Chang Su

Matthew Brendel, Chang Su, Zilong Bai et al.

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.

Zhongkai Hao, Jiachen Yao, Chang Su et al.

While significant progress has been made on Physics-Informed Neural Networks (PINNs), a comprehensive comparison of these methods across a wide range of Partial Differential Equations (PDEs) is still lacking. This study introduces PINNacle, a benchmarking tool designed to fill this gap. PINNacle provides a diverse dataset, comprising over 20 distinct PDEs from various domains, including heat conduction, fluid dynamics, biology, and electromagnetics. These PDEs encapsulate key challenges inherent to real-world problems, such as complex geometry, multi-scale phenomena, nonlinearity, and high dimensionality. PINNacle also offers a user-friendly toolbox, incorporating about 10 state-of-the-art PINN methods for systematic evaluation and comparison. We have conducted extensive experiments with these methods, offering insights into their strengths and weaknesses. In addition to providing a standardized means of assessing performance, PINNacle also offers an in-depth analysis to guide future research, particularly in areas such as domain decomposition methods and loss reweighting for handling multi-scale problems and complex geometry. To the best of our knowledge, it is the largest benchmark with a diverse and comprehensive evaluation that will undoubtedly foster further research in PINNs.

Xinyue Hu, Lin Gu, Kazuma Kobayashi et al.

Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images. This technique has the potential to improve the efficiency of medical professionals while relieving the burden on the public health system, particularly in resource-poor countries. Existing medical VQA methods tend to encode medical images and learn the correspondence between visual features and questions without exploiting the spatial, semantic, or medical knowledge behind them. This is partially because of the small size of the current medical VQA dataset, which often includes simple questions. Therefore, we first collected a comprehensive and large-scale medical VQA dataset, focusing on chest X-ray images. The questions involved detailed relationships, such as disease names, locations, levels, and types in our dataset. Based on this dataset, we also propose a novel baseline method by constructing three different relationship graphs: spatial relationship, semantic relationship, and implicit relationship graphs on the image regions, questions, and semantic labels. The answer and graph reasoning paths are learned for different questions.

Weijie Chen, Yongzhu Chang, Rongsheng Zhang et al.

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.

Xinyue Hu, Lin Gu, Liangchen Liu et al.

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.

Xiang Geng, Ming Zhu, Jiahuan Li et al.

The scarcity of non-English data limits the development of non-English large language models (LLMs). Transforming English-centric LLMs to non-English has been identified as an effective and resource-efficient method. Previous works start from base LLMs and perform knowledge distillation (KD) with data generated by stronger LLMs, e.g. GPT-4. Compared to base LLMs, chat LLMs are further optimized for advanced abilities, e.g. multi-turn conversation and human preference alignment, and thus more powerful in both helpfulness and safety. However, transforming a chat LLM involves two critical issues: (1) How can we effectively transfer advanced abilities without their supervised data? (2) How can we prevent the original knowledge from catastrophic forgetting during transformation? We target these issues by introducing a simple framework called TransLLM. For the first issue, TransLLM divides the transfer problem into some common sub-tasks with the translation chain-of-thought, which uses the translation as the bridge between English and non-English step-by-step. We further enhance the performance of sub-tasks with publicly available data. For the second issue, we propose a method comprising two synergistic components: low-rank adaptation for training to maintain the original LLM parameters, and recovery KD, which utilizes data generated by the chat LLM itself to recover the original knowledge from the frozen parameters. In the experiments, we transform the LLaMA-2-chat-7B to the Thai language. Our method, using only single-turn data, outperforms strong baselines and ChatGPT on multi-turn benchmark MT-bench. Furthermore, our method, without safety data, rejects more harmful queries of safety benchmark AdvBench than both ChatGPT and GPT-4. Code is available at https://github.com/hy5468/TransLLM.

Marianne Arriola, Weishen Pan, Manqi Zhou et al.

Joint analysis of multi-omic single-cell data across cohorts has significantly enhanced the comprehensive analysis of cellular processes. However, most of the existing approaches for this purpose require access to samples with complete modality availability, which is impractical in many real-world scenarios. In this paper, we propose (Single-Cell Cross-Cohort Cross-Category) integration, a novel framework that learns unified cell representations under domain shift without requiring full-modality reference samples. Our generative approach learns rich cross-modal and cross-domain relationships that enable imputation of these missing modalities. Through experiments on real-world multi-omic datasets, we demonstrate that offers a robust solution to single-cell tasks such as cell type clustering, cell type classification, and feature imputation.

Zhengzhe Yu, Jiaxin Guo, Minghan Wang et al.

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 $\mathcal{L}_τ$ 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).

Jiaxin Guo, Minghan Wang, Daimeng Wei et al.

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.

Minghan Wang, Jiaxin Guo, Yuxia Wang et al.

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.