detach().numpy() val = val.detach().numpy() A = scipy.sparse.coo_matrix((val, edge_index), shape=(N, N)) svd = TruncatedSVD(n_components=self.in_channels, n_iter=128) svd.fit(A) x = svd.components_.T return torch.from_numpy(x).to(torch.float).to(pos_edge_index.device) ...
frequency response data form. The main data members are `omega` and `fresp`, where `omega` is a 1D array with the frequency points of the response, and `fresp` is a 3D array, with the first dimension corresponding to the output index of the FRD, the second dimension corresponding to ...
Then, we used the function fisher_exact Python’s scipy package to perform a two-sided Fisher’s exact test comparing the proportions of annotated to unannotated between this set of random anchors and the set of DIVE anchors. Binomial regression...
Mass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface. During the time necessary to perform a single acquisition, it is likely that uncontrollable factors alter the validity of the initial mass calibration of the instrument, resulting...
The enrichment analysis was done by mapping the gene ontology (GO) terms with the gene identifiers, followed by Fisher’s exact and Benjamini-Hochberg-corrected tests using a threshold of 0.05 with SciPy version 1.9.0 [73] and Python Statsmodels version 0.10.2 [74]. The code is available ...
Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns within epigenomic data. However, such annotations are less suitable for gene-based analyses. We present Chr
The workflow of RNAlysis. Top section: a typical analysis with RNAlysis can start at any stage from raw/trimmed FASTQ files, through more processed data tables such as count matrices, differential expression tables, or any form of tabular data. Middle section: data tables can be filtered, nor...
These findings have to be interpreted in the context of the (controversial) discussion about the co-occurrence of BPD and IVH or WMI [21, 39], diagnosed in about 50% of immature preterm infants [19], and its severe form cystic periventricular leukomalacia in 1.3% of preterm infants [50]....
form of abbreviations.nlp.add_pipe("scispacy_linker",config={"resolve_abbreviations":True,"linker_name":"umls"})doc=nlp("Spinal and bulbar muscular atrophy (SBMA) is an\inherited motor neuron disease caused by the expansion\of a polyglutamine tract within the androgen receptor (AR).\SBMA can...
All analysis is performed in Python 3.7.4 with the modules numpy (1.18.1), scipy (1.4.1), and pandas (1.2.3). Kendall's tau was calculated with method set to 'kendall' in pandas.DataFrame.corrwith. The angiogenesis related genes were obtained from GO:0001525. The Gene Ontology (GO) ...