I would like to make a comparison of clustering (heatmap) with the annotation of the genes differently expressed like this :
enter image description here
This picture is from an paper and they used Blast2go to do it. i wish to have free tools or r package or simple tutorials to do it. i have a list of gene as dataset obtained from Deseq2.
your ideas will be a great help to me.
Related
I'm a newbie to NLP and I'm working on NER using OpenNLP. I have a sentence like " We have a dinner party today ". Here "dinner party" is an event type. Similarly consider this sentence- "we have a room reservation" here room reservation is an event type. My goal is to extract such words from sentences and label it as "Event_types" as the final output. This can be fairly achieved by creating custom NER model's by annotating sentences with proper tags in the training dataset. But the event types can be heterogeneous and random and hence it is very hard to label all possible patterns(ie. event types can be anything like "security meeting", "family function","parents teachers meeting", etc,etc,...). So I'm looking for an alternate way to achieve this problem... Immediate response would be appreciated. Thanks ! :)
Basically you have two options: 1) A list-based approach where you have lists of entities you will extract from text. To solve the heterogeneous language use, one can train an embedding (e.g. Word2Vec or FastText) to identify contextually similar phrases for your list. 2) Train a custom CRF with data you have annotated (this obviously requires that you annotate bunch of sentences with corresponding tags). I guess the ideal solution really depends on the data and people's willingness to annotate it.
I have been searching how to create a new entity in google natural language API, and found nothing. Can anybody help how to create a new classifier such that if I pass a sentence and I want to detect suppose 'python' as programming language then how would I get that. Current the API is giving 'python' as 'other'.
I have also looked into cloud auto ml api for my solution and tried to create and train a model but It was only able to do sentiment analysis not entity detection.It was giving me the score rather than telling me that Java is programming language.
Thanks in advance.Your help will be appreciated.
Automl content classification classifies your data into the labels specified in the training set. It does not do entity detection. But it seems like what you need to do is closer to content classification than entity detection. My understanding from the description you provided is that you have content (may be words or phrases or short sentences) and you want to classify them into some labels (e.g. programmingLanguage). If you put together a good training set, the automl model should be able to do this.
The number it provides in eval is not sentiment, it's the probability of the predicted label. As you can see in the eval page you posted, it's telling you that java is a programmingLanguage with probability of 1 (so, it's very certain about it).
I'm really stuck right now. I want to apply LIBSVM for Image Classification. I captured lots of Training-Images (BITMAP-Format), from which I want to extract features.
The Training-Images contain people who are lying on the floor. The classifier should decide if there is a person lying on the floor or not in the given Image.
I read lots of papers, documentary, guides and tutorials, but in none of them is documented how to get a LIBSVM-Package. The only thing that is described is how to convert a LIBSVM-Package from a CSV-File like this one: CSV-File. On the LIBSVM-Website several Example-Data can be downloaded. The Example-Data is either prepared as CSV-Files or as ready-to-use Training- and Testdata.
If you look at the Values which are in the CSV-File, the first column are the labels (lying person or not) and the other Values are the extracted features, but I still can't reconstruct how those values are achieved.
I don't know if it's that simple that nobody has to mention it, but I just can't get trough it, so if anybody knows how to perform the feature extraction from Images, please help me.
Thank you in advance,
Regards
You need to do feature extraction first. There are many methods that are available. These include LBP,Gabor and many more.. These methods will help you get the features to input into libsvm..Hope this helps...
I have tags on my website, and I input them one by one when I create a blog post. I love gmail's new feature, that ask you if you want to include X in a mail, if you type Y's name and that you often include both of them in the same messages.
I'd like to do something similar on my website, but I don't know how to represent the tags "related-ness" in an object or database ... thoughts ?
It all boils down to create associations between certain characteristics of your posts and certain tags, and then - when you press the "publish" button - to analyse the new post and propose all tags matched with your post characteristics.
This can be done in several ways from a "totally hard-coded" association to some sort of "learning AI"... and everything in-between.
Hard-coded solutions
This are the simplest algorithms to implement. You should first decide what characteristics of your post are relevant for tagging (e.g.: it's length if you tag them "short" or "long", the presence of photos or videos if you tag them "multimedia-content", etc...). The most obvious is however to focus on which words are used in posts. For example you could build a mapping like this:
tag_hint_words = {'code-development' : ['programming',
'language', 'python', 'function',
'object', 'method'],
'family' : ['Theresa', 'kids',
'uncle Ben', 'holidays']}
Then you would check your post for the presence of the words in the list (the code between [ and ] ) and propose the tag (the word before :) as a possible candidate.
A common approach is to give "scores", or in other word to put a number that indicates the probability a given tag is the right one. For example: if your post would contain the sentence...
After months of programming, we finally left for the summer holidays at uncle Ben's cottage. Theresa and the kids were ecstatic!
...despite the presence of the word "programming" the program should indicate family as the most likely tag to use, as there are many more words hinting.
Learning AI's
One of the obvious limitations of the above method is that - say one day you pick up java beside python - you would probably need to change your code and include words like "java" or "oracle" too. The same applies if you create new tags.
To circumvent this limitation (and have some fun!!) you could try to implement a learning algorithm. Learning algorithms are those who refine their outcome the more you use them (so they indeed... learn!). Some algorithm requires initial training (many spam filters and voice recognition programs need this initial "primer"). Some don't.
I am absolutely no expert on the subject, but two common AI's are: the Naive Bayes Classifier and some flavour of Neural network.
Although the WP pages might look scary, they are surprisingly easy to implement (at least in Python). Here's the recording of a lecture at PyCon 2009 on the subject "Easy AI with Python". I found it very informative and even somehow inspiring! :)
HTH!
You should have a look at this post :
Any suggestions for a db schema for storing related keywords?
If you're looking for a schema for storing related tags it will help.
Relevancy searches where multiple agents play a part are usually done using Collaborative filtering. You might want to give that a look see.
Look up Clustering (Machine Learning algorithm). Don't be intimidated by math, it's a pretty straightforward algorithm. Check out Machine Learning for Hackers for simpler explanations of many Machine Learning algorithms and methods.
I am trying to get user input from matplotlib XY plot. The plot contains multiple datasets and I need get from user selection of which dataset to use and the range. I need this to fit model to right dataset and range.
Therefore I need two indicators, which would be "attached" to specific dataset, per user choosing. I need to get from them both the dataset info and the range info.
Somehow in line with what commercial plotting packages (Igor Pro, Kaleidagraph, Sigmaplot...) provide as "cursors" and similarly named widgets for control of their fitting interface, which is what I am trying to reproduce.
I have checked various examples with rangeselector and other methods I was able to Google on the web, but none I was able to find seems to be able to provide what I need.
Would anyone have any pointers to where to look or what to start with, please?
You might want to look at this example: http://matplotlib.sourceforge.net/examples/pylab_examples/ginput_manual_clabel.html
The interesting functions are ginput, waitforbuttonpress.