Fault localization is essential to software maintenance tasks such as testing and automated program repair. Many fault localization techniques have been developed, the most common of which are spectrum-based. Most techniques have been designed for traditional programming paradigms that map passing and failing test cases to lines or branches of code, hence specialized programming paradigms which utilize different code abstractions may fail to localize well. In this paper, we study fault localization in the context of a class of programs, molecular programs. Recent research has designed automated testing and repair frameworks for these pro- grams but has ignored the importance of fault localization. As we demonstrate, using existing spectrum-based approaches may not provide much information. Instead we propose a novel approach, Traceback, that leverages temporal trace data. In an empirical study on a set of 89 faulty program variants, we demonstrate that Trace- back provides between a 32-90% improvement in localization over reaction-based mapping, a direct translation of spectrum-based localization. We see little difference in parameter tuning of Trace- back when all tests, or only code-based (invariant) tests are used, however the best depth and weight parameters vary when using specification based tests, which can be either functional or meta- morphic. Overall, invariant-based tests provide the best localization results (either alone or in combination with others), followed by metamorphic and then functional tests.

Chemical reaction networks (CRNs) are an emerging distributed computational paradigm where programs are encoded as a set of abstract chemical reactions. CRNs can be compiled into DNA strands which perform the computations in vitro, creating a foundation for intelligent nanodevices. Recent research proposed a software testing framework for stochastic CRN programs in simulation, however, it relies on existing program specifications. In practice, specifications are often lacking and when they do exist, transforming them into test cases is time-intensive and can be error prone. In this work, we propose an inference technique called ChemFlow which extracts 3 types of invariants from an existing CRN model. The extracted invariants can then be used for test generation or model validation against program implementations. We applied ChemFlow to 13 CRN programs ranging from toy examples to real biological models with hundreds of reactions. We find that the invariants provide strong fault detection and often exhibit less flakiness than specification derived tests. In the biological models we showed invariants to developers and they confirmed that some of these point to parts of the model that are biologically incorrect or incomplete suggesting we may be able to use ChemFlow to improve model quality.

The use of non-traditional computing devices is growing rapidly. One paradigm of interest is chemical reaction networks (CRNs) which can model and use chemical interactions for computation. These CRNs are used to develop programs at the nanoscale for applications such as intelligent drug delivery. In practice, these programs are developed in simulation environments, and then compiled into physical systems. A challenge when designing CRNs for computation is the lack of techniques to verify and validate correctness. In this work, we adapt software testing and repair techniques for use in this domain. In initial work, we designed a testing framework to handle the challenges presented by CRN programs; this includes distributed computation and stochastic behavior. We extended this framework to implement automated program repair of CRN models and automated test generation via program invariants. For future work, we will develop a notion of fault localization for these programs, develop a theory of mutation generation, and address issues regarding flakiness present in this computing paradigm.

In recent years the use of non-traditional computing mechanisms has grown rapidly. One paradigm uses chemical reaction networks (CRNs) to compute via chemical interactions. CRNs are used to prototype molecular devices at the nanoscale such as intelligent drug therapeutics. In practice, these programs are first written and simulated in environments such as MatLab and later compiled into physical molecules such as DNA strands. However, techniques for testing the correctness of CRNs are lacking. Current methods of validating CRNs include model checking and theorem proving, but these are limited in scalability. In this paper we present the first (to the best of our knowledge) testing framework for CRNs, ChemTest. ChemTest evaluates test oracles on individual simulation traces and supports functional, metamorphic, internal and hyper test cases. It also allows for flakiness and programs that are probabilistic. We performed a large case study demonstrating that ChemTest can find seeded faults and scales beyond model checking. Of our tests, 21% are inherently flaky, suggesting that systematic support for this paradigm is needed. On average, functional tests find 66.5% of the faults, while metamorphic tests find 80.4%, showing the benefit of using metamorphic relationships in our test framework. In addition, we show how the time at evaluation impacts fault detection.