User:Ian Helmke/Sandbox: Difference between revisions
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= Machine Learning Additions = | |||
This is text I'd like to add to the [[machine learning]] page (pending heavy editing). This text would go underneath the "Issues in Training and Evaluation" section. | This is text I'd like to add to the [[machine learning]] page (pending | ||
heavy editing). This text would go underneath the "Issues in Training | |||
and Evaluation" section. | |||
== Overfitting == | == Overfitting == | ||
Overfitting occurs when a classifier | Overfitting occurs in classifiers when a classifier creates an extremely accurate [[model_(machine learning)|model]] for classifying the example data used to crate the model, yet is inaccurate on other examples. | ||
This can sometimes occur because a classifier looks at irrelevant data | This can sometimes occur because a classifier looks at irrelevant data | ||
points in the training data. Classifiers often give more weight to | points in the training data. Classifiers often give more weight to | ||
features seen less commonly in the training data, and if data given to | [[feature_(vector)|features]] seen less commonly in the training data, and if data given to | ||
the classifier shares similar uncommon values, it | the classifier shares similar uncommon values, it groups those values | ||
accordingly. | accordingly. As a result, the classifier is extremely accurate when | ||
classifying the training data and appears to be useful, but when used | |||
to organize data outside of the model, it becomes inaccurate. | |||
Machine learning techniques can prevent overfitting | Machine learning techniques can prevent overfitting by | ||
imposing a [[penalty_(machine learning)|penalty]] upon itself for complicated models. A | |||
more consistent with the data in question. | simpler model is oftentimes more consistent with the trends of the | ||
data in question. | |||
== Imbalance of Data == | == Imbalance of Data == | ||
Data within training sets can be imbalanced, where the training set | |||
has more examples of one category of data than another. Many | |||
classifying algorithms assume that the ratio of the different | |||
categories of training data that they receive are roughly equivalent | |||
to the ratio of real data that will belong in each category. | |||
that the ratio of the different categories of training data that they | |||
receive are roughly equivalent to the ratio of real data that will | |||
belong in each category. | |||
One way to prevent this imbalance of data is to use | There may also be characteristics that differentiate members of the | ||
active example selection. Active example selection builds the | minority class that are missed when data is imbalanced. For example, | ||
classifier model slowly, adding a few pieces of sample data of each | a classifier training on examples of cancer patients may fail to | ||
class at a time. The model is tested at every stage, and documents | differentiate between different types of cancer in the minority | ||
which improve the accuracy of the model are kept in the classifier, | class<ref name="ensemble"> | ||
while ones that do not change the model or make its performance worse | {{cite journal | ||
are removed. This ensures that only meaningful pieces of data are used | |author=Sangyoon, Oh et al. | ||
|title=Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification | |||
|journal=IEEE/ACM Trans. Comput. Biol. Bioinformatics | |||
|publisher=IEEE Computer Society Press | |||
|year=2011 | |||
|id=http://dx.doi.org/10.1109/TCBB.2010.96}}</ref>. | |||
One way to prevent this imbalance of data is to use | |||
[[active example selection]]<ref name="ensemble" />. Active example | |||
selection builds the classifier model slowly, adding a few pieces of | |||
sample data of each class at a time. The model is tested at every | |||
stage, and documents which improve the accuracy of the model are kept | |||
in the classifier, while ones that do not change the model or make its | |||
performance worse are removed. This ensures that only meaningful | |||
pieces of data are used to train the classifier, and since the ratio | |||
of documents is closer to 1:1, an imbalance of data is less of an | |||
issue. | |||
== Evaluating Results == | == Evaluating Results == | ||
There are a number of techniques for evaluating the results of a | There are a number of techniques for evaluating the results of a | ||
machine learning algorithm. Some of these techniques are also used in | machine learning [[algorithm]]. Some of these techniques are also used in | ||
natural | [[computational linguistics|natural language processing]]. Machine learning techniques are generally | ||
evaluated by their results, and some methods (such as neural networks) | evaluated by their results, and some methods (such as [[neural networks]]) | ||
are considered "black box" forms of classification, since it is not | are considered "black box" forms of classification, since it is not | ||
easy to understand how or why the underlying implementation is sorting | easy to understand how or why the underlying implementation is sorting | ||
a particular way. | |||
In some cases, particularly with classifiers, the outcome of the | In some cases, particularly with classifiers, the outcome of the | ||
machine learning algorithm is compared to a set of data classified by | machine learning algorithm is compared to a set of data classified by | ||
experts. | experts. The machine learning algorithm creates a model based on a set | ||
of training data, and | of training data, and classifies a second sample set of data. A | ||
experts also annotate | group of experts also annotate the second set of data, marking it | ||
they believe it should be classified (not according to how they | according to how they believe it should be classified (not according | ||
believe a machine would classify it). | to how they believe a machine would classify it). The training and | ||
data is generally a tiny subset of the data available | evaluation data is generally a tiny subset of the data available. | ||
The results of the algorithm are compared to the results of the | The results of the algorithm are compared to the results of the | ||
experts and arranged into two scores: precision and recall. Precision | experts and arranged into two scores: [[precision]] and [[recall]]. Precision | ||
accounts for situations where the classifier put something in a | accounts for situations where the classifier put something in a | ||
category where it did not belong. Recall accounts for situations where | category where it did not belong. Recall accounts for situations where | ||
the classifier did not put something in a category it should have. | the classifier did not put something in a category it should have. | ||
If a classifier is able to produce good results for a subset of data, it | |||
should also be successful at classifying a larger set of similar data. | |||
Classification and clustering algorithms can also be measured against | Classification and clustering algorithms can also be measured against | ||
| Line 77: | Line 91: | ||
== Scalability == | == Scalability == | ||
Modern computers have the ability to [[multitask]] exceptionally | |||
computers | well through the use of multiple cores or [[CPU]]s. Machine learning | ||
well through the use of multiple cores or | algorithms are often used to process large quantities | ||
of data, and optimizing them for multiple CPUs greatly | |||
improves their performance. | |||
= Biclustering = | = Biclustering = | ||
The following material would go on a new page of the above title (probably linked to the ML page) | ''The following material would go on a new page of the above title | ||
(probably linked to the ML page)'' | |||
Biclustering is an unsupervised [[machine learning]] method which searches | '''Biclustering''' is an unsupervised [[machine learning]] method | ||
for | which searches for similarities in specific subsections of the input | ||
machine learning methods because it searches for similarities in | data. Biclustering is unique among machine learning methods because it searches | ||
parts of the data, instead of putting a piece of data into a single | for similarities in small parts of the data, instead of putting a | ||
group. | piece of data into a single group. | ||
Biclustering was first discovered in 1970. | Biclustering was first discovered in 1970. As of 2011, it is a commonly | ||
used technique in bioinformatics, | used technique in [[bioinformatics]], particularly in the area of | ||
expression, or identifying groups of genes that are similar between | [[gene expression]], or identifying groups of [[genes]] that are similar between | ||
different people. | different people. | ||
== Processing == | == Processing == | ||
Clustering algorithms take vectors as input. They sort the vectors | Clustering algorithms take [[vector|vectors]] as input. They sort the | ||
according to how similar they are by comparing all of the | vectors according to how similar they are by comparing all of the | ||
the vector, | [[feature_(vector)|features]] in the vector, creating | ||
each contain a bunch of (hopefully) similar vectors. Biclustering | several groups that each contain a bunch of (hopefully) similar | ||
looks at all of the vectors as a single input matrix, and attempts to | vectors. Biclustering looks at all of the vectors as a single input | ||
find regions of the input which look similar. | matrix, and attempts to find regions of the input which look similar. | ||
Biclustering is a useful technique for finding trends in data when | Biclustering is a useful technique for finding trends in data when | ||
each vector of data is | each vector of data is large because it can spot trends in | ||
specific parts of data that clustering cannot. A normal clustering | specific parts of data that clustering cannot. A normal clustering | ||
algorithm sorts pieces of data according to features that the majority | algorithm sorts pieces of data according to features that the majority | ||
of them share. Biclustering | of them share. Biclustering organizes data according to | ||
parts of them that seem similar. | parts of them that seem similar. | ||
| Line 122: | Line 133: | ||
Biclustering is particularly useful in the medical field, where it can | Biclustering is particularly useful in the medical field, where it can | ||
be used, for example, to find genes related to a specific disease in a | be used, for example, to find genes related to a specific disease in a | ||
group of patients. If each vector represents how a person expresses | group of patients<ref> | ||
{{cite journal | |||
|author=Still, Martin et al. | |||
|title=Robust biclustering by sparse singular value decomposition incorporating stability selection | |||
|publisher=Oxford University Press | |||
|journal=Bioinformatics | |||
|year=2011 | |||
|id=http://dx.doi.org/10.1093/bioinformatics/btr322}}</ref>. | |||
If each vector represents how a person expresses | |||
traits, biclustering can be used to determine a set of genes which is | traits, biclustering can be used to determine a set of genes which is | ||
associated with cancer. It can even be used to find similarities and | associated with cancer. It can even be used to find similarities and | ||
differences between different varieties of cancers. | differences between different varieties of cancers. | ||
== References == | |||
<references /> | |||
Latest revision as of 02:58, 22 November 2023
The account of this former contributor was not re-activated after the server upgrade of March 2022.
Machine Learning Additions
This is text I'd like to add to the machine learning page (pending heavy editing). This text would go underneath the "Issues in Training and Evaluation" section.
Overfitting
Overfitting occurs in classifiers when a classifier creates an extremely accurate model for classifying the example data used to crate the model, yet is inaccurate on other examples.
This can sometimes occur because a classifier looks at irrelevant data points in the training data. Classifiers often give more weight to features seen less commonly in the training data, and if data given to the classifier shares similar uncommon values, it groups those values accordingly. As a result, the classifier is extremely accurate when classifying the training data and appears to be useful, but when used to organize data outside of the model, it becomes inaccurate.
Machine learning techniques can prevent overfitting by imposing a penalty upon itself for complicated models. A simpler model is oftentimes more consistent with the trends of the data in question.
Imbalance of Data
Data within training sets can be imbalanced, where the training set has more examples of one category of data than another. Many classifying algorithms assume that the ratio of the different categories of training data that they receive are roughly equivalent to the ratio of real data that will belong in each category.
There may also be characteristics that differentiate members of the minority class that are missed when data is imbalanced. For example, a classifier training on examples of cancer patients may fail to differentiate between different types of cancer in the minority class[1].
One way to prevent this imbalance of data is to use active example selection[1]. Active example selection builds the classifier model slowly, adding a few pieces of sample data of each class at a time. The model is tested at every stage, and documents which improve the accuracy of the model are kept in the classifier, while ones that do not change the model or make its performance worse are removed. This ensures that only meaningful pieces of data are used to train the classifier, and since the ratio of documents is closer to 1:1, an imbalance of data is less of an issue.
Evaluating Results
There are a number of techniques for evaluating the results of a machine learning algorithm. Some of these techniques are also used in natural language processing. Machine learning techniques are generally evaluated by their results, and some methods (such as neural networks) are considered "black box" forms of classification, since it is not easy to understand how or why the underlying implementation is sorting a particular way.
In some cases, particularly with classifiers, the outcome of the machine learning algorithm is compared to a set of data classified by experts. The machine learning algorithm creates a model based on a set of training data, and classifies a second sample set of data. A group of experts also annotate the second set of data, marking it according to how they believe it should be classified (not according to how they believe a machine would classify it). The training and evaluation data is generally a tiny subset of the data available. The results of the algorithm are compared to the results of the experts and arranged into two scores: precision and recall. Precision accounts for situations where the classifier put something in a category where it did not belong. Recall accounts for situations where the classifier did not put something in a category it should have. If a classifier is able to produce good results for a subset of data, it should also be successful at classifying a larger set of similar data.
Classification and clustering algorithms can also be measured against other algorithms. This is useful when an algorithm is attempting to improve performance (speedwise, for example) while providing similar levels of precision and recall relative to another algorithm. It can also be used to show that an algorithm is an improvement over a previous generation, or to show which algorithm is most useful for organizing data for a particular problem.
Scalability
Modern computers have the ability to multitask exceptionally well through the use of multiple cores or CPUs. Machine learning algorithms are often used to process large quantities of data, and optimizing them for multiple CPUs greatly improves their performance.
Biclustering
The following material would go on a new page of the above title (probably linked to the ML page)
Biclustering is an unsupervised machine learning method which searches for similarities in specific subsections of the input data. Biclustering is unique among machine learning methods because it searches for similarities in small parts of the data, instead of putting a piece of data into a single group.
Biclustering was first discovered in 1970. As of 2011, it is a commonly used technique in bioinformatics, particularly in the area of gene expression, or identifying groups of genes that are similar between different people.
Processing
Clustering algorithms take vectors as input. They sort the vectors according to how similar they are by comparing all of the features in the vector, creating several groups that each contain a bunch of (hopefully) similar vectors. Biclustering looks at all of the vectors as a single input matrix, and attempts to find regions of the input which look similar.
Biclustering is a useful technique for finding trends in data when each vector of data is large because it can spot trends in specific parts of data that clustering cannot. A normal clustering algorithm sorts pieces of data according to features that the majority of them share. Biclustering organizes data according to parts of them that seem similar.
Applications
Biclustering is particularly useful in the medical field, where it can be used, for example, to find genes related to a specific disease in a group of patients[2]. If each vector represents how a person expresses traits, biclustering can be used to determine a set of genes which is associated with cancer. It can even be used to find similarities and differences between different varieties of cancers.
References
- ↑ 1.0 1.1 Sangyoon, Oh et al. (2011). "Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification". IEEE/ACM Trans. Comput. Biol. Bioinformatics. http://dx.doi.org/10.1109/TCBB.2010.96.
- ↑ Still, Martin et al. (2011). "Robust biclustering by sparse singular value decomposition incorporating stability selection". Bioinformatics. http://dx.doi.org/10.1093/bioinformatics/btr322.