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With the rise of large language models (LLMs) for flexibly processing information as strings, a natural application is regression, specifically by preprocessing string representations into LLM embeddings as downstream features for metric…

In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…

This thesis designs a prediction system based on matrix factorization to predict the classification accuracy of a specific model on a particular dataset. In this thesis, we conduct comprehensive empirical research on more than fifty…

Deep learning has become a crucial tool in studying proteins. While the significance of modeling protein structure has been discussed extensively in the literature, amino acid types are typically included in the input as a default operation…

Accurate load forecasting is crucial for maintaining the power balance between generators and consumers,particularly with the increasing integration of renewable energy sources, which introduce significant intermittent volatility. With the…

We surely enjoy the larger the better models for their superior performance in the last couple of years when both the hardware and software support the birth of such extremely huge models. The applied fields include text mining and others.…

We explore how Deep Learning (DL) can be utilized to predict prognosis of acute myeloid leukemia (AML). Out of TCGA (The Cancer Genome Atlas) database, 94 AML cases are used in this study. Input data include age, 10 common cytogenetic and…

Masked Language Modeling (MLM) has been widely used as the denoising objective in pre-training language models (PrLMs). Existing PrLMs commonly adopt a Random-Token Masking strategy where a fixed masking ratio is applied and different…

A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design.…

Machine learning approaches have become popular for molecular modeling tasks, including molecular force fields and properties prediction. Traditional supervised learning methods suffer from scarcity of labeled data for particular tasks,…

Artificial intelligence (AI) methods have become critical in scientific applications to help accelerate scientific discovery. Large language models (LLMs) are being considered as a promising approach to address some of the challenging…

Proteins are complex biomolecules that play a central role in various biological processes, making them critical targets for breakthroughs in molecular biology, medical research, and drug discovery. Deciphering their intricate, hierarchical…

The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on…

The increasing complexity of software systems has driven significant advancements in program analysis, as traditional methods unable to meet the demands of modern software development. To address these limitations, deep learning techniques,…

Large language models (LLMs) have demonstrated unprecedented emergent capabilities, including content generation, translation, and simulation of human behavior. Field experiments, on the other hand, are widely employed in social studies to…

Large language models (LLMs) alignment aims to ensure that the behavior of LLMs meets human preferences. While collecting data from multiple fine-grained, aspect-specific preferences becomes more and more feasible, existing alignment…

Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…

Predicting human behavior in shared environments is crucial for safe and efficient human-robot interaction. Traditional data-driven methods to that end are pre-trained on domain-specific datasets, activity types, and prediction horizons. In…

Recently, large language models (LLMs) have been successfully applied to many fields, showing outstanding comprehension and reasoning capabilities. Despite their great potential, LLMs usually require dedicated pre-training and fine-tuning…