edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page

PTE: Predictive Text Embedding through Large-scale Heterogeneous Text Networks

Unsupervised text embedding methods, such as Skip-gram and Paragraph Vector, have been attracting increasing attention due to their simplicity, scalability, and effectiveness. However, comparing to sophisticated deep learning architectures such as convolutional neural networks, these methods usually yield inferior results when applied to particular machine learning tasks. One possible reason is that these text embedding methods learn the representation of text in a fully unsupervised way, without leveraging the labeled information available for the task. Although the low dimensional representations learned are applicable to many different tasks, they are not particularly tuned for any task. In this paper, we fill this gap by proposing a semi-supervised representation learning method for text data, which we call the \textit{predictive text embedding} (PTE). Predictive text embedding utilizes both labeled and unlabeled data to learn the embedding of text. The labeled information and different levels of word co-occurrence information are first represented as a large-scale heterogeneous text network, which is then embedded into a low dimensional space through a principled and efficient algorithm. This low dimensional embedding not only preserves the semantic closeness of words and documents, but also has a strong predictive power for the particular task. Compared to recent supervised approaches based on convolutional neural networks, predictive text embedding is comparable or more effective, much more efficient, and has fewer parameters to tune.Comment: KDD 201

Recent Advances in Transfer Learning for Cross-Dataset Visual Recognition: A Problem-Oriented Perspective

This paper takes a problem-oriented perspective and presents a comprehensive review of transfer learning methods, both shallow and deep, for cross-dataset visual recognition. Specifically, it categorises the cross-dataset recognition into seventeen problems based on a set of carefully chosen data and label attributes. Such a problem-oriented taxonomy has allowed us to examine how different transfer learning approaches tackle each problem and how well each problem has been researched to date. The comprehensive problem-oriented review of the advances in transfer learning with respect to the problem has not only revealed the challenges in transfer learning for visual recognition, but also the problems (e.g. eight of the seventeen problems) that have been scarcely studied. This survey not only presents an up-to-date technical review for researchers, but also a systematic approach and a reference for a machine learning practitioner to categorise a real problem and to look up for a possible solution accordingly

Transfer Learning for Speech and Language Processing

Transfer learning is a vital technique that generalizes models trained for one setting or task to other settings or tasks. For example in speech recognition, an acoustic model trained for one language can be used to recognize speech in another language, with little or no re-training data. Transfer learning is closely related to multi-task learning (cross-lingual vs. multilingual), and is traditionally studied in the name of `model adaptation'. Recent advance in deep learning shows that transfer learning becomes much easier and more effective with high-level abstract features learned by deep models, and the `transfer' can be conducted not only between data distributions and data types, but also between model structures (e.g., shallow nets and deep nets) or even model types (e.g., Bayesian models and neural models). This review paper summarizes some recent prominent research towards this direction, particularly for speech and language processing. We also report some results from our group and highlight the potential of this very interesting research field.Comment: 13 pages, APSIPA 201

Learning and Transferring IDs Representation in E-commerce

Many machine intelligence techniques are developed in E-commerce and one of the most essential components is the representation of IDs, including user ID, item ID, product ID, store ID, brand ID, category ID etc. The classical encoding based methods (like one-hot encoding) are inefficient in that it suffers sparsity problems due to its high dimension, and it cannot reflect the relationships among IDs, either homogeneous or heterogeneous ones. In this paper, we propose an embedding based framework to learn and transfer the representation of IDs. As the implicit feedbacks of users, a tremendous amount of item ID sequences can be easily collected from the interactive sessions. By jointly using these informative sequences and the structural connections among IDs, all types of IDs can be embedded into one low-dimensional semantic space. Subsequently, the learned representations are utilized and transferred in four scenarios: (i) measuring the similarity between items, (ii) transferring from seen items to unseen items, (iii) transferring across different domains, (iv) transferring across different tasks. We deploy and evaluate the proposed approach in Hema App and the results validate its effectiveness.Comment: KDD'18, 9 page

A Neural Network Approach for Mixing Language Models

The performance of Neural Network (NN)-based language models is steadily improving due to the emergence of new architectures, which are able to learn different natural language characteristics. This paper presents a novel framework, which shows that a significant improvement can be achieved by combining different existing heterogeneous models in a single architecture. This is done through 1) a feature layer, which separately learns different NN-based models and 2) a mixture layer, which merges the resulting model features. In doing so, this architecture benefits from the learning capabilities of each model with no noticeable increase in the number of model parameters or the training time. Extensive experiments conducted on the Penn Treebank (PTB) and the Large Text Compression Benchmark (LTCB) corpus showed a significant reduction of the perplexity when compared to state-of-the-art feedforward as well as recurrent neural network architectures.Comment: Published at IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) 2017. arXiv admin note: text overlap with arXiv:1703.0806