Accurate identification and labeling of biomedical entities, such as diseases, genes, chemical and species, within scientific texts are crucial for understanding complex relationships. We propose Adaptive BERT or AdaBioBERT, a robust named entity recognition (NER) model that builds upon BioBERT (Biomedical Bidirectional Encoded Representation from Transformers) based on an adaptive loss function to learn different types of biomedical token sequence. This adaptive loss function combines the standard Cross Entropy (CE) loss and Conditional Random Field (CRF) loss to optimize both token level accuracy and sequence-level coherence. AdaBioBERT captures rich semantic nuances by leveraging pre-trained contextual embeddings from BioBERT. On the other hand, the CRF loss of AdaBioBERT ensures proper identification of complex multi-token biomedical entities in a sequence and the CE loss can capture the simple unigram entities in a sequence. The empirical analysis on multiple standard biomedical coprora demonstrates that AdaBioBERT performs better than the state of the arts for most of the datasets in terms of macro and micro averaged F1 score.’

The DepSign-LT-EDI-ACL2022 shared task focuses on early prediction of severity of depression over social media posts. The BioNLP group at Department of Data Science and Engineering in Indian Institute of Science Education and Research Bhopal (IISERB) has participated in this challenge and submitted three runs based on three different text mining models. The severity of depression were categorized into three classes, viz., no depression, moderate, and severe and the data to build models were released as part of this shared task. The objective of this work is to identify relevant features from the given social media texts for effective text classification. As part of our investigation, we explored features derived from text data using document embeddings technique and simple bag of words model following different weighting schemes. Subsequently, adaptive boosting, logistic regression, random forest and support vector machine (SVM) classifiers were used to identify the scale of depression from the given texts. The experimental analysis on the given validation data show that the SVM classifier using the bag of words model following term frequency and inverse document frequency weighting scheme outperforms the other models for identifying depression. However, this framework could not achieve a place among the top ten runs of the shared task. This paper describes the potential of the proposed framework as well as the possible reasons behind mediocre performance on the given data.