Gene Mutation Classification through Text Evidence Facilitating Cancer Tumour Detection

Deep-GenMut: Automated genetic mutation classification in oncology: A deep learning comparative study

Early cancer detection and treatment depend on the discovery of specific genes that cause cancer. The classification of genetic mutations was initially done manually. However, this process relies on pathologists and can be a time-consuming task. Therefore, to improve the precision of clinical interpretation, researchers have developed computational algorithms that leverage next-generation sequencing technologies for automated mutation analysis. This paper utilized four deep learning classification models with training collections of biomedical texts. These models comprise bidirectional encoder representations from transformers for Biomedical text mining (BioBERT), a specialized language model implemented for biological contexts. Impressive results in multiple tasks, including text classification, language inference, and question answering, can be obtained by simply adding an extra layer to the BioBERT model. Moreover, bidirectional encoder representations from transformers (BERT), long short-term memory (LSTM), and bidirectional LSTM (BiLSTM) have been leveraged to produce very good results in categorizing genetic mutations based on textual evidence. The dataset used in the work was created by Memorial Sloan Kettering Cancer Center (MSKCC), which contains several mutations. Furthermore, this dataset poses a major classification challenge in the Kaggle research prediction competitions. In carrying out the work, three challenges were identified: enormous text length, biased representation of the data, and repeated data instances. Based on the commonly used evaluation metrics, the experimental results show that the BioBERT model outperforms other models with an F1 score of 0.87 and 0.850 MCC, which can be considered as improved performance compared to similar results in the literature that have an F1 score of 0.70 achieved with the BERT model.

Classification of clinically actionable genetic mutations in cancer patients

Personalized medicine in cancer treatment aims to treat each individual's cancer tumor uniquely based on the genetic sequence of the cancer patient and is a much more effective approach compared to traditional methods which involve treating each type of cancer in the same, generic manner. However, personalized treatment requires the classification of cancer-related genes once profiled, which is a highly labor-intensive and time-consuming task for pathologists making the adoption of personalized medicine a slow progress worldwide. In this paper, we propose an intelligent multi-class classifier system that uses a combination of Natural Language Processing (NLP) techniques and Machine Learning algorithms to automatically classify clinically actionable genetic mutations using evidence from text-based medical literature. The training data set for the classifier was obtained from the Memorial Sloan Kettering Cancer Center and the Random Forest algorithm was applied with TF-IDF for feature extraction and truncated SVD for dimensionality reduction. The results show that the proposed model outperforms the previous research in terms of accuracy and precision scores, giving an accuracy score of approximately 82%. The system has the potential to revolutionize cancer treatment and lead to significant improvements in cancer therapy.