AIMC Topic: Software

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Identification of small molecules using accurate mass MS/MS search.

Mass spectrometry reviews
Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in MS/MS-base...

Towards generalizable entity-centric clinical coreference resolution.

Journal of biomedical informatics
OBJECTIVE: This work investigates the problem of clinical coreference resolution in a model that explicitly tracks entities, and aims to measure the performance of that model in both traditional in-domain train/test splits and cross-domain experiment...

A large-scale benchmark of gene prioritization methods.

Scientific reports
In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. Whi...

Metastasis detection from whole slide images using local features and random forests.

Cytometry. Part A : the journal of the International Society for Analytical Cytology
Digital pathology has led to a demand for automated detection of regions of interest, such as cancerous tissue, from scanned whole slide images. With accurate methods using image analysis and machine learning, significant speed-up, and savings in cos...

S-SulfPred: A sensitive predictor to capture S-sulfenylation sites based on a resampling one-sided selection undersampling-synthetic minority oversampling technique.

Journal of theoretical biology
Protein S-sulfenylation is a reversible post-translational modification involving covalent attachment of hydroxide to the thiol group of cysteine residues, which is involved in various biological processes including cell signaling, response to stress...

Exploiting Linkage Information and Problem-Specific Knowledge in Evolutionary Distribution Network Expansion Planning.

Evolutionary computation
This article tackles the Distribution Network Expansion Planning (DNEP) problem that has to be solved by distribution network operators to decide which, where, and/or when enhancements to electricity networks should be introduced to satisfy the futur...

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.

RNA biology
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are criti...

ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing.

PLoS computational biology
Creating and running realistic models of neural networks has hitherto been a task for computing professionals rather than experimental neuroscientists. This is mainly because such networks usually engage substantial computational resources, the handl...

An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data.

Genes & genetic systems
Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide c...

NegAIT: A new parser for medical text simplification using morphological, sentential and double negation.

Journal of biomedical informatics
Many different text features influence text readability and content comprehension. Negation is commonly suggested as one such feature, but few general-purpose tools exist to discover negation and studies of the impact of negation on text readability ...