An answer recommendation framework for an online cancer community forum.

Health community forums are a kind of online platform to discuss various matters related to management of illness. People are increasingly searching for answers online, particularly when they are diagnosed with cancer like life-threatening diseases. People seek suggestions or advice through these platforms to make decisions during their treatments. However, locating the correct information or similar people is often a great challenge for them. In this scenario, this paper proposes an answer recommendation system in an online breast cancer community forum that provide guidance and valuable references to users while making decisions. The answer is the summary of already discussed topic in the forum, so that they do not need to go through all the answer posts which spans over multiple pages or initiate a thread once again. There are three phases for the answer recommendation system, including query similarity model to retrieve the past similar query, query-answer pair generation and answer recommendation. Query similarity model is employed by a Siamese network with Bi-LSTM architecture which could achieve an F1-score of 85.5%. Also, the paper shows the efficacy of transfer learning technique to generalize the model well in our breast cancer query-query pair data set. The query-answer pairs are generated by an extractive summarization technique that is based on an optimization algorithm. The effectiveness of the generated summary is evaluated based on a manually generated summary, and the result shows a ROUGE-1 score of 49%.

Deep learning based analysis of sentiment dynamics in online cancer community forums: An experience.

Online health communities (OHC) provide various opportunities for patients with chronic or life-threatening illnesses, especially for cancer patients and survivors. A better understanding of the sentiment dynamics of patients in OHCs can help in the precise formulation of the needs during their treatment. The current study investigated the sentiment dynamics in patients' narratives in a Breast Cancer community group (Breastcancer.org) to identify the changes in emotions, thoughts, stress, and coping mechanisms while undergoing treatment options, particularly chemotherapy, radiation, and surgery. Sentiment dynamics of users' posts was performed using a deep learning model. A sentiment change analysis was performed to measure change in the satisfaction level of the users. The deep learning model BiLSTM with sentiment embedding features provided a better F1-score of 91.9%. Sentiment dynamics can assess the difference in satisfaction level the users acquire by interacting with other users in the forum. A comparison of the proposed model with existing models revealed the effectiveness of this methodology.

MicroRNA-mRNA interaction network using TSK-type recurrent neural fuzzy network.

MicroRNAs are short non-coding RNAs that can regulate gene expression during various crucial cell processes such as differentiation, proliferation and apoptosis. Changes in expression profiles of miRNA play an important role in the development of many cancers, including CRC. Therefore, the identification of cancer related miRNAs and their target genes are important for cancer biology research. In this paper, we applied TSK-type recurrent neural fuzzy network (TRNFN) to infer miRNA-mRNA association network from paired miRNA, mRNA expression profiles of CRC patients. We demonstrated that the method we proposed achieved good performance in recovering known experimentally verified miRNA-mRNA associations. Moreover, our approach proved successful in identifying 17 validated cancer miRNAs which are directly involved in the CRC related pathways. Targeting such miRNAs may help not only to prevent the recurrence of disease but also to control the growth of advanced metastatic tumors. Our regulatory modules provide valuable insights into the pathogenesis of cancer.

Gene regulatory network from microarray data of colon cancer patients using TSK-type recurrent neural fuzzy network.

In this work we applied a TSK-type recurrent neural fuzzy approach to extract regulatory relationship among genes and reconstruct gene regulatory network from microarray data. The identified signature has captured the regulatory relationship among 27 differentially expressed genes from microarray dataset. We applied three different methods viz., feed forward neural fuzzy, modified genetic algorithm and recurrent neural fuzzy, on the same data set for the inference of GRNs and the results obtained are almost comparable. In all tested cases, TRNFN identified more biologically meaningful relations. We found that 87.8% of the total interactions extracted by TRNFN are correct in accordance with the biological knowledge. Our analysis resulted in 2 major outcomes. First, upregulated genes are regulated by more genes than downregulated genes. Second, tumor activators activate other tumor activators and suppress tumor suppressers strongly in the disease environment. These findings will help to elucidate the common molecular mechanism of colon cancer, and provide new insights into cancer diagnostics, prognostics and therapy.

Comparative advantages of novel algorithms using MSR threshold and MSR difference threshold for biclustering gene expression data.

The goal of biclustering in gene expression data matrix is to find a submatrix such that the genes in the submatrix show highly correlated activities across all conditions in the submatrix. A measure called mean squared residue (MSR) is used to simultaneously evaluate the coherence of rows and columns within the submatrix. MSR difference is the incremental increase in MSR when a gene or condition is added to the bicluster. In this chapter, three biclustering algorithms using MSR threshold (MSRT) and MSR difference threshold (MSRDT) are experimented and compared. All these methods use seeds generated from K-Means clustering algorithm. Then these seeds are enlarged by adding more genes and conditions. The first algorithm makes use of MSRT alone. Both the second and third algorithms make use of MSRT and the newly introduced concept of MSRDT. Highly coherent biclusters are obtained using this concept. In the third algorithm, a different method is used to calculate the MSRDT. The results obtained on bench mark datasets prove that these algorithms are better than many of the metaheuristic algorithms.

KMeans greedy search hybrid algorithm for biclustering gene expression data.

Microarray technology demands the development of algorithms capable of extracting novel and useful patterns like biclusters. A bicluster is a submatrix of the gene expression datamatrix such that the genes show highly correlated activities across all conditions in the submatrix. A measure called Mean Squared Residue (MSR) is used to evaluate the coherence of rows and columns within the submatrix. In this paper, the KMeans greedy search hybrid algorithm is developed for finding biclusters from the gene expression data. This algorithm has two steps. In the first step, high quality bicluster seeds are generated using KMeans clustering algorithm. In the second step, these seeds are enlarged by adding more genes and conditions using the greedy strategy. Here, the objective is to find the biclusters with maximum size and the MSR value lower than a given threshold. The biclusters obtained from this algorithm on both the bench mark datasets are of high quality. The statistical significance and biological relevance of the biclusters are verified using gene ontology database.