Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states and phenotypes, and has helped elucidate biological processes, such as those occurring during development of complex organisms and improved our understanding of disease states, such as cancer, diabetes, and COVID, among others. Deep learning, a recent advance of artificial intelligence that has been used to address many problems involving large datasets, has also emerged as a promising tool for scRNA-seq data analysis, as it has a capacity to extract informative, compact features from noisy, heterogeneous, and high-dimensional scRNA-seq data to improve downstream analysis. The present review aims at surveying recently developed deep learning techniques in scRNA-seq data analysis, identifying key steps within the scRNA-seq data analysis pipeline that have been advanced by deep learning, and explaining the benefits of deep learning over more conventional analysis tools. Finally, we summarize the challenges in current deep learning approaches faced within scRNA-seq data and discuss potential directions for improvements in deep algorithms for scRNA-seq data analysis.
Existing video domain adaption (DA) methods need to store all temporal combinations of video frames or pair the source and target videos, which are memory cost expensive and can't scale up to long videos. To address these limitations, we propose a memory-efficient graph-based video DA approach as follows. At first our method models each source or target video by a graph: nodes represent video frames and edges represent the temporal or visual similarity relationship between frames. We use a graph attention network to learn the weight of individual frames and simultaneously align the source and target video into a domain-invariant graph feature space. Instead of storing a large number of sub-videos, our method only constructs one graph with a graph attention mechanism for one video, reducing the memory cost substantially. The extensive experiments show that, compared with the state-of-art methods, we achieved superior performance while reducing the memory cost significantly.
Simile interpretation (SI) and simile generation (SG) are challenging tasks for NLP because models require adequate world knowledge to produce predictions. Previous works have employed many hand-crafted resources to bring knowledge-related into models, which is time-consuming and labor-intensive. In recent years, pre-trained language models (PLMs) based approaches have become the de-facto standard in NLP since they learn generic knowledge from a large corpus. The knowledge embedded in PLMs may be useful for SI and SG tasks. Nevertheless, there are few works to explore it. In this paper, we probe simile knowledge from PLMs to solve the SI and SG tasks in the unified framework of simile triple completion for the first time. The backbone of our framework is to construct masked sentences with manual patterns and then predict the candidate words in the masked position. In this framework, we adopt a secondary training process (Adjective-Noun mask Training) with the masked language model (MLM) loss to enhance the prediction diversity of candidate words in the masked position. Moreover, pattern ensemble (PE) and pattern search (PS) are applied to improve the quality of predicted words. Finally, automatic and human evaluations demonstrate the effectiveness of our framework in both SI and SG tasks.
Autoregressive (AR) and Non-autoregressive (NAR) models have their own superiority on the performance and latency, combining them into one model may take advantage of both. Current combination frameworks focus more on the integration of multiple decoding paradigms with a unified generative model, e.g. Masked Language Model. However, the generalization can be harmful to the performance due to the gap between training objective and inference. In this paper, we aim to close the gap by preserving the original objective of AR and NAR under a unified framework. Specifically, we propose the Directional Transformer (Diformer) by jointly modelling AR and NAR into three generation directions (left-to-right, right-to-left and straight) with a newly introduced direction variable, which works by controlling the prediction of each token to have specific dependencies under that direction. The unification achieved by direction successfully preserves the original dependency assumption used in AR and NAR, retaining both generalization and performance. Experiments on 4 WMT benchmarks demonstrate that Diformer outperforms current united-modelling works with more than 1.5 BLEU points for both AR and NAR decoding, and is also competitive to the state-of-the-art independent AR and NAR models.
Deep encoders have been proven to be effective in improving neural machine translation (NMT) systems, but it reaches the upper bound of translation quality when the number of encoder layers exceeds 18. Worse still, deeper networks consume a lot of memory, making it impossible to train efficiently. In this paper, we present Symbiosis Networks, which include a full network as the Symbiosis Main Network (M-Net) and another shared sub-network with the same structure but less layers as the Symbiotic Sub Network (S-Net). We adopt Symbiosis Networks on Transformer-deep (m-n) architecture and define a particular regularization loss $\mathcal{L}_{\tau}$ between the M-Net and S-Net in NMT. We apply joint-training on the Symbiosis Networks and aim to improve the M-Net performance. Our proposed training strategy improves Transformer-deep (12-6) by 0.61, 0.49 and 0.69 BLEU over the baselines under classic training on WMT'14 EN->DE, DE->EN and EN->FR tasks. Furthermore, our Transformer-deep (12-6) even outperforms classic Transformer-deep (18-6).
Recently, non-autoregressive (NAT) models predict outputs in parallel, achieving substantial improvements in generation speed compared to autoregressive (AT) models. While performing worse on raw data, most NAT models are trained as student models on distilled data generated by AT teacher models, which is known as sequence-level Knowledge Distillation. An effective training strategy to improve the performance of AT models is Self-Distillation Mixup (SDM) Training, which pre-trains a model on raw data, generates distilled data by the pre-trained model itself and finally re-trains a model on the combination of raw data and distilled data. In this work, we aim to view SDM for NAT models, but find directly adopting SDM to NAT models gains no improvements in terms of translation quality. Through careful analysis, we observe the invalidation is correlated to Modeling Diversity and Confirmation Bias between the AT teacher model and the NAT student models. Based on these findings, we propose an enhanced strategy named SDMRT by adding two stages to classic SDM: one is Pre-Rerank on self-distilled data, the other is Fine-Tune on Filtered teacher-distilled data. Our results outperform baselines by 0.6 to 1.2 BLEU on multiple NAT models. As another bonus, for Iterative Refinement NAT models, our methods can outperform baselines within half iteration number, which means 2X acceleration.
This paper describes our work in participation of the IWSLT-2021 offline speech translation task. Our system was built in a cascade form, including a speaker diarization module, an Automatic Speech Recognition (ASR) module and a Machine Translation (MT) module. We directly use the LIUM SpkDiarization tool as the diarization module. The ASR module is trained with three ASR datasets from different sources, by multi-source training, using a modified Transformer encoder. The MT module is pretrained on the large-scale WMT news translation dataset and fine-tuned on the TED corpus. Our method achieves 24.6 BLEU score on the 2021 test set.
Over the past several years there has been a considerable research investment into learning-based approaches to industrial assembly, but despite significant progress these techniques have yet to be adopted by industry. We argue that it is the prohibitively large design space for Deep Reinforcement Learning (DRL), rather than algorithmic limitations per se, that are truly responsible for this lack of adoption. Pushing these techniques into the industrial mainstream requires an industry-oriented paradigm which differs significantly from the academic mindset. In this paper we define criteria for industry-oriented DRL, and perform a thorough comparison according to these criteria of one family of learning approaches, DRL from demonstration, against a professional industrial integrator on the recently established NIST assembly benchmark. We explain the design choices, representing several years of investigation, which enabled our DRL system to consistently outperform the integrator baseline in terms of both speed and reliability. Finally, we conclude with a competition between our DRL system and a human on a challenge task of insertion into a randomly moving target. This study suggests that DRL is capable of outperforming not only established engineered approaches, but the human motor system as well, and that there remains significant room for improvement. Videos can be found on our project website: https://sites.google.com/view/shield-nist.
When the dimension of data is comparable to or larger than the number of available data samples, Principal Components Analysis (PCA) is known to exhibit problematic phenomena of high-dimensional noise. In this work, we propose an Empirical Bayes PCA method that reduces this noise by estimating a structural prior for the joint distributions of the principal components. This EB-PCA method is based upon the classical Kiefer-Wolfowitz nonparametric MLE for empirical Bayes estimation, distributional results derived from random matrix theory for the sample PCs, and iterative refinement using an Approximate Message Passing (AMP) algorithm. In theoretical "spiked" models, EB-PCA achieves Bayes-optimal estimation accuracy in the same settings as the oracle Bayes AMP procedure that knows the true priors. Empirically, EB-PCA can substantially improve over PCA when there is strong prior structure, both in simulation and on several quantitative benchmarks constructed using data from the 1000 Genomes Project and the International HapMap Project. A final illustration is presented for an analysis of gene expression data obtained by single-cell RNA-seq.