Valery Trifonov

Predicting interactions in protein networks by completing defective cliques

UNLABELLED Datasets obtained by large-scale, high-throughput methods for detecting protein-protein interactions typically suffer from a relatively high level of noise. We describe a novel method for improving the quality of these datasets by predicting missed protein-protein interactions, using only the topology of the protein interaction network observed by the large-scale experiment. The central idea of the method is to search the protein interaction network for defective cliques (nearly complete complexes of pairwise interacting proteins), and predict the interactions that complete them. We formulate an algorithm for applying this method to large-scale networks, and show that in practice it is efficient and has good predictive performance. More information can be found on our website http://topnet.gersteinlab.org/clique/ CONTACT Mark.Gerstein@yale.edu SUPPLEMENTARY INFORMATION Supplementary Materials are available at Bioinformatics online.

A syntactic approach to foundational proof-carrying code

Proof-carrying code (PCC) is a general framework for verifying the safety properties of machine-language programs. PCC proofs are usually written in a logic extended with language-specific typing rules. In foundational proof-carrying code (FPCC), on the other hand, proofs are constructed and verified using strictly the foundations of mathematical logic, with no type-specific axioms. FPCC is more flexible and secure because it is not tied to any particular type system and it has a smaller trusted base. Foundational proofs, however are much harder to construct. Previous efforts on FPCC all required building sophisticated semantic models for types. In this paper, we present a syntactic approach to FPCC that avoids the difficulties of previous work. Under our new scheme, the foundational proof for a typed machine program simply consists of the typing derivation plus the formalized syntactic soundness proof for the underlying type system. We give a translation from a typed assembly language into FPCC and demonstrate the advantages of our new system via an implementation in the Coq proof assistant.

Subtyping Constrained Types

A constrained type is a type that comes with a set of subtyping constraints on variables occurring in the type. Constrained type inference systems are a natural generalization of Hindley/Milner type inference to languages with subtyping. This paper develops several subtyping relations on polymorphic constrained types of a general form that allows recursive constraints and multiple bounds on type variables. Subtyping constrained types has applications to signature matching and to constrained type simplification.

Type Inference for Recursively Constrained Types and its Application to OOP

Abstract We define a powerful type inference mechanism with application to object-oriented programming. The types inferred are recursively constrained types, types that come with a system of constraints. These types may be viewed as generalizations of recursive types and F-bounded polymorphic types, the forms of type that are necessary to properly encode object typings. The base language we study, I-Soop, incorporates state and records, the two features critical to encode objects in a non-object-oriented language. Soundness and completeness of the type inference algorithm are established by operational means. Our method for establishing these properties is somewhat novel. We illustrate how the algorithm may be fruitfully applied to infer types of object-oriented programs.

Fully reflexive intensional type analysis

Compilers for polymorphic languages can use runtime type inspection to support advanced implementation techniques such as tagless garbage collection, polymorphic marshalling, and flattened data structures. Intensional type analysis is a type-theoretic framework for expressing and certifying such type-analyzing computations. Unfortunately, existing approaches to intensional analysis do not work well on types with universal, existential, or fixpoint quantifiers. This makes it impossible to code applications such as garbage collection, persistence, or marshalling which must be able to examine the type of any runtime value.We present a typed intermediate language that supports fully reflexive intensional type analysis. By fully reflexive, we mean that type-analyzing operations are applicable to the type of any runtime value in the language. In particular, we provide both type-level and term-level constructs for analyzing quantified types. Our system supports structural induction on quantified types yet type checking remains decidable. We show how to use reflexive type analysis to support type-safe marshalling and how to generate certified type-analyzing object code.

Representing Java classes in a typed intermediate language

We propose a conservative extension of the polymorphic lambda calculus (Fω) as an intermediate language for compiling languages with name-based class and interface hierarchies. Our extension enriches standard Fω with recursive types, existential types, and row polymorphism, but only ordered records with no subtyping. Basing our language on Fω makes it also a suitable target for translation from other higher-order languages; this enables the safe interoperation between class-based and higher-order languages and the reuse of common type-directed optimization techniques, compiler back ends, and runtime support.We present the formal semantics of our intermediate language and illustrate its features by providing a formal translation from a subset of Java, including classes, interfaces, and private instance variables. The translation preserves the name-based hierarchical relation between Java classes and interfaces, and allows access to private instance variables of parameters of the same class as the one defining the method. It also exposes the details of method invocation and instance variable access and allows many standard optimizations to be performed on the object-oriented code.

Type-preserving compilation of Featherweight Java

We present an efficient encoding of core Java constructs in a simple, implementable typed intermediate language. The encoding, after type erasure, has the same operational behavior as a standard implementation using vtables and self-application for method invocation. Classes inherit super-class methods with no overhead. We support mutually recursive classes while preserving separate compilation. Our strategy extends naturally to a significant subset of Java, including interfaces and privacy. The formal translation using Featherweight Java allows comprehensible type-preservation proofs and serves as a starting point for extending the translation to new features. Our work provides a foundation for supporting certifying compilation of Java-like class-based languages in a type-theoretic framework.

A Syntactic Approach to Foundational Proof-Carrying Code

Proof-carrying code (PCC) is a general framework for verifying the safety properties of machine-language programs. PCC proofs are usually written in a logic extended with language-specific typing rules; they certify safety but only if there is no bug in the typing rules. In foundational proof-carrying code (FPCC), on the other hand, proofs are constructed and verified by using strictly the foundations of mathematical logic, with no type-specific axioms. FPCC is more flexible and secure because it is not tied to any particular type system and it has a smaller trusted base. Foundational proofs, however, are much harder to construct. Previous efforts on FPCC all required building sophisticated semantic models for types. Furthermore, none of them can be easily extended to support mutable fields and recursive types. In this article, we present a syntactic approach to FPCC that avoids all of these difficulties. Under our new scheme, the foundational proof for a typed machine program simply consists of the typing derivation plus the formalized syntactic soundness proof for the underlying type system. The former can be readily obtained from a type-checker, while the latter is known to be much easier to construct than the semantic soundness proofs. We give a translation from a typed assembly language into FPCC and demonstrate the advantages of our new system through an implementation in the Coq proof assistant.

Precision in practice: a type-preserving java compiler

Popular mobile code architectures (Java and .NET) include verifiers to check for memory safety and other security properties. Since their formats are relatively high level, supporting a wide range of source language features is awkward. Further compilation and optimization, necessary for efficiency, must be trusted. We describe the design and implementation of a fully type-preserving compiler for Java and ML. Its strongly-typed intermediate language provides a low-level abstract machine model and a type system general enough to prove the safety of a variety of implementation techniques. We show that precise type preservation is within reach for real-world Java systems.

Safe and Principled Language Interoperation

Safety of interoperation of program fragments written in different safe languages may fail when the languages have different systems of computational effects: an exception raised by an ML function may have no valid semantic interpretation in the context of a Safe-C caller. Sandboxing costs performance and still may violate the semantics if effects are not taken into account. We show that effect annotations alone are insufficient to guarantee safety, and we present a type system with bounded effect polymorphism designed to verify the compatibility of abstract resources required by the computational models of the interoperating languages. The type system ensures single address space interoperability of statically typed languages with effect mechanisms built of modules for control and state. It is shown sound for safety with respect to the semantics of a language with constructs for selection, simulation, and blocking of resources, targeted as an intermediate language for optimization of resource handling.