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Background: Single-stranded whole-genome bisulfite sequencing (ssWGBS) enables DNA methylation profiling in low-input and highly fragmented material, including cell-free DNA. In widely used post-bisulfite protocols, Adaptase-mediated…

Genomics · Quantitative Biology 2026-02-10 Yihan Fang

Keyphrases, that concisely summarize the high-level topics discussed in a document, can be categorized into present keyphrase which explicitly appears in the source text, and absent keyphrase which does not match any contiguous subsequence…

Computation and Language · Computer Science 2021-10-14 Jing Zhao , Junwei Bao , Yifan Wang , Youzheng Wu , Xiaodong He , Bowen Zhou

It is often useful, if not necessary, to reason about the syntactic structure of an expression in an interpreted language (i.e., a language with a semantics). This paper introduces a mathematical structure called a syntax framework that is…

Logic in Computer Science · Computer Science 2014-06-27 William M. Farmer , Pouya Larjani

The unification algorithm has long been a target for program synthesis research, but a fully automatic derivation remains a research goal. In deductive program synthesis, computer programming is phrased as a task in theorem proving; a…

Logic in Computer Science · Computer Science 2025-09-16 Richard Waldinger

A recent strand of research in structural proof theory aims at exploring the notion of analytic calculi (i.e. those calculi that support general and modular proof-strategies for cut elimination), and at identifying classes of logics that…

Logic in Computer Science · Computer Science 2021-02-24 Jinsheng Chen , Giuseppe Greco , Alessandra Palmigiano , Apostolos Tzimoulis

The workflow satisfiability problem is concerned with determining whether it is possible to find an allocation of authorized users to the steps in a workflow in such a way that all constraints are satisfied. The problem is NP-hard in…

Cryptography and Security · Computer Science 2012-10-16 J. Crampton , R. Crowston , G. Gutin , M. Jones , M. S. Ramanujan

The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is "constructed from scratch" rather than composed from reusable components. However, this is rare in…

Logic in Computer Science · Computer Science 2015-02-18 Krishnendu Chatterjee , Laurent Doyen , Moshe Y. Vardi

We present a device for specifying and reasoning about syntax for datatypes, programming languages, and logic calculi. More precisely, we study a notion of "signature" for specifying syntactic constructions. In the spirit of Initial…

Logic in Computer Science · Computer Science 2023-06-22 Benedikt Ahrens , André Hirschowitz , Ambroise Lafont , Marco Maggesi

We introduce an approach that aims to combine the usage of satisfiability modulo theories (SMT) solvers with the Combinatory Logic Synthesizer (CL)S framework. (CL)S is a tool for the automatic composition of software components from a…

Logic in Computer Science · Computer Science 2019-08-27 Fadil Kallat , Tristan Schäfer , Anna Vasileva

In this article we show how the problem of neural text generation can be constructively reformulated in terms of transitions between the states of a finite-state machine. This framework leads to an efficient approach to guiding text…

Computation and Language · Computer Science 2023-08-22 Brandon T. Willard , Rémi Louf

Evaluation metrics play a vital role in the growth of an area as it defines the standard of distinguishing between good and bad models. In the area of code synthesis, the commonly used evaluation metric is BLEU or perfect accuracy, but they…

Software Engineering · Computer Science 2020-09-29 Shuo Ren , Daya Guo , Shuai Lu , Long Zhou , Shujie Liu , Duyu Tang , Neel Sundaresan , Ming Zhou , Ambrosio Blanco , Shuai Ma

LLMs are widely used in complex AI applications. These applications underscore the need for LLM outputs to adhere to a specific format, for their integration with other components in the systems. Typically the format rules e.g., for data…

Machine Learning · Computer Science 2024-11-07 Shubham Ugare , Tarun Suresh , Hangoo Kang , Sasa Misailovic , Gagandeep Singh

The reactive synthesis problem is to compute a system satisfying a given specification in temporal logic. Bounded synthesis is the approach to bound the maximum size of the system that we accept as a solution to the reactive synthesis…

Logic in Computer Science · Computer Science 2018-03-28 Peter Faymonville , Bernd Finkbeiner , Markus N. Rabe , Leander Tentrup

When giving automated feedback to a student working on a beginner's exercise, many programming tutors run into a completeness problem. On the one hand, we want a student to experiment freely. On the other hand, we want a student to write…

Human-Computer Interaction · Computer Science 2020-11-17 Niek Mulleners , Johan Jeuring , Bastiaan Heeren

Synthesis is a particularly challenging problem for concurrent programs. At the same time it is a very promising approach, since concurrent programs are difficult to get right, or to analyze with traditional verification techniques. This…

Formal Languages and Automata Theory · Computer Science 2015-06-09 Anca Muscholl

We introduce E3Solver, a unification-based solver for programming-by-example (PBE) participating in the 2017 edition of the SyGuS Competition. Our tool proceeds in two phases. First, for each individual example, we enumerate a terminal…

Programming Languages · Computer Science 2017-10-20 M. Ammar Ben Khadra

A uniformization of a binary relation is a function that is contained in the relation and has the same domain as the relation. The synthesis problem asks for effective uniformization for classes of relations and functions that can be…

Formal Languages and Automata Theory · Computer Science 2018-05-08 Sarah Winter

Counterexample-guided inductive synthesis CEGIS is used to synthesize programs from a candidate space of programs. The technique is guaranteed to terminate and synthesize the correct program if the space of candidate programs is finite. But…

Logic in Computer Science · Computer Science 2014-07-22 Susmit Jha , Sanjit A. Seshia

Runtime efficiency and termination are crucial properties in the studies of program verification. Instead of dealing with these issues in an ad hoc manner, it would be useful to develop a robust framework in which such properties are…

Programming Languages · Computer Science 2026-04-06 Weijun Chen , Yuxi Fu , Huan Long

The unrealizability of a specification is often due to the assumption that the behavior of the environment is unrestricted. In this paper, we present algorithms for synthesis in bounded environments, where the environment can only generate…

Logic in Computer Science · Computer Science 2021-01-01 Rayna Dimitrova , Bernd Finkbeiner , Hazem Torfah