Recent developments in single-cell omics technologies have enabled the quantification of molecular profiles in individual cells at an unparalleled resolution. Deep learning, a rapidly evolving sub-field of machine learning, has instilled a significant interest in single-cell omics research due to its remarkable success in analysing heterogeneous high-dimensional single-cell omics data. Nevertheless, the inherent multi-layer nonlinear architecture of deep learning models often makes them `black boxes' as the reasoning behind predictions is often unknown and not transparent to the user. This has stimulated an increasing body of research for addressing the lack of interpretability in deep learning models, especially in single-cell omics data analyses, where the identification and understanding of molecular regulators are crucial for interpreting model predictions and directing downstream experimental validations. In this work, we introduce the basics of single-cell omics technologies and the concept of interpretable deep learning. This is followed by a review of the recent interpretable deep learning models applied to various single-cell omics research. Lastly, we highlight the current limitations and discuss potential future directions. We anticipate this review to bring together the single-cell and machine learning research communities to foster future development and application of interpretable deep learning in single-cell omics research.

Extracting meaningful drug-related information chunks, such as adverse drug events (ADE), is crucial for preventing morbidity and saving many lives. Most ADEs are reported via an unstructured conversation with the medical context, so applying a general entity recognition approach is not sufficient enough. In this paper, we propose a new multi-aspect cross-integration framework for drug entity/event detection by capturing and aligning different context/language/knowledge properties from drug-related documents. We first construct multi-aspect encoders to describe semantic, syntactic, and medical document contextual information by conducting those slot tagging tasks, main drug entity/event detection, part-of-speech tagging, and general medical named entity recognition. Then, each encoder conducts cross-integration with other contextual information in three ways: the key-value cross, attention cross, and feedforward cross, so the multi-encoders are integrated in depth. Our model outperforms all SOTA on two widely used tasks, flat entity detection and discontinuous event extraction.

Natural language understanding typically maps single utterances to a dual level semantic frame, sentence level intent and slot labels at the word level. The best performing models force explicit interaction between intent detection and slot filling. We present a novel tri-level joint natural language understanding approach, adding domain, and explicitly exchange semantic information between all levels. This approach enables the use of multi-turn datasets which are a more natural conversational environment than single utterance. We evaluate our model on two multi-turn datasets for which we are the first to conduct joint slot-filling and intent detection. Our model outperforms state-of-the-art joint models in slot filling and intent detection on multi-turn data sets. We provide an analysis of explicit interaction locations between the layers. We conclude that including domain information improves model performance.

When a human communicates with a machine using natural language on the web and online, how can it understand the human's intention and semantic context of their talk? This is an important AI task as it enables the machine to construct a sensible answer or perform a useful action for the human. Meaning is represented at the sentence level, identification of which is known as intent detection, and at the word level, a labelling task called slot filling. This dual-level joint task requires innovative thinking about natural language and deep learning network design, and as a result, many approaches and models have been proposed and applied. This tutorial will discuss how the joint task is set up and introduce Spoken Language Understanding/Natural Language Understanding (SLU/NLU) with Deep Learning techniques. We will cover the datasets, experiments and metrics used in the field. We will describe how the machine uses the latest NLP and Deep Learning techniques to address the joint task, including recurrent and attention-based Transformer networks and pre-trained models (e.g. BERT). We will then look in detail at a network that allows the two levels of the task, intent classification and slot filling, to interact to boost performance explicitly. We will do a code demonstration of a Python notebook for this model and attendees will have an opportunity to watch coding demo tasks on this joint NLU to further their understanding.

We propose a PiggyBack, a Visual Question Answering platform that allows users to apply the state-of-the-art visual-language pretrained models easily. The PiggyBack supports the full stack of visual question answering tasks, specifically data processing, model fine-tuning, and result visualisation. We integrate visual-language models, pretrained by HuggingFace, an open-source API platform of deep learning technologies; however, it cannot be runnable without programming skills or deep learning understanding. Hence, our PiggyBack supports an easy-to-use browser-based user interface with several deep learning visual language pretrained models for general users and domain experts. The PiggyBack includes the following benefits: Free availability under the MIT License, Portability due to web-based and thus runs on almost any platform, A comprehensive data creation and processing technique, and ease of use on deep learning-based visual language pretrained models. The demo video is available on YouTube and can be found at https://youtu.be/iz44RZ1lF4s.

Recommender systems typically operate on high-dimensional sparse user-item matrices. Matrix completion is a very challenging task to predict one's interest based on millions of other users having each seen a small subset of thousands of items. We propose a Global-Local Kernel-based matrix completion framework, named GLocal-K, that aims to generalise and represent a high-dimensional sparse user-item matrix entry into a low dimensional space with a small number of important features. Our GLocal-K can be divided into two major stages. First, we pre-train an auto encoder with the local kernelised weight matrix, which transforms the data from one space into the feature space by using a 2d-RBF kernel. Then, the pre-trained auto encoder is fine-tuned with the rating matrix, produced by a convolution-based global kernel, which captures the characteristics of each item. We apply our GLocal-K model under the extreme low-resource setting, which includes only a user-item rating matrix, with no side information. Our model outperforms the state-of-the-art baselines on three collaborative filtering benchmarks: ML-100K, ML-1M, and Douban.

Text-to-image multimodal tasks, generating/retrieving an image from a given text description, are extremely challenging tasks since raw text descriptions cover quite limited information in order to fully describe visually realistic images. We propose a new visual contextual text representation for text-to-image multimodal tasks, VICTR, which captures rich visual semantic information of objects from the text input. First, we use the text description as initial input and conduct dependency parsing to extract the syntactic structure and analyse the semantic aspect, including object quantities, to extract the scene graph. Then, we train the extracted objects, attributes, and relations in the scene graph and the corresponding geometric relation information using Graph Convolutional Networks, and it generates text representation which integrates textual and visual semantic information. The text representation is aggregated with word-level and sentence-level embedding to generate both visual contextual word and sentence representation. For the evaluation, we attached VICTR to the state-of-the-art models in text-to-image generation.VICTR is easily added to existing models and improves across both quantitative and qualitative aspects.