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Using Relational Structure for Learning and Modeling in Biomedical and Social Domains. Mark Goadrich Computer Science and Mathematics Centenary College of Louisiana Natural Science Colloquium November 6th, 2007. Overview. First-Order Logic and Machine Learning The world is full of Objects
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Using Relational Structure for Learning and Modeling in Biomedical and Social Domains Mark Goadrich Computer Science and Mathematics Centenary College of Louisiana Natural Science Colloquium November 6th, 2007
Overview • First-Order Logic and Machine Learning • The world is full of Objects • Model these Objects to understand the world • Inductive Logic Programming • Objects and Relations/Properties • Agent-Based Modeling • Objects and Interactions/Behaviors
Bongard Problems • 6 positive examples of a concept on left • 6 negative examples on right • How to learn this concept using a computer?
First-Order Logic using PROLOG • Objects • e3, t1, t2, c1 • Types • example(e3) • triangle(t1) • triangle(t2) • circle(c1) • Relations • has_shape(e3, t1) • has_shape(e3, t2) • has_shape(e3, c1) • inside(t2, c1) • left(t2, t1) • size(c1, 2.5) • above(t2, t1) • … Positive Example 3 Repeat this process for each example in dataset
Inductive Logic Programming (ILP) • Search the space of possible rules “positive(E) :- …” • Judge rule quality by positive - negative coverage positive(E):- has_shape(E, A) positive(E) positive(E):- has_shape(E, A), triangle(A) positive(E) :- has_shape(E, A), has_shape(E, B), triangle(A), circle(B), inside(A, B).
Research Issues in ILP • Enormous space to search for rules • Enormous number of examples • Incorporation of continuous features • Learning of probabilistic rules • Evaluation of rule quality • Survey of ILP domains and future interests
Mutagenesis • Designing effective and selective drugs • Represent chemicals as atoms and bonds between them atm(127, 127_1, c, 22, 0.191 ) bond(127, 127_1, 127_6, 7 ) • Learned mutagenic rule: mutagenic(A) :- atm(A, B, c, 27, C), bond(A, D, E, 1), bond(A, B, E, 7).
Breast CancerDetection • Large dataset of abnormalities found in mammograms • Not enough radiologists • Relational features • More than one abnormality per mammogram • More than one mammogram per person over time malignant(A) :- not asymmetric(A), in_same_mammorgram(A, A2), spiculated_margin(A2), not distorted(A2)
Robot Scientist • Represent Metabolic Pathways as a Regulatory Network Graph • Knock out genes, and then systematically deduce the unknown function • Try to learn the network from time-series microarray data
Social Networks • People are connected by friendships into networks • Each person has likes/dislikes, possibly influenced by their network • Can we learn your interests based on who you know and what they like? Targeted advertisements?
Netflix Prize • What movies should Netflix recommend you watch next? • Large relational dataset • Movies • Titles • Ratings • Friends • Friend’s ratings • Genre • $1 million if you achieve 10% improvement over their algorithm Cinematch
Zendo • Board game about inductive logic • Master creates a rule which some 3-D pyramid structures fit and others do not • Players build structures and try to guess the Master rule • Easier to design computer Master to decide if a structure fits the rule • Harder to design computer Player that must efficiently guess the rule
Crab Claws • What physical characteristics distinguish between two species? • Within the same species, what changes due to growth, diet and their relation to predation? • Find the “shock graph” of each image • Use ILP to learn differences based on these graphs
Agent-Based Modeling • Objects have interactions with each other • Flocks of Birds, Schools of Fish • Separation • Alignment • Cohesion • Objects interact with their environment • Ant Foraging, Pheromones, Traffic Laws • Agent-Based Modeling (ABM) • Create discrete-time computational simulation • Align models with known behavior • Vary parameters to test new hypotheses
Social Science Cellular Process
Conclusions • First-Order Logic combines with ILP and ABM to create a powerful representation of the world • Research Opportunities • Social Networks • Zendo Player • Claws and Shock Graphs • Cellular Simulation • Social Simulation • [Insert your favorite dataset here]