Dynamic Dependency Pairs for Algebraic Functional Systems

We extend the higher-order termination method of dynamic dependency pairs to Algebraic Functional Systems (AFSs). In this setting, simply typed lambda-terms with algebraic reduction and separate {\beta}-steps are considered. For left-linear AFSs, the method is shown to be complete. For so-called local AFSs we define a variation of usable rules and an extension of argument filterings. All these techniques have been implemented in the higher-order termination tool WANDA

Arabic parsing using grammar transforms

We investigate Arabic Context Free Grammar parsing with dependency annotation comparing lexicalised and unlexicalised parsers. We study how morphosyntactic as well as function tag information percolation in the form of grammar transforms (Johnson, 1998, Kulick et al., 2006) affects the performance of a parser and helps dependency assignment. We focus on the three most frequent functional tags in the Arabic Penn Treebank: subjects, direct objects and predicates . We merge these functional tags with their phrasal categories and (where appropriate) percolate case information to the non-terminal (POS) category to train the parsers. We then automatically enrich the output of these parsers with full dependency information in order to annotate trees with Lexical Functional Grammar (LFG) f-structure equations with produce f-structures, i.e. attribute-value matrices approximating to basic predicate-argument-adjunct structure representations. We present a series of experiments evaluating how well lexicalized, history-based, generative (Bikel) as well as latent variable PCFG (Berkeley) parsers cope with the enriched Arabic data. We measure quality and coverage of both the output trees and the generated LFG f-structures. We show that joint functional and morphological information percolation improves both the recovery of trees as well as dependency results in the form of LFG f-structures

The Budget-Constrained Functional Dependency

Armstrong's axioms of functional dependency form a well-known logical system that captures properties of functional dependencies between sets of database attributes. This article assumes that there are costs associated with attributes and proposes an extension of Armstrong's system for reasoning about budget-constrained functional dependencies in such a setting. The main technical result of this article is the completeness theorem for the proposed logical system. Although the proposed axioms are obtained by just adding cost subscript to the original Armstrong's axioms, the proof of the completeness for the proposed system is significantly more complicated than that for the Armstrong's system

LFG without C-structures

We explore the use of two dependency parsers, Malt and MST, in a Lexical Functional Grammar parsing pipeline. We compare this to the traditional LFG parsing pipeline which uses constituency parsers. We train the dependency parsers not on classical LFG f-structures but rather on modified dependency-tree versions of these in which all words in the input sentence are represented and multiple heads are removed. For the purposes of comparison, we also modify the existing CFG-based LFG parsing pipeline so that these "LFG-inspired" dependency trees are produced. We find that the differences in parsing accuracy over the various parsing architectures is small

Characterizing genomic alterations in cancer by complementary functional associations.

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes