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From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning
A step towards a reinforcement learning de novo genome assembler
The use of reinforcement learning has proven to be very promising for solving
complex activities without human supervision during their learning process.
However, their successful applications are predominantly focused on fictional
and entertainment problems - such as games. Based on the above, this work aims
to shed light on the application of reinforcement learning to solve this
relevant real-world problem, the genome assembly. By expanding the only
approach found in the literature that addresses this problem, we carefully
explored the aspects of intelligent agent learning, performed by the Q-learning
algorithm, to understand its suitability to be applied in scenarios whose
characteristics are more similar to those faced by real genome projects. The
improvements proposed here include changing the previously proposed reward
system and including state space exploration optimization strategies based on
dynamic pruning and mutual collaboration with evolutionary computing. These
investigations were tried on 23 new environments with larger inputs than those
used previously. All these environments are freely available on the internet
for the evolution of this research by the scientific community. The results
suggest consistent performance progress using the proposed improvements,
however, they also demonstrate the limitations of them, especially related to
the high dimensionality of state and action spaces. We also present, later, the
paths that can be traced to tackle genome assembly efficiently in real
scenarios considering recent, successfully reinforcement learning applications
- including deep reinforcement learning - from other domains dealing with
high-dimensional inputs
Machine learning meets genome assembly
International audienceMotivation: With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequencing projects remain unsolved. Among them is the task of assembling DNA fragments from previously unsequenced organisms, which is classified as an NP-hard (nondeterministic polynomial time hard) problem, for which no efficient computational solution with reasonable execution time exists. However, several tools that produce approximate solutions have been used with results that have facilitated scientific discoveries, although there is ample room for improvement. As with other NP-hard problems, machine learning algorithms have been one of the approaches used in recent years in an attempt to find better solutions to the DNA fragment assembly problem, although still at a low scale.Results: This paper presents a broad review of pioneering literature comprising artificial intelligence-based DNA assemblers—particularly the ones that use machine learning—to provide an overview of state-of-the-art approaches and to serve as a starting point for further study in this field
Machine learning meets genome assembly
International audienceMotivation: With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequencing projects remain unsolved. Among them is the task of assembling DNA fragments from previously unsequenced organisms, which is classified as an NP-hard (nondeterministic polynomial time hard) problem, for which no efficient computational solution with reasonable execution time exists. However, several tools that produce approximate solutions have been used with results that have facilitated scientific discoveries, although there is ample room for improvement. As with other NP-hard problems, machine learning algorithms have been one of the approaches used in recent years in an attempt to find better solutions to the DNA fragment assembly problem, although still at a low scale.Results: This paper presents a broad review of pioneering literature comprising artificial intelligence-based DNA assemblers—particularly the ones that use machine learning—to provide an overview of state-of-the-art approaches and to serve as a starting point for further study in this field