A Context Free TAG Variant

Engineering and Applied Science

CRISPR/Cas9-based precision tagging of essential genes in bloodstream form African trypanosomes

Proteins of interest are frequently expressed with a fusion-tag to facilitate experimental analysis. In trypanosomatids, which are typically diploid, a tag-encoding DNA fragment is typically fused to one native allele. However, since recombinant cells represent ≪0.1% of the population following transfection, these DNA fragments also incorporate a marker cassette for positive selection. Consequently, native mRNA untranslated regions (UTRs) are replaced, potentially perturbing gene expression; in trypanosomatids, UTRs often impact gene expression in the context of widespread and constitutive polycistronic transcription. We sought to develop a tagging strategy that preserves native UTRs in bloodstream-form African trypanosomes, and here we describe a CRISPR/Cas9-based knock-in approach to drive precise and marker-free tagging of essential genes. Using simple tag-encoding amplicons, we tagged four proteins: a histone acetyltransferase, HAT2; a histone deacetylase, HDAC3; a cleavage and polyadenylation specificity factor, CPSF3; and a variant surface glycoprotein exclusion factor, VEX2. The approach maintained the native UTRs and yielded clonal strains expressing functional recombinant proteins, typically with both alleles tagged. We demonstrate utility for both immunofluorescence-based localisation and for enriching protein complexes; GFPHAT2 or GFPHDAC3 complexes in this case. This precision tagging approach facilitates the assembly of strains expressing essential recombinant genes with their native UTRs preserved

Modular session types for objects

Session types allow communication protocols to be specified type-theoretically so that protocol implementations can be verified by static type checking. We extend previous work on session types for distributed object-oriented languages in three ways. (1) We attach a session type to a class definition, to specify the possible sequences of method calls. (2) We allow a session type (protocol) implementation to be modularized, i.e. partitioned into separately-callable methods. (3) We treat session-typed communication channels as objects, integrating their session types with the session types of classes. The result is an elegant unification of communication channels and their session types, distributed object-oriented programming, and a form of typestate supporting non-uniform objects, i.e. objects that dynamically change the set of available methods. We define syntax, operational se-mantics, a sound type system, and a sound and complete type checking algorithm for a small distributed class-based object-oriented language with structural subtyping. Static typing guarantees that both sequences of messages on channels, and sequences of method calls on objects, conform to type-theoretic specifications, thus ensuring type-safety. The language includes expected features of session types, such as delegation, and expected features of object-oriented programming, such as encapsulation of local state.Comment: Logical Methods in Computer Science (LMCS), International Federation for Computational Logic, 201

Developing a TT-MCTAG for German with an RCG-based parser

Developing linguistic resources, in particular grammars, is known to be a complex task in itself, because of (amongst others) redundancy and consistency issues. Furthermore some languages can reveal themselves hard to describe because of specific characteristics, e.g. the free word order in German. In this context, we present (i) a framework allowing to describe tree-based grammars, and (ii) an actual fragment of a core multicomponent tree-adjoining grammar with tree tuples (TT-MCTAG) for German developed using this framework. This framework combines a metagrammar compiler and a parser based on range concatenation grammar (RCG) to respectively check the consistency and the correction of the grammar. The German grammar being developed within this framework already deals with a wide range of scrambling and extraction phenomena

Primitives for Contract-based Synchronization

We investigate how contracts can be used to regulate the interaction between processes. To do that, we study a variant of the concurrent constraints calculus presented in [1], featuring primitives for multi-party synchronization via contracts. We proceed in two directions. First, we exploit our primitives to model some contract-based interactions. Then, we discuss how several models for concurrency can be expressed through our primitives. In particular, we encode the pi-calculus and graph rewriting.Comment: In Proceedings ICE 2010, arXiv:1010.530

Improving PARMA Trailing

Taylor introduced a variable binding scheme for logic variables in his PARMA system, that uses cycles of bindings rather than the linear chains of bindings used in the standard WAM representation. Both the HAL and dProlog languages make use of the PARMA representation in their Herbrand constraint solvers. Unfortunately, PARMA's trailing scheme is considerably more expensive in both time and space consumption. The aim of this paper is to present several techniques that lower the cost. First, we introduce a trailing analysis for HAL using the classic PARMA trailing scheme that detects and eliminates unnecessary trailings. The analysis, whose accuracy comes from HAL's determinism and mode declarations, has been integrated in the HAL compiler and is shown to produce space improvements as well as speed improvements. Second, we explain how to modify the classic PARMA trailing scheme to halve its trailing cost. This technique is illustrated and evaluated both in the context of dProlog and HAL. Finally, we explain the modifications needed by the trailing analysis in order to be combined with our modified PARMA trailing scheme. Empirical evidence shows that the combination is more effective than any of the techniques when used in isolation. To appear in Theory and Practice of Logic Programming.Comment: 36 pages, 7 figures, 8 table

Modeling Target-Side Inflection in Neural Machine Translation

NMT systems have problems with large vocabulary sizes. Byte-pair encoding (BPE) is a popular approach to solving this problem, but while BPE allows the system to generate any target-side word, it does not enable effective generalization over the rich vocabulary in morphologically rich languages with strong inflectional phenomena. We introduce a simple approach to overcome this problem by training a system to produce the lemma of a word and its morphologically rich POS tag, which is then followed by a deterministic generation step. We apply this strategy for English-Czech and English-German translation scenarios, obtaining improvements in both settings. We furthermore show that the improvement is not due to only adding explicit morphological information.Comment: Accepted as a research paper at WMT17. (Updated version with corrected references.

Edge-Based Best-First Chart Parsing

Best-first probabilistic chart parsing attempts to parse efficiently by working on edges that are judged 'best' by some probabilistic figure of merit (FOM). Recent work has used proba- bilistic context-free grammars (PCFGs) to sign probabilities to constituents, and to use these probabilities as the starting point for the FOM. This paper extends this approach to us- ing a probabilistic FOM to judge edges (incomplete constituents), thereby giving a much finergrained control over parsing effort. We show how this can be accomplished in a particularly simple way using the common idea of binarizing the PCFG. The results obtained are about a factor of twenty improvement over the best prior results -- that is, our parser achieves equivalent results using one twentieth the number of edges. Furthermore we show that this improvement is obtained with parsing precision and recall levels superior to those achieved by exhaustive parsing