Farzaneh Esmaili

Farzaneh Esmaili, Mahdi Pourmirzaei, Shahin Ramazi et al.

Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays significant roles in many biological processes. Disorders in the phosphorylation process lead to multiple diseases including neurological disorders and cancers. At first, this study comprehensively reviewed all databases related to phosphorylation sites (p-sites). Secondly, we introduced all steps regarding dataset creation, data preprocessing and method evaluation in p-sites prediction. Next, we investigated p-sites prediction methods which fall into two computational and Machine Learning (ML) groups. Additionally, it was shown that there are basically two main approaches for p-sites prediction by ML: conventional and End-to-End learning, which were given an overview for both of them. Moreover, this study introduced the most important feature extraction techniques which have mostly been used in ML approaches. Finally, we created three test sets from new proteins related to the 2022th released version of the dbPTM database based on general and human species. After evaluating available online tools on the test sets, results showed that the performance of online tools for p-sites prediction are quite weak on new reported phospho-proteins.

Mahdi Pourmirzaei, Farzaneh Esmaili, Ebrahim Mousavi et al.

The cost of head pose labeling is the main challenge of improving the fine-grained Head Pose Estimation (HPE). Although Self-Supervised Learning (SSL) can be a solution to the lack of huge amounts of labeled data, its efficacy for fine-grained HPE is not yet fully explored. This study aims to assess the usage of SSL in fine-grained HPE based on two scenarios: (1) using SSL for weights pre-training procedure, and (2) leveraging auxiliary SSL losses besides HPE. We design a Hybrid Multi-Task Learning (HMTL) architecture based on the ResNet50 backbone in which both strategies are applied. Our experimental results reveal that the combination of both scenarios is the best for HPE. Together, the average error rate is reduced up to 23.1% for AFLW2000 and 14.2% for BIWI benchmark compared to the baseline. Moreover, it is found that some SSL methods are more suitable for transfer learning, while others may be effective when they are considered as auxiliary tasks incorporated into supervised learning. Finally, it is shown that by using the proposed HMTL architecture, the average error is reduced with different types of initial weights: random, ImageNet and SSL pre-trained weights.

Mahdi Pourmirzaei, Gholam Ali Montazer, Farzaneh Esmaili

Facial emotion recognition (FER) is a fine-grained problem where the value of transfer learning is often assumed. We first quantify this assumption and show that, on AffectNet, training from random initialization with sufficiently strong augmentation consistently matches or surpasses fine-tuning from ImageNet. Motivated by this result, we propose Hybrid Multi-Task Learning (HMTL) for FER in the wild. HMTL augments supervised learning (SL) with self-supervised learning (SSL) objectives during training, while keeping the inference-time model unchanged. We instantiate HMTL with two tailored pretext tasks, puzzling and inpainting with a perceptual loss, that encourage part-aware and expression-relevant features. On AffectNet, both HMTL variants achieve state-of-the-art accuracy in the eight-emotion setting without any additional pretraining data, and they provide larger gains under low-data regimes. Compared with conventional SSL pretraining, HMTL yields stronger downstream performance. Beyond FER, the same strategy improves fine-grained facial analysis tasks, including head pose estimation and gender recognition. These results suggest that aligned SSL auxiliaries are an effective and simple way to strengthen supervised fine-grained facial representation without adding extra computation cost during inference time.