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

Epitope profiling via mixture modeling of ranked data

We propose the use of probability models for ranked data as a useful alternative to a quantitative data analysis to investigate the outcome of bioassay experiments, when the preliminary choice of an appropriate normalization method for the raw numerical responses is difficult or subject to criticism. We review standard distance-based and multistage ranking models and in this last context we propose an original generalization of the Plackett-Luce model to account for the order of the ranking elicitation process. The usefulness of the novel model is illustrated with its maximum likelihood estimation for a real data set. Specifically, we address the heterogeneous nature of experimental units via model-based clustering and detail the necessary steps for a successful likelihood maximization through a hybrid version of the Expectation-Maximization algorithm. The performance of the mixture model using the new distribution as mixture components is compared with those relative to alternative mixture models for random rankings. A discussion on the interpretation of the identified clusters and a comparison with more standard quantitative approaches are finally provided.Comment: (revised to properly include references