Saturday, April 28, 2007

PRESENT TEXT MINING FOCUS ON ENTITIES

Named Entity Recognizer:

The present day text mining tools aims in identifying the named entity within a collection of text. For e.g. all the drug names within a group of articles. The goal is to identify, within a collection of text, all of the instances of a name for a specific type of thing: for example, the entire set of drug names within a collection of journal articles, or all of the gene names and symbols within a collection of abstracts.

The idea behind this is that by recognizing biological entities within a group of articles allows further extraction of relationship and other information by identifying the key concept of interest; by doing so they can be represented in a normalized form. This has however been challenging due to several reasons.

Since there is no complete dictionary for most type of biological entities so simple text matching algorithms do not suffice, apart from this some phrases can refer to two different things depending on the context. A known fact is that biological entities have more than a single name. To top up this is that many biological entities have several multi-words; which complicates the process for defining name boundaries that would overlap the candidate gene.


Text Classification

Text classification attempts to automatically determine whether a document or part of a document has particular characteristics of interest, usually based on whether the document discusses a given topic or contains a certain type of information. Typically the information of interest is not specified explicitly by the users and, instead, they provide a set of documents that have been found to contain the characteristics of interest (the positive training set), and another set that does not (the negative training set). Text classification systems must automatically extract the features that help determine positives from negatives and apply those features to candidate documents using some kind of decision-making process. Accurate text classification systems can be especially valuable to database curators, who may have to review many documents to find a few that contain the kind of information they are collecting in their database. Because more biomedical information is being created in text form then ever before, and because there are more ongoing database curation efforts to organise this information into coded databases than before, there is a strong need to find useful ways to apply text classification methods to biomedical text.

Synonym And Abbreviation

There has been a tremendous growth seen in the biological terminologies seen accompanied with the increase in biological literature. Complicating this is that many biological entities have multiple names and abbreviation. By including these synonyms and abbreviations in the search would result in higher efficiency of the text mining tool. This is one area which has been developed recently, and improvements are being made. One such would be by collecting these synonyms and abbreviation to aid the user to perform literature searches.

Relationship Extraction

This helps in detecting specific relationship between a pair of named entities or more. Though the entities are related and specific, the relationship established between the two might be either very specific or general. Depending on the type of entity; the extraction of relationship between them is found on text. This helps to uncover the preciously unrecognized relationship between the two entities.

Natural Language Processing (NLP) For Text Mining

The field of Natural Language Processing is concerned with the analysis of free textual information and has been applied recently in the context of molecular biology. Text-mining approaches involve analyzing and extracting information from large collections of free textual data by using automatic or semiautomatic systems. Currently, text-mining applications are being employed in the identification of biological entities such as protein or gene names, automated protein annotation, analysis of microarrays and extraction of protein–protein interactions. In general, text-mining applications take advantage of a range of domain-independent methods such as part-of speech (POS) taggers, which label each word with its corresponding part of speech (e.g. noun, verb or adjective), or stemmers, which are algorithms that return the morphological root of a word form. Also, domain-specific tools and resources such as protein taggers and ontologies are employed.

Tuesday, April 3, 2007

Schizophrenia

Schizophrenia is often described in terms of "positive" and "negative" symptoms. Positive symptoms include delusions, auditory hallucinations and thought disorder and are typically regarded as manifestations of psychosis. Negative symptoms are so named because they are considered to be the loss or absence of normal traits or abilities, and include features such as flat, blunted or constricted affect and emotion, poverty of speech and lack of motivation. Additionally, a 'disorganization syndrome' and neurocognitive deficits may be present. These may take the form of reduced or impaired psychological functions such as memory, attention, problem-solving, executive function or social cognition.

Onset of schizophrenia typically occurs in late adolescence or early adulthood, with males tending to show symptoms earlier than females.

In 1893 psychiatrist Emil Kraepelin was the first to draw a distinction between what he termed dementia praecox ("premature dementia") and other psychotic illnesses. In 1908, "dementia praecox" was renamed "schizophrenia" by psychiatrist Eugen Bleuler, who discovered that the disorder is not a form of dementia.

The diagnostic category of schizophrenia has been widely criticised as lacking in scientific validity or reliability, consistent with evidence of poor levels of consistency in diagnostic practices and the use of criteria. One alternative suggests that the problems and issues making up the diagnosis of schizophrenia would be better addressed as individual dimensions along which everyone varies, such that there is a spectrum or continuum rather than a cut-off between normal and ill. This approach appears consistent with research on schizotypy and of a relatively high prevalence of psychotic experiences and delusional beliefs amongst the general public.

Although no common cause of schizophrenia has been identified in all individuals diagnosed with the condition, currently most researchers and clinicians believe it results from a combination of both brain vulnerabilities (either inherited or acquired) and stressful life-events. This widely-adopted approach is known as the 'stress-vulnerability' model, and much scientific debate now focuses on how much each of these factors contributes to the development and maintenance of schizophrenia.

It is also thought that processes in early neurodevelopment are important, particularly prenatal processes. In adult life, particular importance has been placed upon the function (or malfunction) of dopamine in the mesolimbic pathway in the brain. This theory, known as the dopamine hypothesis of schizophrenia largely resulted from the accidental finding that a drug group which blocks dopamine function, known as the phenothiazines, reduced psychotic symptoms. However, this theory is now thought to be overly simplistic as a complete explanation. These drugs have now been developed further and antipsychotic medication is commonly used as a first-line treatment. Although effective in many cases, these medications are not well tolerated by some patients due to significant side-effects. The positive symptoms are more responsive to medications; negative symptoms being less so.

Differences in brain structure have been found between people with schizophrenia and those without. However, these tend only to be reliable on the group level and, due to the significant variability between individuals, may not be reliably present in any particular individual. Significant brain atrophy and enlarged ventricles are the most conspicuous of such differences.

Causes

The causes of schizophrenia are not known. However, an interplay of genetic, biological, environmental, and psychological factors are thought to be involved. We do not yet understand all the causes and other issues involved, but current research is making steady progress towards elucidating and defining causes of schizophrenia.

In biological models of schizophrenia, genetic (familial) predisposition, infectious agents, allergies, and disturbances in metabolism have all been investigated.

Schizophrenia is known to run in families. Thus, the risk of illness in an identical twin of a person with schizophrenia is 40-50%. A child of a parent suffering from schizophrenia has a 10% chance of developing the illness. The risk of schizophrenia in the general population is about 1%.

The current concept is that multiple genes are involved in the development of schizophrenia and that factors such as prenatal (intrauterine), perinatal, and nonspecific stressors are involved in creating a disposition or vulnerability to develop the illness. Neurotransmitters (chemicals allowing the communication between nerve cells) have also been implicated in the development of schizophrenia. The list of neurotransmitters under scrutiny is long, but special attention has been given to dopamine, serotonin, and glutamate.

Also, recent studies have identified subtle changes in brain structure and function, indicating that, at least in part, schizophrenia could be a disorder of the development of the brain.

It is important for doctors to investigate all reasonable medical causes for any acute change in someone’s mental health or behavior. Sometimes a medical condition that might be treated easily, if diagnosed, is responsible for symptoms that resemble those of schizophrenia.


Symptoms

Usually with schizophrenia, the person's inner world and behavior change notably. Behavior changes might include the following:

  • Social withdrawal

  • Depersonalization (intense anxiety and a feeling of being unreal)

  • Loss of appetite

  • Loss of hygiene

  • Delusions

  • Hallucinations (eg, hearing things not actually present)

  • The sense of being controlled by outside forces

A person with schizophrenia may not have any outward appearance of being ill. In other cases, the illness may be more apparent, causing bizarre behaviors. For example, a person with schizophrenia may wear aluminum foil in the belief that it will stop one's thoughts from being broadcasted and protect against malicious waves entering the brain.

People with schizophrenia vary widely in their behavior as they struggle with an illness beyond their control. In active stages, those affected may ramble in illogical sentences or react with uncontrolled anger or violence to a perceived threat. People with schizophrenia may also experience relatively passive phases of the illness in which they seem to lack personality, movement, and emotion (also called a flat affect). People with schizophrenia may alternate in these extremes. Their behavior may or may not be predictable.

In order to better understand schizophrenia, the concept of clusters of symptoms is often used. Thus, people with schizophrenia can experience symptoms that may be grouped under the following categories:

  • Positive symptoms - Hearing voices, suspiciousness, feeling under constant surveillance, delusions, or making up words without a meaning (neologisms).

  • Negative (or deficit) symptoms - Social withdrawal, difficulty in expressing emotions (in extreme cases called blunted affect), difficulty in taking care of themselves, inability to feel pleasure (These symptoms cause severe impairment and are often mistaken for laziness.)

  • Cognitive symptoms - Difficulties attending to and processing of information, in understanding the environment, and in remembering simple tasks

  • Affective (or mood) symptoms - Most notably depression, accounting for a very high rate of attempted suicide in people suffering from schizophrenia

Helpful definitions in understanding schizophrenia include the following:

  • Psychosis: Psychosis is defined as being out of touch with reality. During this phase, one can experience delusions or prominent hallucinations. People with psychoses are not aware that what they are experiencing or some of the things that they believe are not real. Psychosis is a prominent feature of schizophrenia but is not unique to this illness.

  • Schizoid: This term is often used to describe a personality disorder characterized by almost complete lack of interest in social relationships and a restricted range of expression of emotions in interpersonal settings, making a person with this disorder appear cold and aloof.

  • Schizotypal: This term defines a more severe personality disorder characterized by acute discomfort with close relationships as well as disturbances of perception and bizarre behaviors, making people with schizophrenia seem odd and eccentric because of unusual mannerisms.

  • Hallucinations: A person with schizophrenia may have strong sensations of objects or events that are real only to him or her. These may be in the form of things that they believe strongly that they see, hear, smell, taste, or touch. Hallucinations have no outside source, and are sometimes described as "the person's mind playing tricks" on him or her.

  • Illusion: An illusion is a mistaken perception for which there is an actual external stimulus. For example, a visual illusion might be seeing a shadow and misinterpreting it as a person. The words "illusion" and "hallucination" are sometimes confused with each other.

  • Delusion: A person with a delusion has a strong belief about something despite evidence that the belief is false. For instance, a person may listen to a radio and believe the radio is giving a coded message about an impending extraterrestrial invasion. All of the other people who listen to the same radio program would hear, for example, a feature story about road repair work taking place in the area.

Types of schizophrenia are as follows:

  • Paranoid-type schizophrenia is characterized by delusions and auditory hallucinations but relatively normal intellectual functioning and expression of affect. The delusions can often be about being persecuted unfairly or being some other person who is famous. People with paranoid-type schizophrenia can exhibit anger, aloofness, anxiety, and argumentativeness.

  • Disorganized-type schizophrenia is characterized by speech and behavior that are disorganized or difficult to understand, and flattening or inappropriate emotions. People with disorganized-type schizophrenia may laugh at the changing color of a traffic light or at something not closely related to what they are saying or doing. Their disorganized behavior may disrupt normal activities, such as showering, dressing, and preparing meals.

  • Catatonic-type schizophrenia is characterized by disturbances of movement. People with catatonic-type schizophrenia may keep themselves completely immobile or move all over the place. They may not say anything for hours, or they may repeat anything you say or do senselessly. Either way, the behavior is putting these people at high risk because it impairs their ability to take care of themselves.

  • Undifferentiated-type schizophrenia is characterized by some symptoms seen in all of the above types but not enough of any one of them to define it as another particular type of schizophrenia.

  • Residual-type schizophrenia is characterized by a past history of at least one episode of schizophrenia, but the person currently has no positive symptoms (delusions, hallucinations, disorganized speech or behavior). It may represent a transition between a full-blown episode and complete remission, or it may continue for years without any further psychotic episodes.