Higher-order Syntax Research Articles

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.

Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood, and de novo enhancer design has been challenging. Here, we built a deep-learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. The model learned relevant TF motifs and higher-order syntax rules, including functionally nonequivalent instances of the same TF motif that are determined by motif-flanking sequence and intermotif distances. We validated these rules experimentally and demonstrated that they can be generalized to humans by testing more than 40,000 wildtype and mutant Drosophila and human enhancers. Finally, we designed and functionally validated synthetic enhancers with desired activities de novo.

Skipping the binder bureaucracy with mixed embeddings in a semantics course (functional pearl)

Rigorous reasoning about programs calls for some amount of bureaucracy in managing details like variable binding, but, in guiding students through big ideas in semantics, we might hope to minimize the overhead. We describe our experiment introducing a range of such ideas, using the Coq proof assistant, without any explicit representation of variables, instead using a higher-order syntax encoding that we dub "mixed embedding": it is neither the fully explicit syntax of deep embeddings nor the syntax-free programming of shallow embeddings. Marquee examples include different takes on concurrency reasoning, including in the traditions of model checking (partial-order reduction), program logics (concurrent separation logic), and type checking (session types) -- all presented without any side conditions on variables.

HO$$\pi $$ in Coq

We present a formalization of HOπ in Coq, a process calculus where messages carry processes. Such a higher-order calculus features two very different kinds of binder: process input, similar to λ-abstraction, and name restriction, whose scope can be expanded by communication. For the latter, we compare four approaches to represent binders: locally nameless, de Bruijn indices, nominal, and Higher-Order Abstract Syntax. In each case, we formalize strong context bisimi-larity and prove it is compatible, i.e., closed under every context, using Howe's method, based on several proof schemes we developed in a previous paper.

A Weakly Initial Algebra for Higher-Order Abstract Syntax in Cedille

Cedille is a relatively recent tool based on a Curry-style pure type theory, without a primitive datatype system. Using novel techniques based on dependent intersection types, inductive datatypes with their induction principles are derived. One benefit of this approach is that it allows exploration of new or advanced forms of inductive datatypes. This paper reports work in progress on one such form, namely higher-order abstract syntax (HOAS). We consider the nature of HOAS in the setting of pure type theory, comparing with the traditional concept of environment models for lambda calculus. We see an alternative, based on what we term Kripke function-spaces, for which we can derive a weakly initial algebra in Cedille. Several examples are given using the encoding.

Formalization of Metatheory of the Quipper Quantum Programming Language in a Linear Logic

We develop a linear logical framework within the Hybrid system and use it to reason about the type system of a quantum lambda calculus. In particular, we consider a practical version of the calculus called Proto-Quipper, which contains the core of Quipper. Quipper is a quantum programming language under active development and recently has gained much popularity among the quantum computing communities. Hybrid is a system that is designed to support the use of higher-order abstract syntax for representing and reasoning about formal systems implemented in the Coq Proof Assistant. In this work, we extend the system with a linear specification logic (SL) in order to reason about the linear type system of Quipper. To this end, we formalize the semantics of Proto-Quipper by encoding the typing and evaluation rules in the SL, and prove type soundness.

Formal Meta-level Analysis Framework for Quantum Programming Languages

The design and development of quantum programming languages (QPLs) is an important and active area of quantum computing. This paper addresses the problem of developing a standard methodology for verifying a QPL against major quantum computing concepts. We propose a framework dedicated to the meta-level analysis of QPLs, in particular, functional quantum languages. To this aim, we choose the Hybrid system as the tool in which to build our framework. Hybrid is a logical framework that supports higher-order abstract syntax, on top of which we develop an intuitionistic linear specification logic used for reasoning about QPLs. We provide a formal proof of some important meta-theoretic properties of this logic, and in addition, showcase a number of examples that can be tackled under the proposed framework.

Mechanizing proofs with logical relations – Kripke-style

Proofs with logical relations play a key role to establish rich properties such as normalization or contextual equivalence. They are also challenging to mechanize. In this paper, we describe two case studies using the proof environmentBeluga: First, we explain the mechanization of the weak normalization proof for the simply typed lambda-calculus; second, we outline how to mechanize the completeness proof of algorithmic equality for simply typed lambda-terms where we reason about logically equivalent terms. The development of these proofs inBelugarelies on three key ingredients: (1) we encode lambda-terms together with their typing rules, operational semantics, algorithmic and declarative equality using higher order abstract syntax (HOAS) thereby avoiding the need to manipulate and deal with binders, renaming and substitutions, (2) we take advantage ofBeluga's support for representing derivations that depend on assumptions and first-class contexts to directly state inductive properties such as logical relations and inductive proofs, (3) we exploitBeluga's rich equational theory for simultaneous substitutions; as a consequence, users do not need to establish and subsequently use substitution properties, and proofs are not cluttered with references to them. We believe these examples demonstrate thatBelugaprovides the right level of abstractions and primitives to mechanize challenging proofs using HOAS encodings. It also may serve as a valuable benchmark for other proof environments.

Abstract Representation of Binders in OCaml using the Bindlib Library

The Bindlib library for OCaml provides a set of tools for the manipulation of data structures with variable binding. It is very well suited for the representation of abstract syntax trees, and has already been used for the implementation of half a dozen languages and proof assistants (including a new version of the logical framework Dedukti). Bindlib is optimised for fast substitution, and it supports variable renaming. Since the representation of binders is based on higher-order abstract syntax, variable capture cannot arise during substitution. As a consequence, variable names are not updated at substitution time. They can however be explicitly recomputed to avoid "visual capture" (i.e., distinct variables with the same apparent name) when a data structure is displayed.

QWIRE Practice: Formal Verification of Quantum Circuits in Coq

We describe an embedding of the QWIRE quantum circuit language in the Coq proof assistant. This allows programmers to write quantum circuits using high-level abstractions and to prove properties of those circuits using Coq's theorem proving features. The implementation uses higher-order abstract syntax to represent variable binding and provides a type-checking algorithm for linear wire types, ensuring that quantum circuits are well-formed. We formalize a denotational semantics that interprets QWIRE circuits as superoperators on density matrices, and prove the correctness of some simple quantum programs.

Canonical HybridLF: Extending Hybrid with Dependent Types

We introduce Canonical HybridLF (CHLF), a metalogic for proving properties of deductive systems, implemented in Isabelle HOL. CHLF is closely related to two other metalogics. The first is the Edinburgh Logical Framework (LF) by Harper, Honsell and Plotkin. The second is the Hybrid system developed by Ambler, Crole and Momigliano which provides a Higher-Order Abstract Syntax (HOAS) based on un-typed lambda calculus.Historically there are two problems with HOAS: its incompatibility with inductive types and the presence of exotic terms. Hybrid provides a partial solution to these problems whereby HOAS functions that include bound variables in the metalogic are automatically converted to a machine-friendly de Bruijn representation hidden from the user.The key innovation of CHLF is the replacement of the un-typed lambda calculus with a dependently-typed lambda calculus in the style of LF. CHLF allows signatures containing constants representing the judgements and syntax of an object logic, together with proofs of metatheorems about its judgements, to be entered using a HOAS interface. Proofs that metatheorems defined in the signature are valid are created using the M2 metalogic of Schurmann and Pfenning.We make a number of advances over existing versions of Hybrid: we now have the utility of dependent types; the unitary bound variable capability of Hybrid is now potentially finitary; a type system performs the role of Hybrid well-formedness predicates; and the old method of indicating errors using special elements of core datatypes is replaced with a more streamlined one that uses the Isabelle option type.

Combinators for impure yet hygienic code generation

Code generation is the leading approach to making high-performance software reusable. Effects are indispensable in code generators, whether to report failures or to insert let-statements and if-guards. Extensive painful experience shows that unrestricted effects interact with generated binders in undesirable ways to produce unexpectedly unbound variables, or worse, unexpectedly bound ones. These subtleties hinder domain experts in using and extending the generator. A pressing problem is thus to express the desired effects while regulating them so that the generated code is correct, or at least correctly scoped, by construction.We present a code-combinator framework that lets us express arbitrary monadic effects, including mutable references and delimited control, that move open code across generated binders. The static types of our generator expressions not only ensure that a well-typed generator produces well-typed and well-scoped code. They also express the lexical scopes of generated binders and prevent mixing up variables with different scopes. For the first time ever we demonstrate statically safe and well-scoped loop interchange and constant factoring from arbitrarily nested loops.Our framework is implemented as a Haskell library that embeds an extensible typed higher-order domain-specific language. It may be regarded as ‘staged Haskell.’ To become practical, the library relies on higher-order abstract syntax and polymorphism over generated type environments, and is written in a mature language.

Embedding a full linear Lambda calculus in Haskell

We present an encoding of full linear lambda calculus in Haskell using higher order abstract syntax. By making use of promoted data kinds, multi-parameter type classes and functional dependencies, the encoding allows Haskell to do both linear type checking and linear type inference.

A Case Study on Logical Relations using Contextual Types

Proofs by logical relations play a key role to establish rich properties such as normalization or contextual equivalence. They are also challenging to mechanize. In this paper, we describe the completeness proof of algorithmic equality for simply typed lambda-terms by Crary where we reason about logically equivalent terms in the proof environment Beluga. There are three key aspects we rely upon: 1) we encode lambda-terms together with their operational semantics and algorithmic equality using higher-order abstract syntax 2) we directly encode the corresponding logical equivalence of well-typed lambda-terms using recursive types and higher-order functions 3) we exploit Beluga's support for contexts and the equational theory of simultaneous substitutions. This leads to a direct and compact mechanization, demonstrating Beluga's strength at formalizing logical relations proofs.

An Open Challenge Problem Repository for Systems Supporting Binders

A variety of logical frameworks support the use of higher-order abstract syntax in representing formal systems; however, each system has its own set of benchmarks. Even worse, general proof assistants that provide special libraries for dealing with binders offer a very limited evaluation of such libraries, and the examples given often do not exercise and stress-test key aspects that arise in the presence of binders. In this paper we design an open repository ORBI (Open challenge problem Repository for systems supporting reasoning with BInders). We believe the field of reasoning about languages with binders has matured, and a common set of benchmarks provides an important basis for evaluation and qualitative comparison of different systems and libraries that support binders, and it will help to advance the field.

The Next 700 Challenge Problems for Reasoning with Higher-Order Abstract Syntax Representations

Over the past three decades, a variety of meta-reasoning systems which support reasoning about higher-order abstract specifications have been designed and developed. In this paper, we survey and compare four meta-reasoning systems, Twelf, Beluga, Abella and Hybrid, using several benchmarks from the open repository ORBI that describes challenge problems for reasoning with higher-order abstract syntax representations. In particular, we investigate how these systems mechanize and support reasoning using a context of assumptions. This highlights commonalities and differences in these systems and is a first step towards translating between them.

Effect handlers in scope

Algebraic effect handlers are a powerful means for describing effectful computations. They provide a lightweight and orthogonal technique to define and compose the syntax and semantics of different effects. The semantics is captured by handlers, which are functions that transform syntax trees. Unfortunately, the approach does not support syntax for scoping constructs, which arise in a number of scenarios. While handlers can be used to provide a limited form of scope, we demonstrate that this approach constrains the possible interactions of effects and rules out some desired semantics. This paper presents two different ways to capture scoped constructs in syntax, and shows how to achieve different semantics by reordering handlers. The first approach expresses scopes using the existing algebraic handlers framework, but has some limitations. The problem is fully solved in the second approach where we introduce higher-order syntax.

Using circular programs for higher-order syntax

This pearl presents a novel technique for constructing a first-order syntax tree directly from a higher-order interface. We exploit circular programming to generate names for new variables, resulting in a simple yet efficient method. Our motivating application is the design of embedded languages supporting variable binding, where it is convenient to use higher-order syntax when constructing programs, but first-order syntax when processing or transforming programs.

A weak HOAS approach to the POPLmark Challenge

Capitalizing on previous encodings and formal developments about nominal calculi and type systems, we propose a weak Higher-Order Abstract Syntax formalization of the type language of pure System F<: within Coq, a proof assistant based on the Calculus of Inductive Constructions. Our encoding allows us to accomplish the proof of the transitivity property of algorithmic subtyping, which is in fact the first of the three tasks stated by the POPLmark Challenge, a set of problems that capture the most critical issues in formalizing programming language metatheory.

Cut elimination for a logic with induction and co-induction

Proof search has been used to specify a wide range of computation systems. In order to build a framework for reasoning about such specifications, we make use of a sequent calculus involving induction and co-induction. These proof principles are based on a proof-theoretic (rather than set-theoretic) notion of definition (Hallnäs, 1991 [18], Eriksson, 1991 [11], Schroeder-Heister, 1993 [38], McDowell and Miller, 2000 [22]). Definitions are akin to logic programs, where the left and right rules for defined atoms allow one to view theories as “closed” or defining fixed points. The use of definitions and free equality makes it possible to reason intensionally about syntax. We add in a consistent way rules for pre- and post-fixed points, thus allowing the user to reason inductively and co-inductively about properties of computational system making full use of higher-order abstract syntax. Consistency is guaranteed via cut-elimination, where we give a direct cut-elimination procedure in the presence of general inductive and co-inductive definitions via the parametric reducibility technique.

Parametric Compositional Data Types

In previous work we have illustrated the benefits that compositional data types (CDTs) offer for implementing languages and in general for dealing with abstract syntax trees (ASTs). Based on Swierstra's data types \'a la carte, CDTs are implemented as a Haskell library that enables the definition of recursive data types and functions on them in a modular and extendable fashion. Although CDTs provide a powerful tool for analysing and manipulating ASTs, they lack a convenient representation of variable binders. In this paper we remedy this deficiency by combining the framework of CDTs with Chlipala's parametric higher-order abstract syntax (PHOAS). We show how a generalisation from functors to difunctors enables us to capture PHOAS while still maintaining the features of the original implementation of CDTs, in particular its modularity. Unlike previous approaches, we avoid so-called exotic terms without resorting to abstract types: this is crucial when we want to perform transformations on CDTs that inspect the recursively computed CDTs, e.g. constant folding.