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Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans
[article]
2017
bioRxiv
pre-print
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Here we use ~36 million singleton variants from 3,560 whole-genome sequences to infer fine-scale patterns of mutation rate heterogeneity. ...
Remarkably, GC content, DNase hypersensitivity, CpG islands, and H3K36 trimethylation are associated with both increased and decreased mutation rates depending on nucleotide context. ...
Let K be the index across all 7-552 mer subtypes with more than 10 observed singletons ( ∈ { , … , , }). ...
doi:10.1101/108290
fatcat:puvydu3bajhdpnnmzgj762tuoq
A syntactic account of singleton types via hereditary substitution
2009
Proceedings of the Fourth International Workshop on Logical Frameworks and Meta-Languages Theory and Practice - LFMTP '09
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We give a syntactic proof of decidability and consistency of equivalence for the singleton type calculus, which lies at the foundation of modern module systems such as that of ML. ...
The proof works by translation of the singleton type calculus into a canonical presentation, adapted from work on logical frameworks, in which equivalent terms are written identically. ...
Subtyping Subtyping in the EL is associated with a subsumption rule, as is typical for type systems with subtyping. However, the IL cannot support a subsumption rule. ...
doi:10.1145/1577824.1577829
dblp:conf/lfmtp/Crary09
fatcat:q2n5ephm3rf7pcrhbtyjsrvz3y
Coming to Terms with Your Choices: An Existential Take on Dependent Types
[article]
2020
arXiv
pre-print
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We propose a new dependently-typed system with subtyping and singleton types whose goal is to enable type-level programming in an accessible style. ...
Furthermore, we show that singleton types combined with the choice operator can serve as a replacement for many type functions of interest in practice. ...
In [Aspinall 1994 ] Aspinall introduces ≤ , a dependently-typed system with subtyping and singleton types that resembles ours in its type language. ...
arXiv:2011.07653v1
fatcat:cejcks5iwbb77lkcxx3ztt2gdu
A Core Calculus for Scala Type Checking
[chapter]
2006
Lecture Notes in Computer Science
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Both calculi model a simple, purely functional core language of objects with fields and methods in a nominal class-based type system. ...
All presented deduction rules are syntax-directed and thus lead directly to procedures for subtyping and type assignment. ...
This rule therefore allows us to unfold a subtyping problem referring to a singleton type to a subtyping problem between non-singleton types in a single step. ...
doi:10.1007/11821069_1
fatcat:j4jct4vgrbel5fa7osuzdhmomq
Omni-word Feature and Soft Constraint for Chinese Relation Extraction
2014
Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)
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The results show a significant improvement in Chinese relation extraction, outperforming other methods in F-score by 10% in 6 relation types and 15% in 18 relation subtypes. ...
In Row 2, with only the F ow feature, the F-score already reaches 77.74% in 6 types and 60.31% in 18 subtypes. ...
Zhang et al. (2011) was based on the ACE 2005 corpus with 75% data for training and 25% for testing. Performances about the 7 types and 19 subtypes were given. ...
doi:10.3115/v1/p14-1054
dblp:conf/acl/ChenZZ14
fatcat:cga4jamk55dvdhucmb4cwubssy
Protocol Specialization
[chapter]
2004
Lecture Notes in Computer Science
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Each channel acts as a component connector with the interface determined by the channel's protocol. ...
We present an analysis that determines the minimum protocol required for each process and specify the specialization of a process with respect to a desired protocol, thereby removing unnecessary code. ...
The type system underlying our work relies on recursive types with singleton types and subtyping. The combination with singleton types is a novel contribution to session type systems. ...
doi:10.1007/978-3-540-30477-7_17
fatcat:dxcr3gsttfaaxdl5qmkh7lspn4
A Path To DOT: Formalizing Fully Path-Dependent Types
[article]
2019
arXiv
pre-print
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This paper presents the pDOT calculus, which generalizes DOT to support types that depend on paths of arbitrary length, as well as singleton types to track path equality. ...
The Dependent Object Types (DOT) calculus aims to formalize the Scala programming language with a focus on path-dependent types - types such as x.a_1... a_n.T that depend on the runtime value of a path ...
Path Alias Typing. In pDOT singleton-type related typing and subtyping rules are responsible for the handling of aliased paths and equivalent types. Singleton Type Creation. ...
arXiv:1904.07298v4
fatcat:ufd3sxdicjdgxih2mbgius6gcy
External Dispatch: Yet Another Object-Oriented Single and Multiple Dispatch Mechanism
2017
Journal of Object Technology
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A more complete realization for external dispatch motivated the definition of a new singleton language mechanism that is also presented. ...
This mechanism is compatible with existing object-oriented language constructs, and provides a simple, expressive, and universal dispatch tool. ...
For example: Listing 7 -Import dispatch grammar If successfully compiled and run, this expression creates an object with type T<Integer> subtype of A<Integer>, and T<> is the best conforming type match ...
doi:10.5381/jot.2017.16.2.a1
fatcat:llei27a2gjfalfmclm3u5gblby
Recency Types for Analyzing Scripting Languages
[chapter]
2010
Lecture Notes in Computer Science
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Unlike with linear types, summary types may refer to singleton types and vice versa. We prove the soundness of the type system and present a constraintbased inference algorithm. ...
With the current surge of scripting technologies, large programs are being built with dynamically typed languages. ...
Fig. 7 (b) defines the subtyping relation. Besides the rules dealing with reflexivity and top, one summary object type is a subtype of another, if it encompasses fewer locations. ...
doi:10.1007/978-3-642-14107-2_10
fatcat:tn2grzmdync63dk3jasgctrgu4
Comparative Population Analysis of Klebsiella pneumoniae Strains with Extended-Spectrum β-Lactamases Colonizing Patients in Rehabilitation Centers in Four Countries
2013
Antimicrobial Agents and Chemotherapy
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High genetic diversity ofK. pneumoniaepopulations was observed, with specific characteristics at each center. ...
Then, 100 isolates, including representatives of all PFGE types and of multiple subtypes for each larger PFGE type with subtypes, were typed by MLST (8) . ...
An interesting exception was the Israeli CC147 isolates, split by MLST into ST147 and ST392 (SLVs differing by tonB alleles) but clustered by PFGE into 1 type with 23 subtypes. ...
doi:10.1128/aac.02571-12
pmid:23403417
pmcid:PMC3623323
fatcat:crt24iku2rczhnfvpkfl75yr2u
Increased HIV Subtype Diversity Reflecting Demographic Changes in the HIV Epidemic in New South Wales, Australia
2020
Viruses
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In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons. ...
However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only. ...
The proportion of sequences associated with each cluster type or singleton is shown as a pie chart for the four subtype groups analysed. ...
doi:10.3390/v12121402
pmid:33291330
fatcat:pbm3a3uyufar5pzbskwnkasn4i
Relating Church-Style and Curry-Style Subtyping
2011
Electronic Proceedings in Theoretical Computer Science
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2011 pre-print arXiv:1101.4423v1 fatcat:tvie6b6mybfq5pz7z6vmwy7c54
Type theories with higher-order subtyping or singleton types are examples of systems where computation rules for variables are affected by type information in the context. ...
The algorithm for subtyping in F-Omega-Sub can then be given on types without context or kind information. ...
Examples where this may occur are type systems with singleton types, where a variable of a singleton type is equal to the unique element of the type, or subtyping, where a type variable may be replaced ...
doi:10.4204/eptcs.45.1
fatcat:e75aonjtu5fi5gkfbioujqglbi
Extensional equivalence and singleton types
2006
ACM Transactions on Computational Logic
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The system includes dependent types for pairs and functions ( and ) and a subtyping relation induced by regarding singletons as subtypes of the base type. ...
We study the λ S ≤ calculus, which contains singleton types S(M ) classifying terms of base type provably equivalent to the term M . ...
Later, he used an extremely simple form of singleton type (with no elimination rule or subtyping) in order to prove parametricity results [Crary 1999 ]. ...
doi:10.1145/1166109.1166112
fatcat:wklyh5yuvvau7onwbhctjnyihu
Extensional equivalence and singleton types
2006
ACM Transactions on Computational Logic
Preserved Fulltext
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The file type is application/pdf.
The system includes dependent types for pairs and functions ( and ) and a subtyping relation induced by regarding singletons as subtypes of the base type. ...
We study the λ S ≤ calculus, which contains singleton types S(M ) classifying terms of base type provably equivalent to the term M . ...
Later, he used an extremely simple form of singleton type (with no elimination rule or subtyping) in order to prove parametricity results [Crary 1999 ]. ...
doi:10.1145/1183278.1183281
fatcat:tpyi53ceujel7mvp7u5qp52fie
Obesity Subtypes and Risk of Spontaneous versus Medically Indicated Preterm Births in Singletons and Twins
2008
American Journal of Epidemiology
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By contrast, obese mothers with singleton gestation had about 50% greater odds of medically indicated preterm (odds ratio ¼ 1.46, 95% confidence interval: 1.39, 1.54) and very preterm (odds ratio ¼ 1.49 ...
Using data from the Missouri maternally linked files (1989)(1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997), the authors examined the association among maternal obesity, obesity subtypes, and spontaneous ...
All tests of hypothesis were two tailed with a type 1 error rate fixed at 5 percent. SAS, version 9.1, software (SAS Institute, Inc., Cary, North Carolina) was used to perform all analyses. ...
doi:10.1093/aje/kwn092
pmid:18456643
fatcat:hmwjvafev5d4dkfxxtbl7vaczi
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