I have a cancer patients data from mass spectrometry which consists of more than half million features and my task is to apply feature selection algorithm to extract the most relevant features from it. My question is which feature selection model would me more appropriate in this case... Any suggestions will be more appreciated...
Use a support vector machine, a type of machine learning model. Perhaps Python and Tensorflow would be useful here!
All the best,
OL
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I'm now in the middle of the semester and trying to understand the background of the algorithms and features.
I would like to understand some theory.
If I have a dataset with N samples.
each sample has 5 features for example.
I have done 3 kinds of classifications algorithms for example : SVM, decision tree and kMeans.
In all 3, I got nice results
In a mystery way, a new feature added to the dataset. The value of the features for every sample selected randomly.
I restarted the algorithms on the dataset ( with the new feature)
Are the classification results gonna change from the first results without the new feature? If yes, why are they gonna change and by how much ?
In addition, if I do not have the dataset how can I know how to recognize that new feature?
The results of your classification algorithm are going to either change or stay the same depending on how much information the model gains from the feature. If the feature for instance is random noise then it will have little to no effect on your model, other than slowing it down. If it contains useful information it might be able to increase parameters such as recall and precision. Hope this might help.
I've been currently working on my FYP on Brain tumor classification.Extracted features using wavelet transform ,glcm ,polynomial transform etc.
IS IT RIGHT TO APPEND THESE FEATURE VECTORS (columnwise) for training? like combinations of these feature vectors eg: glcm+wavelet
Can you suggest me any papers related to this?
THANK YOU FOR THE HELP
Yes, this method is known as early fusion.
In other words, early fusion is when you are concatenating 2 or more features sets prior to model training.
There are a number of other methods for feature fusion, including model-, and late-fusion.
Take a look at these papers which might help you:
Specific to a health-based application
figure which might help you to grasp the concept
I am building a model that will predict the lead time of products flowing through a pipeline.
I have a lot of different features, one is a string containing a few words about the purpose of the product (often abbreviations, name of the application it will be a part of and so forth). I have previously not used this field at all when doing feature engineering.
I was thinking that it would be nice to do some type of clustering on this data, and then use the cluster ID as a feature for my model, perhaps the lead time is correlated with the type of info present in that field.
Here was my line of thinking)
1) Cleaning & tokenizing text.
2) TF-IDF
3) Clustering
But after thinking more about it, is it a bad idea? Because the clustering was based on the old data, if new words are introduced in the new data this will not be captured by the clustering algorithm, and the data should perhaps be clustered differently now. Does this mean that I would have to retrain the entire model (k-means model and then the supervised model) whenever I want to predict new data points? Are there any best practices for this?
Are there better ways of finding clusters for text data to use as features in a supervised model?
I understand the urge to use an unsupervised clustering algorithm first to see for yourself, which clusters were found. And of course you can try if such a way helps your task.
But as you have labeled data, you can pass the product description without an intermediate clustering. Your supervised algorithm shall then learn for itself if and how this feature helps in your task (of course preprocessing such as removal of stopwords, cleaining, tokenizing and feature extraction needs to be done).
Depending of your text descriptions, I could also imagine that some simple sequence embeddings could work as feature-extraction. An embedding is a vector of for example 300 dimensions, which describes the words in a manner that hp office printer and canon ink jet shall be close to each other but nice leatherbag shall be farer away from the other to phrases. For example fasText-Word-Embeddings are already trained in english. To get a single embedding for a sequence of hp office printerone can take the average-vector of the three vectors (there are more ways to get an embedding for a whole sequence, for example doc2vec).
But in the end you need to run tests to choose your features and methods!
I've got a problem where I've potentially got a huge number of features. Essentially a mountain of data points (for discussion let's say it's in the millions of features). I don't know what data points are useful and what are irrelevant to a given outcome (I guess 1% are relevant and 99% are irrelevant).
I do have the data points and the final outcome (a binary result). I'm interested in reducing the feature set so that I can identify the most useful set of data points to collect to train future classification algorithms.
My current data set is huge, and I can't generate as many training examples with the mountain of data as I could if I were to identify the relevant features, cut down how many data points I collect, and increase the number of training examples. I expect that I would get better classifiers with more training examples given fewer feature data points (while maintaining the relevant ones).
What machine learning algorithms should I focus on to, first,
identify the features that are relevant to the outcome?
From some reading I've done it seems like SVM provides weighting per feature that I can use to identify the most highly scored features. Can anyone confirm this? Expand on the explanation? Or should I be thinking along another line?
Feature weights in a linear model (logistic regression, naive Bayes, etc) can be thought of as measures of importance, provided your features are all on the same scale.
Your model can be combined with a regularizer for learning that penalises certain kinds of feature vectors (essentially folding feature selection into the classification problem). L1 regularized logistic regression sounds like it would be perfect for what you want.
Maybe you can use PCA or Maximum entropy algorithm in order to reduce the data set...
You can go for Chi-Square tests or Entropy depending on your data type. Supervized discretization highly reduces the size of your data in a smart way (take a look into Recursive Minimal Entropy Partitioning algorithm proposed by Fayyad & Irani).
If you work in R, the SIS package has a function that will do this for you.
If you want to do things the hard way, what you want to do is feature screening, a massive preliminary dimension reduction before you do feature selection and model selection from a sane-sized set of features. Figuring out what is the sane-size can be tricky, and I don't have a magic answer for that, but you can prioritize what order you'd want to include the features by
1) for each feature, split the data in two groups by the binary response
2) find the Komogorov-Smirnov statistic comparing the two sets
The features with the highest KS statistic are most useful in modeling.
There's a paper "out there" titled "A selctive overview of feature screening for ultrahigh-dimensional data" by Liu, Zhong, and Li, I'm sure a free copy is floating around the web somewhere.
4 years later I'm now halfway through a PhD in this field and I want to add that the definition of a feature is not always simple. In the case that your features are a single column in your dataset, the answers here apply quite well.
However, take the case of an image being processed by a convolutional neural network, for example, a feature is not one pixel of the input, rather it's much more conceptual than that. Here's a nice discussion for the case of images:
https://medium.com/#ageitgey/machine-learning-is-fun-part-3-deep-learning-and-convolutional-neural-networks-f40359318721
I am new in machine learning. My problem is to make a machine to select a university for the student according to his location and area of interest. i.e it should select the university in the same city as in the address of the student. I am confused in selection of the algorithm can I use Perceptron algorithm for this task.
There are no hard rules as to which machine learning algorithm is the best for which task. Your best bet is to try several and see which one achieves the best results. You can use the Weka toolkit, which implements a lot of different machine learning algorithms. And yes, you can use the perceptron algorithm for your problem -- but that is not to say that you would achieve good results with it.
From your description it sounds like the problem you're trying to solve doesn't really require machine learning. If all you want to do is match a student with the closest university that offers a course in the student's area of interest, you can do this without any learning.
I second the first remark that you probably don't need machine learning if the student has to live in the same area as the university. If you want to use an ML algorithm, maybe it would best to think about what data you would have to start with. The thing that comes to mind is a vector for a university that has certain subjects/areas for each feature. Then compute a distance from a vector which is like an ideal feature vector for the student. Minimize this distance.
The first and formost thing you need is a labeled dataset.
It sounds like the problem could be decomposed into a ML problem however you first need a set of positive and negative examples to train from.
How big is your dataset? What features do you have available? Once you answer these questions you can select an algorithm that bests fits the features of your data.
I would suggest using decision trees for this problem which resembles a set of if else rules. You can just take the location and area of interest of the student as conditions of if and else if statements and then suggest a university for him. Since its a direct mapping of inputs to outputs, rule based solution would work and there is no learning required here.
Maybe you can use a "recommender system"or a clustering approach , you can investigate more deeply the techniques like "collaborative filtering"(recommender system) or k-means(clustering) but again, as some people said, first you need data to learn from, and maybe your problem can be solved without ML.
Well, there is no straightforward and sure-shot answer to this question. The answer depends on many factors like the problem statement and the kind of output you want, type and size of the data, the available computational time, number of features, and observations in the data, to name a few.
Size of the training data
Accuracy and/or Interpretability of the output
Accuracy of a model means that the function predicts a response value for a given observation, which is close to the true response value for that observation. A highly interpretable algorithm (restrictive models like Linear Regression) means that one can easily understand how any individual predictor is associated with the response while the flexible models give higher accuracy at the cost of low interpretability.
Speed or Training time
Higher accuracy typically means higher training time. Also, algorithms require more time to train on large training data. In real-world applications, the choice of algorithm is driven by these two factors predominantly.
Algorithms like Naïve Bayes and Linear and Logistic regression are easy to implement and quick to run. Algorithms like SVM, which involve tuning of parameters, Neural networks with high convergence time, and random forests, need a lot of time to train the data.
Linearity
Many algorithms work on the assumption that classes can be separated by a straight line (or its higher-dimensional analog). Examples include logistic regression and support vector machines. Linear regression algorithms assume that data trends follow a straight line. If the data is linear, then these algorithms perform quite good.
Number of features
The dataset may have a large number of features that may not all be relevant and significant. For a certain type of data, such as genetics or textual, the number of features can be very large compared to the number of data points.