alo cse f buf Knowledge Representation and Reasoning

alo @ cse f buf Knowledge Representation and Reasoning in SNe. PS for Bioinformatics Stuart C. Shapiro Department of Computer Science and Engineering, and Center for Cognitive Science University at Buffalo, The State University of New York 201 Bell Hall, Buffalo, NY 14260 -2000 shapiro@cse. buffalo. edu http: //www. cse. buffalo. edu/~shapiro/ http: //www. cse. buffalo. edu/sneps/ November, 2003 S. C. Shapiro

alo f buf @ cse SNe. PS Ø A logic- and network-based Ø Knowledge representation Ø Reasoning Ø and Acting Ø System 2 November, 2003 S. C. Shapiro

alo f buf @ cse Examples of SNe. PS for Bioinformatics Ø Neurological Diagnostic Expert System Ø System for Understanding NF 1 Literature 3 November, 2003 S. C. Shapiro

alo f buf @ cse NEUREX: A Neurological Diagnostic Expert System Ø Ca. 1983 – 1986 Ø See: Z. Xiang, J. G. Chutkow, S. C. Shapiro, and S. N. Srihari, Computerized neurological diagnosis: a paradigm of modeling and reasoning, Health Care Instrumentation 1, 3 (1986), 90 -105. 4 November, 2003 S. C. Shapiro

alo f buf @ cse Strengths of SNe. PS for This Task Ø Integrated Analogical, Propositional, Functional Knowledge Ø Access to Procedural Knowledge via Acting System 5 November, 2003 S. C. Shapiro

alo f buf @ cse Analogical/Propositional Representation Proposition, Ventral root is proximal to spinal nerve. is represented by {<p “ventral root”> <d “spinal nerve”>} also have {<p “ganglion”> <d “spinal nerve”>} {<p “spinal nerve”> <d “dorsal ramus”>} {<p “spinal nerve”> <d “ventral ramus-1”>} 6 November, 2003 S. C. Shapiro

alo f buf @ cse Analogical/Propositional Propositions form a relational graph. From Z. Xiang, S. N. Srihari, S. C. Shapiro, and J. G. Chutkow, A modeling scheme for diagnosis, Expert Systems in Government Symposium, IEEE Computer Society Press, Silver Spring, MD, 1985, 538 -547. 7 November, 2003 S. C. Shapiro

alo f buf @ cse A Knowledge-Based Approach to Understanding the NF 1 Literature Ø A proposal to Do. D § PI: Gary R. Skuse, Director of Bioinformatics, RIT § Co. PIs: • Debra T. Burhans, Director, Bioinformatics, Canisius College • Alistair E. R. Campbell, Computer Science, Hamilton College • Stuart C. Shapiro, CSE, UB 8 November, 2003 S. C. Shapiro

alo f buf @ cse Goals Discover new linkages in information across Medline abstracts of research literature about Neurofibromatosis 1 (NF 1, or von Recklinghausen disease) 9 November, 2003 S. C. Shapiro

alo f buf @ cse Strengths of SNe. PS for This Task Ø Inconsistency Tolerance/Discovery/Repair Ø Contexts Ø Multiple Sources Ø Amenable to Backend DB Storage 10 November, 2003 S. C. Shapiro

alo f buf @ cse Inconsistent Knowledge Base wff 3: free(Willy) and whale(Willy) wff 10: all(x)(whale(x) => mammal(x)) wff 19: all(x)(whale(x) => fish(x)) wff 20: all(x)(andor(0, 1){mammal(x), fish(x)}) wff 21: all(x)(fish(x) <=> has(x, scales)) 11 November, 2003 S. C. Shapiro

alo @ cse f buf Finding the Contradiction During Query Answering : has(Willy, scales)? I infer fish(Willy) I infer it is not the case that wff 23: fish(Willy) 12 November, 2003 S. C. Shapiro

alo f buf @ cse BR Advice In order to make the context consistent you must delete at least one hypothesis from the set listed below. 1 : wff 20: all(x)(andor(0, 1){mammal(x), fish(x)}) (1 dependent proposition: (wff 24)) 2 : wff 19: all(x)(whale(x) => fish(x)) (2 dependent propositions: (wff 23 wff 22)) 3 : wff 10: all(x)(whale(x) => mammal(x)) (3 dependent propositions: (wff 24 wff 15 wff 11)) 4 : wff 3: free(Willy) and whale(Willy) (8 dependent propositions: (wff 24 wff 23 wff 22 wff 11 wff 9 wff 5 wff 2 wff 1)) User deletes #2: wff 19. 13 November, 2003 S. C. Shapiro

alo f buf @ cse Continuing with Repaired KB I infer it is not the case that wff 22: has(Willy, scales) wff 26: ~has(Willy, scales) 14 November, 2003 S. C. Shapiro

alo f buf @ cse Multiple Sources wff 1: all(x)(andor(0, 1){mammal(x), fish(x)}) wff 2: all(x)(fish(x) <=> has(x, scales)) wff 4: all(x)(whale(x) => fish(x)) wff 5: Source(Melville, all(x)(whale(x) => fish(x))) wff 6: all(x)(whale(x) => mammal(x)) wff 7: Source(Darwin, all(x)(whale(x) => mammal(x))) wff 8: Sgreater(Darwin, Melville) wff 11: free(Willy) and whale(Willy) Note: Source & Sgreater props are regular object-language props. 15 November, 2003 S. C. Shapiro

alo f buf @ cse Finding the Contradiction : has(Willy, scales)? I infer fish(Willy) I infer has(Willy, scales) I infer mammal(Willy) I infer it is not the case that wff 14: fish(Willy) 16 November, 2003 S. C. Shapiro

alo f buf @ cse Using Source Credibility A contradiction was detected within context default-defaultct. The contradiction involves the newly derived proposition: wff 17: ~fish(Willy) {<der, {wff 1, wff 6, wff 11}>} and the previously existing proposition: wff 14: fish(Willy) {<der, {wff 4, wff 11}>} The least believed hypothesis: (wff 4) The most common hypothesis: (nil) The hypothesis supporting the fewest wffs: (wff 1) I removed the following belief: wff 4: all(x)(whale(x) => fish(x)) I no longer believe the following 2 propositions: wff 14: fish(Willy) wff 13: has(Willy, scales) 17 November, 2003 S. C. Shapiro

alo f buf @ cse Backend DB Storage Ø A proposal Ø All propositions represented with keyword arguments Ø Each keyword set a Relation in an RDB Ø Or in XML 18 November, 2003 S. C. Shapiro

alo f buf @ cse P m 1 m 2 m 3 m 4 m 5 m 6 m 7 m 8 m 9 m 10 m 11 m 12 m 13 NEUREX Data as Relation Proximal dorsal root ganglion ventral root spinal nerve dorsal ramus medial branch of d. r. dorsal ramus spinal nerve ventral ramus-1 cutaneous branch of v. r. November, 2003 Distal ganglion spinal nerve dorsal ramus medial branch of d. r. medial cutaneous branch lateral branch of d. r. ventral ramus-1 ventral ramus-2 lateral cutaneous branch of v. r. posterior branch lateral anterior branch lateral 19 S. C. Shapiro

alo @ cse f buf Reasoning in Different Contexts Ø A context is a set of hypotheses and all propositions derived from them. Ø Reasoning is performed within a context. Ø A conclusion is available in every context that is a superset of its origin set. Ø Contradictions across contexts are noticed. 20 November, 2003 S. C. Shapiro

alo f buf @ cse Darwin Context : set-context Darwin () : set-default-context Darwin wff 1: all(x)(andor(0, 1){mammal(x), fish(x)}) wff 2: all(x)(fish(x) <=> has(x, scales)) wff 3: all(x)(orca(x) => whale(x)) wff 4: all(x)(whale(x) => mammal(x)) wff 7: free(Willy) and whale(Willy) 21 November, 2003 S. C. Shapiro

alo f buf @ cse Melville Context : set-context Melville (wff 8 wff 7 wff 3 wff 2 wff 1) : set-default-context Melville wff 9: all(x)(whale(x) => fish(x)) 22 November, 2003 S. C. Shapiro

alo f buf @ cse Melville: Willy has scales : has(Willy, scales)? I infer wff 10: fish(Willy) has(Willy, scales) 23 November, 2003 S. C. Shapiro

alo f buf @ cse Darwin: No scales : set-default-context Darwin : has(Willy, scales)? I infer mammal(Willy) I infer it is not the case that wff 10: has(Willy, scales) wff 15: wff 11: fish(Willy) ~has(Willy, scales) 24 November, 2003 S. C. Shapiro

alo @ cse f buf Summary Ø SNe. PS is useful for Bioinformatics reasoning. Ø Analogical/Propositional/DB Representation. Ø Notifies user about inconsistencies. Ø Resolves inconsistencies from differently credible sources. Ø Can reason in one context, even if another is inconsistent with it. 25 November, 2003 S. C. Shapiro