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 a single model to master numerous tasks with improved efficiency. We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Tokens strong predictive power in different types of protein-prediction tasks. Key results include significant speedups (e.g., near 1000x over AlphaFold2 with MSA) and performance often matching or exceeding specialized approaches. Beyond that, we introduce an auxiliary self-supervised decoder pre-training approach to improve spatially sensitive task performance. Prot2Token thus offers a significant step towards a versatile, high-throughput paradigm for protein modeling, promising to accelerate biological discovery and the development of novel therapeutics. The code is available at https://github.com/mahdip72/prot2token .

A comparison between Recurrent Neural Networks and classical machine learning approaches In Laser induced breakdown spectroscopy

Recurrent Neural Networks are classes of Artificial Neural Networks that establish connections between different nodes form a directed or undirected graph for temporal dynamical analysis. In this research, the laser induced breakdown spectroscopy (LIBS) technique is used for quantitative analysis of aluminum alloys by different Recurrent Neural Network (RNN) architecture. The fundamental harmonic (1064 nm) of a nanosecond Nd:YAG laser pulse is employed to generate the LIBS plasma for the prediction of constituent concentrations of the aluminum standard samples. Here, Recurrent Neural Networks based on different networks, such as Long Short Term Memory (LSTM), Gated Recurrent Unit (GRU), Simple Recurrent Neural Network (Simple RNN), and as well as Recurrent Convolutional Networks comprising of Conv-SimpleRNN, Conv-LSTM and Conv-GRU are utilized for concentration prediction. Then a comparison is performed among prediction by classical machine learning methods of support vector regressor (SVR), the Multi Layer Perceptron (MLP), Decision Tree algorithm, Gradient Boosting Regression (GBR), Random Forest Regression (RFR), Linear Regression, and k-Nearest Neighbor (KNN) algorithm. Results showed that the machine learning tools based on Convolutional Recurrent Networks had the best efficiencies in prediction of the most of the elements among other multivariate methods.