AIMC Topic: Software

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Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories.

Bioinformatics (Oxford, England)
MOTIVATION: The recent emergence of cloud laboratories-collections of automated wet-lab instruments that are accessed remotely, presents new opportunities to apply Artificial Intelligence and Machine Learning in scientific research. Among these is th...

DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.

Bioinformatics (Oxford, England)
MOTIVATION: Mapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods wit...

keras_dna: a wrapper for fast implementation of deep learning models in genomics.

Bioinformatics (Oxford, England)
SUMMARY: Prediction of genomic annotations from DNA sequences using deep learning is today becoming a flourishing field with many applications. Nevertheless, there are still difficulties in handling data in order to conveniently build and train model...

eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping.

Nucleic acids research
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the d...

Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning.

Nucleic acids research
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-bas...

ModFOLD8: accurate global and local quality estimates for 3D protein models.

Nucleic acids research
Methods for estimating the quality of 3D models of proteins are vital tools for driving the acceptance and utility of predicted tertiary structures by the wider bioscience community. Here we describe the significant major updates to ModFOLD, which ha...

Unsupervised flow cytometry analysis in hematological malignancies: A new paradigm.

International journal of laboratory hematology
Ever since hematopoietic cells became "events" enumerated and characterized in suspension by cell counters or flow cytometers, researchers and engineers have strived to refine the acquisition and display of the electronic signals generated. A large a...

Moral Status for Malware! The Difficulty of Defining Advanced Artificial Intelligence.

Cambridge quarterly of healthcare ethics : CQ : the international journal of healthcare ethics committees
The suggestion has been made that future advanced artificial intelligence (AI) that passes some consciousness-related criteria should be treated as having moral status, and therefore, humans would have an ethical obligation to consider its well-being...

Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study.

Database : the journal of biological databases and curation
Producing findable, accessible, interoperable and reusable (FAIR) data cannot be accomplished solely by data curators in all disciplines. In biology, we have shown that phenotypic data curation is not only costly, but it is burdened with inter-curato...