Related papers: In Search of Lost DNA Sequence Pretraining
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
With the success of large-scale pre-training in language tasks, there is an increasing trend of applying it to the domain of life sciences. In particular, pre-training methods based on DNA sequences have received increasing attention…
Code writing is repetitive and predictable, inspiring us to develop various code intelligence techniques. This survey focuses on code search, that is, to retrieve code that matches a given query by effectively capturing the semantic…
Decision-making is a dynamic process requiring perception, memory, and reasoning to make choices and find optimal policies. Traditional approaches to decision-making suffer from sample efficiency and generalization, while large-scale…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient…
Genomic foundation models trained on DNA sequences have demonstrated remarkable capabilities across diverse biological tasks, from variant effect prediction to genome design. These models are typically trained on massive, publicly sourced…
Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is…
Extracting informative representations of molecules using Graph neural networks (GNNs) is crucial in AI-driven drug discovery. Recently, the graph research community has been trying to replicate the success of self-supervised pretraining in…
Self-supervised pretraining (SSP) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the…
With the evolution of self-supervised learning, the pre-training paradigm has emerged as a predominant solution within the deep learning landscape. Model providers furnish pre-trained encoders designed to function as versatile feature…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
A pretrain-finetune strategy is widely used to reduce the overfitting that can occur when data is insufficient for CNN training. First few layers of a CNN pretrained on a large-scale RGB dataset are capable of acquiring general image…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
Deep learning models are widely used for solving challenging code processing tasks, such as code generation or code summarization. Traditionally, a specific model architecture was carefully built to solve a particular code processing task.…