We develop a pipeline to mine complex drug interactions by combining different similarities and interaction types (molecular, structural, phenotypic, genomic etc). Our goal is to learn an optimal kernel from these heterogeneous similarities in a supervised manner. We formulate an extensible framework that can easily integrate new interaction types into a rich model. The core of our pipeline features a novel kernel-learning approach that tunes the weights of the heterogeneous similarities, and fuses them into a Similarity-based Kernel for Identifying Drug-Drug interactions and Discovery, or SKID3. Experimental evaluation on the DrugBank database shows that SKID3 effectively combines similarities generated from chemical reaction pathways (which generally improve precision) and molecular and structural fingerprints (which generally improve recall) into a single kernel that gets the best of both worlds, and consequently demonstrates the best performance.

No abstract

Counting the number of true instances of a clause is arguably a major bottleneck in relational probabilistic inference and learning. We approximate counts in two steps: (1) transform the fully grounded relational model to a large hypergraph, and partially-instantiated clauses to hypergraph motifs; (2) since the expected counts of the motifs are provably the clause counts, approximate them using summary statistics (in/outdegrees, edge counts, etc). Our experimental results demonstrate the efficiency of these approximations, which can be applied to many complex statistical relational models, and can be significantly faster than state-of-the-art, both for inference and learning, without sacrificing effectiveness.

Agents that communicate back and forth with humans to help them execute nonlinguistic tasks are a long sought goal of AI. These agents need to translate between utterances and actionable meaning representations that can be interpreted by task-specific problem solvers in a contextdependent manner. They should also be able to learn such actionable interpretations for new predicates on the fly. We define an agent architecture for this scenario and present a series of experiments in the Blocks World domain that illustrate how our architecture supports language learning and problem solving in this domain.

One of the key advantages of Inductive Logic Programming systems is the ability of the domain experts to provide background knowledge as modes that allow for efficient search through the space of hypotheses. However, there is an inherent assumption that this expert should also be an ILP expert to provide effective modes. We relax this assumption by designing a graphical user interface that allows the domain expert to interact with the system using Entity Relationship diagrams. These interactions are used to construct modes for the learning system. We evaluate our algorithm on a probabilistic logic learning system where we demonstrate that the user is able to construct effective background knowledge on par with the expert-encoded knowledge on five data sets.