TLGP: a flexible transfer learning algorithm for gene prioritization based on heterogeneous source domain

BackgroundGene prioritization (gene ranking) aims to obtain the centrality of genes, which is critical for cancer diagnosis and therapy since keys genes correspond to the biomarkers or targets of drugs. Great efforts have been devoted to the gene ranking problem by exploring the similarity between candidate and known disease-causing genes. However, when the number of disease-causing genes is limited, they are not applicable largely due to the low accuracy. Actually, the number of disease-causing genes for cancers, particularly for these rare cancers, are really limited. Therefore, there is a critical needed to design effective and efficient algorithms for gene ranking with limited prior disease-causing genes.ResultsIn this study, we propose a transfer learning based algorithm for gene prioritization (called TLGP) in the cancer (target domain) without disease-causing genes by transferring knowledge from other cancers (source domain). The underlying assumption is that knowledge shared by similar cancers improves the accuracy of gene prioritization. Specifically, TLGP first quantifies the similarity between the target and source domain by calculating the affinity matrix for genes. Then, TLGP automatically learns a fusion network for the target cancer by fusing affinity matrix, pathogenic genes and genomic data of source cancers. Finally, genes in the target cancer are prioritized. The experimental results indicate that the learnt fusion network is more reliable than gene co-expression network, implying that transferring knowledge from other cancers improves the accuracy of network construction. Moreover, TLGP outperforms state-of-the-art approaches in terms of accuracy, improving at least 5%.ConclusionThe proposed model and method provide an effective and efficient strategy for gene ranking by integrating genomic data from various cancers

ResumeNet: A Learning-based Framework for Automatic Resume Quality Assessment

Recruitment of appropriate people for certain positions is critical for any companies or organizations. Manually screening to select appropriate candidates from large amounts of resumes can be exhausted and time-consuming. However, there is no public tool that can be directly used for automatic resume quality assessment (RQA). This motivates us to develop a method for automatic RQA. Since there is also no public dataset for model training and evaluation, we build a dataset for RQA by collecting around 10K resumes, which are provided by a private resume management company. By investigating the dataset, we identify some factors or features that could be useful to discriminate good resumes from bad ones, e.g., the consistency between different parts of a resume. Then a neural-network model is designed to predict the quality of each resume, where some text processing techniques are incorporated. To deal with the label deficiency issue in the dataset, we propose several variants of the model by either utilizing the pair/triplet-based loss, or introducing some semi-supervised learning technique to make use of the abundant unlabeled data. Both the presented baseline model and its variants are general and easy to implement. Various popular criteria including the receiver operating characteristic (ROC) curve, F-measure and ranking-based average precision (AP) are adopted for model evaluation. We compare the different variants with our baseline model. Since there is no public algorithm for RQA, we further compare our results with those obtained from a website that can score a resume. Experimental results in terms of different criteria demonstrate the effectiveness of the proposed method. We foresee that our approach would transform the way of future human resources management.Comment: ICD

Advances in Processing, Mining, and Learning Complex Data: From Foundations to Real-World Applications

Processing, mining, and learning complex data refer to an advanced study area of data mining and knowledge discovery concerning the development and analysis of approaches for discovering patterns and learning models from data with a complex structure (e.g., multirelational data, XML data, text data, image data, time series, sequences, graphs, streaming data, and trees) [1–5]. These kinds of data are commonly encountered in many social, economic, scientific, and engineering applications. Complex data pose new challenges for current research in data mining and knowledge discovery as they require new methods for processing, mining, and learning them. Traditional data analysis methods often require the data to be represented as vectors [6]. However, many data objects in real-world applications, such as chemical compounds in biopharmacy, brain regions in brain health data, users in business networks, and time-series information in medical data, contain rich structure information (e.g., relationships between data and temporal structures). Such a simple feature-vector representation inherently loses the structure information of the objects. In reality, objects may have complicated characteristics, depending on how the objects are assessed and characterized. Meanwhile, the data may come from heterogeneous domains [7], such as traditional tabular-based data, sequential patterns, graphs, time-series information, and semistructured data. Novel data analytics methods are desired to discover meaningful knowledge in advanced applications from data objects with complex characteristics. This special issue contributes to the fundamental research in processing, mining, and learning complex data, focusing on the analysis of complex data sources

SplitPlace: AI augmented splitting and placement of large-scale neural networks in mobile edge environments

In recent years, deep learning models have become ubiquitous in industry and academia alike. Deep neural networks can solve some of the most complex pattern-recognition problems today, but come with the price of massive compute and memory requirements. This makes the problem of deploying such large-scale neural networks challenging in resource-constrained mobile edge computing platforms, specifically in mission-critical domains like surveillance and healthcare. To solve this, a promising solution is to split resource-hungry neural networks into lightweight disjoint smaller components for pipelined distributed processing. At present, there are two main approaches to do this: semantic and layer-wise splitting. The former partitions a neural network into parallel disjoint models that produce a part of the result, whereas the latter partitions into sequential models that produce intermediate results. However, there is no intelligent algorithm that decides which splitting strategy to use and places such modular splits to edge nodes for optimal performance. To combat this, this work proposes a novel AI-driven online policy, SplitPlace, that uses Multi-Armed-Bandits to intelligently decide between layer and semantic splitting strategies based on the input task's service deadline demands. SplitPlace places such neural network split fragments on mobile edge devices using decision-aware reinforcement learning for efficient and scalable computing. Moreover, SplitPlace fine-tunes its placement engine to adapt to volatile environments. Our experiments on physical mobile-edge environments with real-world workloads show that SplitPlace can significantly improve the state-of-the-art in terms of average response time, deadline violation rate, inference accuracy, and total reward by up to 46, 69, 3 and 12 percent respectively

New Techniques for Learning Parameters in Bayesian Networks.

PhDOne of the hardest challenges in building a realistic Bayesian network (BN) model is to construct the node probability tables (NPTs). Even with a fixed predefined model structure and very large amounts of relevant data, machine learning methods do not consistently achieve great accuracy compared to the ground truth when learning the NPT entries (parameters). Hence, it is widely believed that incorporating expert judgment or related domain knowledge can improve the parameter learning accuracy. This is especially true in the sparse data situation. Expert judgments come in many forms. In this thesis we focus on expert judgment that specifies inequality or equality relationships among variables. Related domain knowledge is data that comes from a different but related problem. By exploiting expert judgment and related knowledge, this thesis makes novel contributions to improve the BN parameter learning performance, including: • The multinomial parameter learning model with interior constraints (MPL-C) and exterior constraints (MPL-EC). This model itself is an auxiliary BN, which encodes the multinomial parameter learning process and constraints elicited from the expert judgments. • The BN parameter transfer learning (BNPTL) algorithm. Given some potentially related (source) BNs, this algorithm automatically explores the most relevant source BN and BN fragments, and fuses the selected source and target parameters in a robust way. • A generic BN parameter learning framework. This framework uses both expert judgments and transferred knowledge to improve the learning accuracy. This framework transfers the mined data statistics from the source network as the parameter priors of the target network. Experiments based on the BNs from a well-known repository as well as two realworld case studies using different data sample sizes demonstrate that the proposed new approaches can achieve much greater learning accuracy compared to other state-of-theart methods with relatively sparse data.China Scholarship Counci