Machine learning techniques are steadily becoming more important in modern biology, and are used to build predictive models, discover patterns, and investigate biological problems. However, models trained on one dataset are often not generalizable to other datasets from different cohorts or laboratories, due to differences in the statistical properties of these datasets. These could stem from technical differences, such as the measurement technique used, or from relevant biological differences between the populations studied. Domain adaptation, a type of transfer learning, can alleviate this problem by aligning the statistical distributions of features and samples among different datasets so that similar models can be applied across them. However, a majority of state-of-the-art domain adaptation methods are designed to work with large-scale data, mostly text and images, while biological datasets often suffer from small sample sizes, and possess complexities such as heterogeneity of the feature space. This Review aims to synthetically discuss domain adaptation methods in the context of small-scale and highly heterogeneous biological data. We describe the benefits and challenges of domain adaptation in biological research and critically discuss some of its objectives, strengths, and weaknesses through key representative methodologies. We argue for the incorporation of domain adaptation techniques to the computational biologist's toolkit, with further development of customized approaches. Keywords: Machine learning; biological-scale datasets; small datasets; neuroimaging; microbiome; domain adaptation; transfer learning.

Deep learning (DL) techniques are highly effective for defect detection from images. Training DL classification models, however, requires vast amounts of labeled data which is often expensive to collect. In many cases, not only the available training data is limited but may also imbalanced. In this paper, we propose a novel domain adaptation (DA) approach to address the problem of labeled training data scarcity for a target learning task by transferring knowledge gained from an existing source dataset used for a similar learning task. Our approach works for scenarios where the source dataset and the dataset available for the target learning task have same or different feature spaces. We combine our DA approach with an autoencoder-based data augmentation approach to address the problem of imbalanced target datasets. We evaluate our combined approach using image data for wafer defect prediction. The experiments show its superior performance against other algorithms when the number of labeled samples in the target dataset is significantly small and the target dataset is imbalanced.

The presence of domain shift in medical imaging is a common issue, which can greatly impact the performance of segmentation models when dealing with unseen image domains. Adversarial-based deep learning models, such as Cycle-GAN, have become a common model for approaching unsupervised domain adaptation of medical images. These models however, have no ability to enforce the preservation of structures of interest when translating medical scans, which can lead to potentially poor results for unsupervised domain adaptation within the context of segmentation. This work introduces the Structure Preserving Cycle-GAN (SP Cycle-GAN), which promotes medical structure preservation during image translation through the enforcement of a segmentation loss term in the overall Cycle-GAN training process. We demonstrate the structure preserving capability of the SP Cycle-GAN both visually and through comparison of Dice score segmentation performance for the unsupervised domain adaptation models. The SP Cycle-GAN is able to outperform baseline approaches and standard Cycle-GAN domain adaptation for binary blood vessel segmentation in the STARE and DRIVE datasets, and multi-class Left Ventricle and Myocardium segmentation in the multi-modal MM-WHS dataset. SP Cycle-GAN achieved a state of the art Myocardium segmentation Dice score (DSC) of 0.7435 for the MR to CT MM-WHS domain adaptation problem, and excelled in nearly all categories for the MM-WHS dataset. SP Cycle-GAN also demonstrated a strong ability to preserve blood vessel structure in the DRIVE to STARE domain adaptation problem, achieving a 4% DSC increase over a default Cycle-GAN implementation.

We present three large-scale experiments on binary text matching classification task both in Chinese and English to evaluate the effectiveness and generalizability of random text perturbations as a data augmentation approach for NLP. It is found that the augmentation can bring both negative and positive effects to the test set performance of three neural classification models, depending on whether the models train on enough original training examples. This remains true no matter whether five random text editing operations, used to augment text, are applied together or separately. Our study demonstrates with strong implication that the effectiveness of random text perturbations is task specific and not generally positive.

To investigate the role of linguistic knowledge in data augmentation (DA) for Natural Language Processing (NLP), we designed two adapted DA programs and applied them to LCQMC (a Large-scale Chinese Question Matching Corpus) for a binary Chinese question matching classification task. The two DA programs produce augmented texts by five simple text editing operations (or DA techniques), largely irrespective of language generation rules, but one is enhanced with a pre-trained n-gram language model to fuse it with prior linguistic knowledge. We then trained four neural network models (BOW, CNN, LSTM, and GRU) and a pre-trained model (ERNIE-Gram) on the LCQMCs train sets of varying size as well as the related augmented train sets produced by the two DA programs. The results show that there are no significant performance differences between the models trained on the two types of augmented train sets, both when the five DA techniques are applied together or separately. Moreover, due to the inability of the five DA techniques to make strictly paraphrastic augmented texts, the results indicate the need of sufficient amounts of training examples for the classification models trained on them to mediate the negative impact of false matching augmented text pairs and improve performance, a limitation of random text editing perturbations used as a DA approach. Similar results were also obtained for English.

A brain-computer interface (BCI) system usually needs a long calibration session for each new subject/task to adjust its parameters, which impedes its transition from the laboratory to real-world applications. Domain adaptation, which leverages labeled data from auxiliary subjects/tasks (source domains), has demonstrated its effectiveness in reducing such calibration effort. Currently, most domain adaptation approaches require the source domains to have the same feature space and label space as the target domain, which limits their applications, as the auxiliary data may have different feature spaces and/or different label spaces. This paper considers different set domain adaptation for BCIs, i.e., the source and target domains have different label spaces. We introduce a practical setting of different label sets for BCIs, and propose a novel label alignment (LA) approach to align the source label space with the target label space. It has three desirable properties: 1) LA only needs as few as one labeled sample from each class of the target subject; 2) LA can be used as a preprocessing step before different feature extraction and classification algorithms; and, 3) LA can be integrated with other domain adaptation approaches to achieve even better performance. Experiments on two motor imagery datasets demonstrated the effectiveness of LA.

Point cloud data from 3D LiDAR sensors are one of the most crucial sensor modalities for versatile safety-critical applications such as self-driving vehicles. Since the annotations of point cloud data is an expensive and time-consuming process, therefore recently the utilisation of simulated environments and 3D LiDAR sensors for this task started to get some popularity. With simulated sensors and environments, the process for obtaining an annotated synthetic point cloud data became much easier. However, the generated synthetic point cloud data are still missing the artefacts usually exist in point cloud data from real 3D LiDAR sensors. As a result, the performance of the trained models on this data for perception tasks when tested on real point cloud data is degraded due to the domain shift between simulated and real environments. Thus, in this work, we are proposing a domain adaptation framework for bridging this gap between synthetic and real point cloud data. Our proposed framework is based on the deep cycle-consistent generative adversarial networks (CycleGAN) architecture. We have evaluated the performance of our proposed framework on the task of vehicle detection from a bird's eye view (BEV) point cloud images coming from real 3D LiDAR sensors. The framework has shown competitive results with an improvement of more than 7% in average precision score over other baseline approaches when tested on real BEV point cloud images.