arXiv subjects

Farzaneh Esmaili

Publications and source records attributed to Farzaneh Esmaili.

6 recordsLinked to original sources

arXiv2026

Learning Latent Protein Languages for Autoregressive Generation

Autoregressive transformers remain comparatively weak for protein sequence and structure generation. We study the role of target representation: amino acid tokens encode residue identities without explicit contextual semantics, while backbone coordinates require a discrete representation in our framework. We introduce two learned latent protein languages. Protein Latent Language (PLL) maps sequences to a 4,096-state contextual alphabet built on a frozen ESM-2 encoder, with one token per residue. Structure Latent Language (SLL) adapts GCP-VQVAE Lite with auxiliary sequence and confidence supervision while retaining decoding to backbone coordinates. We separately pretrain autoregressive transformer models on PLL and SLL tokens using next-token prediction, yielding PLLM and SLLM. Under matched downstream sequence training, PLLM has a fitted compute-scaling exponent of 0.038 versus 0.020 for the amino acid autoregressive model. In unconditional sequence generation, PLLM reduces the fraction of samples below a heuristic 1.5-bit residue-composition entropy threshold by 54% relative to the amino acid model across sampling temperatures. For sequence-to-structure prediction, replacing the original GCP-VQVAE Lite tokenizer with SLL reduces best validation perplexity by 34% under matched training. For long proteins, latent-token sampling is approximately 1,000 times faster than MSA-based AlphaFold2 in our measurements. In backbone generation, SLLM compares favorably with other generative models on diversity and novelty. We also observe early signs that using SLLM's internal token confidence for inference-time sampling can improve sequence-to-structure prediction quality beyond a single decoded sample. These results position learned latent protein languages as a promising substrate for autoregressive transformer scaling and inference-time sampling in protein generation.

cs.LG↗

arXiv2025

Prot2Token: A Unified Framework for Protein Modeling via Next-Token Prediction

The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce Prot2Token, a unified framework that overcomes these challenges by converting a wide spectrum of protein-related predictions-from sequence-level properties and residue-specific attributes to complex inter-protein interactions-into a standardized next-token prediction format. At its core, Prot2Token employs an autoregressive decoder, conditioned on embeddings from pre-trained protein encoders and guided by learnable task tokens, to perform diverse predictions. This architecture uniquely facilitates multi-task learning, enabling general-purpose decoders to generalize across five distinct categories. We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Token's predictive power in different types of protein-prediction tasks. In 3D structure prediction, Prot2Token delivers substantial speedups (up to 1000x faster than AlphaFold2 with MSA on the same hardware) while, across other numerous tasks, matching or surpassing specialized methods. Beyond that, we introduce an auxiliary self-supervised decoder pre-training approach to improve spatially sensitive task performance. Prot2Token thus offers a step towards standardizing biological prediction into a generative interface, promising to accelerate biological discovery and the development of novel therapeutics. The code is available at https://github.com/mahdip72/prot2token .

cs.LG↗

arXiv2025

Using Self-Supervised Auxiliary Tasks to Improve Fine-Grained Facial Representation

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.

cs.CV↗

arXiv2022

A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Sites Prediction

Post-translational modifications (PTMs) have key 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 a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases including neurological disorders and cancers. The purpose of this review paper is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively reviewed all related databases and introduced all steps regarding dataset creation, data preprocessing and method evaluation in p-site prediction. Next, we investigated p-sites prediction methods which fall into two computational groups: Algorithmic and Machine Learning (ML). Additionally, it was shown that there are basically two main approaches for p-sites prediction by ML: conventional and End-to-End deep learning methods, 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 p-site prediction. 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. Evaluation of the available online tools on the test sets showed quite poor performance for p-sites prediction. Keywords: Phosphorylation, Machine Learning, Deep Learning, Post Translation Modification, Databases

q-bio.QM↗

arXiv2022

How Self-Supervised Learning Can be Used for Fine-Grained Head Pose Estimation?

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.

cs.CV↗

arXiv2022

A Brief Review of Machine Learning Techniques for Protein Phosphorylation Sites Prediction

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.

q-bio.QM↗