasks demonstrate the effectiveness of our approach, leading to state-of-the-art segmentation performance. Our proposed data-dependent initialization approach performs favorably as compared to the Swin-UNETR model pretrained using large-scale datasets on multi-organ segmentation task. Our source code and models are available at: //github.com/ShahinaKK/LWI-VMS.
One of the most significant challenges in the field of deep learning and medical image segmentation is to determine an appropriate threshold for classifying each pixel. This threshold is a value above which the model's output is considered to belong to a specific class. Manual thresholding based on personal experience is error-prone and time-consuming, particularly for complex problems such as medical images. Traditional methods for thresholding are not effective for determining the threshold value for such problems. To tackle this challenge, automatic thresholding methods using deep learning have been proposed. However, the main issue with these methods is that they often determine the threshold value statically without considering changes in input data. Since input data can be dynamic and may change over time, threshold determination should be adaptive and consider input data and environmental conditions.
Transfer learning aims to make the most of existing pre-trained models to achieve better performance on a new task in limited data scenarios. However, it is unclear which models will perform best on which task, and it is prohibitively expensive to try all possible combinations. If transferability estimation offers a computation-efficient approach to evaluate the generalisation ability of models, prior works focused exclusively on classification settings. To overcome this limitation, we extend transferability metrics to object detection. We design a simple method to extract local features corresponding to each object within an image using ROI-Align. We also introduce TLogME, a transferability metric taking into account the coordinates regression task. In our experiments, we compare TLogME to state-of-the-art metrics in the estimation of transfer performance of the Faster-RCNN object detector. We evaluate all metrics on source and target selection tasks, for real and synthetic datasets, and with different backbone architectures. We show that, over different tasks, TLogME using the local extraction method provides a robust correlation with transfer performance and outperforms other transferability metrics on local and global level features.
Deep learning has been widely used in medical image segmentation and other aspects. However, the performance of existing medical image segmentation models has been limited by the challenge of obtaining sufficient high-quality labeled data due to the prohibitive data annotation cost. To alleviate this limitation, we propose a new text-augmented medical image segmentation model LViT (Language meets Vision Transformer). In our LViT model, medical text annotation is incorporated to compensate for the quality deficiency in image data. In addition, the text information can guide to generate pseudo labels of improved quality in the semi-supervised learning. We also propose an Exponential Pseudo label Iteration mechanism (EPI) to help the Pixel-Level Attention Module (PLAM) preserve local image features in semi-supervised LViT setting. In our model, LV (Language-Vision) loss is designed to supervise the training of unlabeled images using text information directly. For evaluation, we construct three multimodal medical segmentation datasets (image + text) containing X-rays and CT images. Experimental results show that our proposed LViT has superior segmentation performance in both fully-supervised and semi-supervised setting. The code and datasets are available at //github.com/HUANGLIZI/LViT.
Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.
Current models for event causality identification (ECI) mainly adopt a supervised framework, which heavily rely on labeled data for training. Unfortunately, the scale of current annotated datasets is relatively limited, which cannot provide sufficient support for models to capture useful indicators from causal statements, especially for handing those new, unseen cases. To alleviate this problem, we propose a novel approach, shortly named CauSeRL, which leverages external causal statements for event causality identification. First of all, we design a self-supervised framework to learn context-specific causal patterns from external causal statements. Then, we adopt a contrastive transfer strategy to incorporate the learned context-specific causal patterns into the target ECI model. Experimental results show that our method significantly outperforms previous methods on EventStoryLine and Causal-TimeBank (+2.0 and +3.4 points on F1 value respectively).
We study the problem of named entity recognition (NER) from electronic medical records, which is one of the most fundamental and critical problems for medical text mining. Medical records which are written by clinicians from different specialties usually contain quite different terminologies and writing styles. The difference of specialties and the cost of human annotation makes it particularly difficult to train a universal medical NER system. In this paper, we propose a label-aware double transfer learning framework (La-DTL) for cross-specialty NER, so that a medical NER system designed for one specialty could be conveniently applied to another one with minimal annotation efforts. The transferability is guaranteed by two components: (i) we propose label-aware MMD for feature representation transfer, and (ii) we perform parameter transfer with a theoretical upper bound which is also label aware. We conduct extensive experiments on 12 cross-specialty NER tasks. The experimental results demonstrate that La-DTL provides consistent accuracy improvement over strong baselines. Besides, the promising experimental results on non-medical NER scenarios indicate that La-DTL is potential to be seamlessly adapted to a wide range of NER tasks.
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