Kaushik Acharya

This enables reading text of languages written in non-ascii characters. Reference: https://stackoverflow.com/a/22288895/282155

While exploring nearest neighbors, have seen many words which seem to be invalid words. ``` import fasttext model = fasttext.load_model('./BioSentVec/models/BioWordVec_PubMed_MIMICIII_d200.bin') model.get_nearest_neighbors('kidney', 30) ``` This gives the following output: ``` [(0.9160109162330627,...

JPype1 has released version 0.7 as mentioned in https://github.com/jpype-project/jpype/releases For the issue: https://github.com/ncbi-nlp/NegBio/issues/27 it was [mentioned](https://github.com/jpype-project/jpype/issues/395#issuecomment-502723967) that JPype1 version: 0.7 would resolve the issue I tried testing(in usual way by...

Detecting negation for one CUI but failing to detect negation for other CUIs

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Environment: Using MetaMap 2016v2 Sentence: > There is no spinal canal hematoma. Among other CUIs, these are the ones I am focusing on: ``` Hematoma patf C0018944 MetaMap hematoma spinal...

--chemdnersldi option not available

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./metamaplite.sh --chemdnersldi input_file.txt This returns > unknown option: --chemdnersldi Content of input_file.txt 1|'Heart Attack' 2|'John had a huge heart attack' **Update**: After going through the source code: https://github.com/lhncbc/metamaplite/blob/master/src/main/java/gov/nih/nlm/nls/ner/MetaMapLite.java found that...

For the input file: [00000086.txt](https://github.com/ncbi-nlp/NegBio/blob/master/examples/00000086.txt) In MetaMap, the outputs used to come like these: '00000086-0'|MMI|17.80|Mediastinum|C0025066|[blor]|["MEDIASTINUM"-tx-2-"mediastinum"-noun-0]|TX|50/11|A01.923.761.800.500 '00000086-73'|MMI|8.34|Lung|C0024109|[bpoc]|["LUNGS"-tx-1-"lungs"-noun-0]|TX|1/5|A04.411 But the output in MetaMapLite comes like these: 00000000.tx|MMI|2.37|Mediastinum|C0025066|[blor]|"Mediastinum"-text-0-"mediastinum"-NN-0|63/11|A01.923.761.800.500 00000000.tx|MMI|0.98|Lung|C0024109|[bpoc]|"Lungs"-text-0-"lungs"-NNS-0|103/5|A04.411 The first field in...

"Location" field was provided in MetaMap (mmi output). But this seems to be missing in MetaMapLite. Any plans to introduce that to make it consistent with MetaMap? I was facing...

In README.md: For MetaMapLite 3.6.1p1 (with Category 0+4+9 (USAbase) 2017AA UMLS dataset), it should be --indexdir=public_mm_lite/data/ivf/2017AA/USAbase/strict

TypeError: sequence index must be integer, not 'slice'

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Environment: > OS: Windows 7 > RunSnakeRun 2.0.5 > Python 2.7.15 :: Anaconda, Inc. I had followed the example to dump profile output as mentioned in https://kupczynski.info/2015/01/16/profiling-python-scripts.html ``` import multiprocessing...

https://six.readthedocs.io/#module-six.moves (**Renamed modules and attributes compatibility**) `range` in `six.moves` refers to [xrange](https://docs.python.org/2/library/functions.html#xrange) in python 2 and [range](https://docs.python.org/3.3/library/stdtypes.html?highlight=range#ranges) in python 3 In my opinion, `range(self.GetColumnCount())[::-1]` is not a proper usage. Though...