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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Causal Discovery from Medical Textual Data Subramani Mani and Gregory F. Cooper Proceedings of the AMIA annual fall symposium, 2000, pp.542--546. Hanley and Belfus Publishers, Philadelphia, PA. Available at: http://omega.cbmi.upmc.edu/~mani/pub/amia_fs2000.pdf Presentation for the Bayesian Networks Reading Club Marco Valtorta mgv@cse.sc.edu January 28, 2005

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Learning from Textual Data Text is ubiquitous Causal knowledge aids in planning and decision making –Because it supports manipulation Causal relations may represent prior and tacit knowledge Learning from textual data is a new and difficult area of research “[T]he present paper reports the first investigation of causal knowledge discovery from text.”

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Causal BNs A causal BN is a BN in which each arc is interpreted as a direct causal influence between parent and child node Casual (why?) Markov condition: a variable is independent of its non-descendants given its parents Causal (why?) faithfulness condition: variables are independent only if their independence is implied by the causal Markov condition Statistical testing assumption: independence tests on a finite dataset are correct with respect to the underlying causal process that generated the dataset

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering LCD Algorithm Algorithm for finding causal links between pairs of variables Assumes Markov condition, faithfulness condition, and statistical testing assumption, and an additional assumption

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Assumption 4 Given measured variables X,Y, and Z, if Y causes Z, and Y and Z are not confounded (i.e., they do not have a common unmeasured cause), then one of the causal networks below must hold: In case (1), X and Y are independent; in case (2), they are dependent due to X causing Y; and in cases (3) and (4), they are confounded

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Local Causal Discovery Consider three measured variables W,X, and Y. We will model the ways in which each pair can be causally related as in the tables above. The H variables are unmeasured (latent, hidden) variables. There are 96 ways in which W,X, and Y can interact. This is not a complete list, but Cooper argues that very little is lost. Based on: Cooper, Gregory F. “A Simple Constraint-Based Algorithm for Efficiently Mining Observational Databases for Causal Relationships.” Data Mining and Knowledge Discovery 1, 203-224 (1997).

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Three Tests D(W, X) or: Dependent(X,Y) D(X,Y) or: Dependent(Y,Z) I(W,Y|X) or: Independent(X, Z given Y)

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering D-Separation Conditions for the 96 Causal Graphs..................... Graphs 18, 19, and 20 are the only ones for which all three tests D(W,X), D(X,Y), and I(W,Y|X) hold. In each of the three graphs, X causes Y.

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering The three Graphs for Which All Tests Are Positive

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Example: No Causal Link There is no causal link between Y causes Z. Independent (X, Z given Y) fails.

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering LCD Pseudocode

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Extra Test D(W,Y) Dependent(X,Y) Why? Redundancy, if I understand Cooper correctly.

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Limitations of LCD Many causal networks are missed, e.g: LCD only returns separate pairwise causal relationships, which may need to be assembled.

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Time Complexity Not too bad, because only three variables at a time are considered O(mnnr), where m is the number of cases in the database, n is the number of variables, and r is the number of variables such as X (W in Cooper’s paper), i.e., variables that have no cause (“acausal”) –O(mn) if “few” acausal variables and potential effects (like Z, or Y in Cooper’s paper) Space complexity: O(mn), which is the size of the database

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Text Dataset 2060 ICU discharge summaries (documents) 1808 unique words appeared in the documents Age, gender, and race appeared in 1611 documents and were considered causeless (“acausal”) Each of the 1808 words was coded as present (1) or absent (0): in total 1811 variables m=1611, n=1811, r=3 only 18 variables of type Z (possible effects) were considered: nausea, cyrrhosis, dyspnea,…

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Results One good causal relation was recovered One bad causal relation was also obtained A study from infant birth and death records led to more causal relations. Ref.: Subramani Mani, Gregory F. Cooper “A Study in Causal Discovery from Population-Based Infant Birth and Death Records.” Proceedings of the AMIA Annual Fall Symposium, 1999, p315--319. Hanley and Belfus Publishers, Philadelphia, PA.

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Suggested Improvements Multi-word phrases More records Multivariate causes or effects (?) Encoding variable-value pairs (e.g.: serum sodium = high) (?) The number of occurrences of phrases in a documents The location of phrases in a document

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UNIVERSITY OF SOUTH CAROLINA Department of Computer Science and Engineering Limitations of the Text Study Words, not phrases Present or absent only Context of a word is not considered “hypertensive” and “not hypertensive” are treated the same way! Synonyms are treated as different words More generally: no linguistic analysis, no domain (semantic, ontological?) information is used

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