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Neural sequence-to-sequence models are finding increasing use in editing of documents, for example in correcting a text document or repairing source code. In this paper, we argue that common seq2seq models (with a facility to copy single tokens) are not a natural fit for such tasks, as they have to explicitly copy each unchanged token. We present an extension of seq2seq models capable of copying entire spans of the input to the output in one step, greatly reducing the number of decisions required during inference. This extension means that there are now many ways of generating the same output, which we handle by deriving a new objective for training and a variation of beam search for inference that explicitly handles this problem. In our experiments on a range of editing tasks of natural language and source code, we show that our new model consistently outperforms simpler baselines., Published in AAAI 2021

Causal inference is essential for data-driven decision making across domains such as business engagement, medical treatment and policy making. However, research on causal discovery has evolved separately from inference methods, preventing straight-forward combination of methods from both fields. In this work, we develop Deep End-to-end Causal Inference (DECI), a single flow-based non-linear additive noise model that takes in observational data and can perform both causal discovery and inference, including conditional average treatment effect (CATE) estimation. We provide a theoretical guarantee that DECI can recover the ground truth causal graph under standard causal discovery assumptions. Motivated by application impact, we extend this model to heterogeneous, mixed-type data with missing values, allowing for both continuous and discrete treatment decisions. Our results show the competitive performance of DECI when compared to relevant baselines for both causal discovery and (C)ATE estimation in over a thousand experiments on both synthetic datasets and causal machine learning benchmarks across data-types and levels of missingness.

Semantic code search is the task of retrieving a code snippet given a textual description of its functionality. Recent work has been focused on using similarity metrics between neural embeddings of text and code. However, current language models are known to struggle with longer, compositional text, and multi-step reasoning. To overcome this limitation, we propose supplementing the query sentence with a layout of its semantic structure. The semantic layout is used to break down the final reasoning decision into a series of lower-level decisions. We use a Neural Module Network architecture to implement this idea. We compare our model - NS3 (Neuro-Symbolic Semantic Search) - to a number of baselines, including state-of-the-art semantic code retrieval methods, and evaluate on two datasets - CodeSearchNet and Code Search and Question Answering. We demonstrate that our approach results in more precise code retrieval, and we study the effectiveness of our modular design when handling compositional queries.

Learning from structured data is a core machine learning task. Commonly, such data is represented as graphs, which normally only consider (typed) binary relationships between pairs of nodes. This is a substantial limitation for many domains with highly-structured data. One important such domain is source code, where hypergraph-based representations can better capture the semantically rich and structured nature of code. In this work, we present HEAT, a neural model capable of representing typed and qualified hypergraphs, where each hyperedge explicitly qualifies how participating nodes contribute. It can be viewed as a generalization of both message passing neural networks and Transformers. We evaluate HEAT on knowledge base completion and on bug detection and repair using a novel hypergraph representation of programs. In both settings, it outperforms strong baselines, indicating its power and generality., Comment: Published in TMLR

Code completion is usually cast as a language modelling problem, i.e., continuing an input in a left-to-right fashion. However, in practice, some parts of the completion (e.g., string literals) may be very hard to predict, whereas subsequent parts directly follow from the context. To handle this, we instead consider the scenario of generating code completions with "holes" inserted in places where a model is uncertain. We develop Grammformer, a Transformer-based model that guides code generation by the programming language grammar, and compare it to a variety of more standard sequence models. We train the models on code completion for C# and Python given partial code context. To evaluate models, we consider both ROUGE as well as a new metric RegexAcc that measures success of generating completions matching long outputs with as few holes as possible. In our experiments, Grammformer generates 10-50% more accurate completions compared to traditional generative models and 37-50% longer sketches compared to sketch-generating baselines trained with similar techniques., Comment: Published in ICLR 2022

Machine learning-based program analyses have recently shown the promise of integrating formal and probabilistic reasoning towards aiding software development. However, in the absence of large annotated corpora, training these analyses is challenging. Towards addressing this, we present BugLab, an approach for self-supervised learning of bug detection and repair. BugLab co-trains two models: (1) a detector model that learns to detect and repair bugs in code, (2) a selector model that learns to create buggy code for the detector to use as training data. A Python implementation of BugLab improves by up to 30% upon baseline methods on a test dataset of 2374 real-life bugs and finds 19 previously unknown bugs in open-source software., Comment: Published in NeurIPS 2021

Learning structures between groups of variables from data with missing values is an important task in the real world, yet difficult to solve. One typical scenario is discovering the structure among topics in the education domain to identify learning pathways. Here, the observations are student performances for questions under each topic which contain missing values. However, most existing methods focus on learning structures between a few individual variables from the complete data. In this work, we propose VISL, a novel scalable structure learning approach that can simultaneously infer structures between groups of variables under missing data and perform missing value imputations with deep learning. Particularly, we propose a generative model with a structured latent space and a graph neural network-based architecture, scaling to a large number of variables. Empirically, we conduct extensive experiments on synthetic, semi-synthetic, and real-world education data sets. We show improved performances on both imputation and structure learning accuracy compared to popular and recent approaches.

The challenge of automatically determining the correctness of test executions is referred to as the test oracle problem and is one of the key remaining issues for automated testing. The goal in this paper is to solve the test oracle problem in a way that is general, scalable and accurate. To achieve this, we use supervised learning over test execution traces. We label a small fraction of the execution traces with their verdict of pass or fail. We use the labelled traces to train a neural network (NN) model to learn to distinguish runtime patterns for passing versus failing executions for a given program. Our approach for building this NN model involves the following steps, 1. Instrument the program to record execution traces as sequences of method invocations and global state, 2. Label a small fraction of the execution traces with their verdicts, 3. Designing a NN component that embeds information in execution traces to fixed length vectors, 4. Design a NN model that uses the trace information for classification, 5. Evaluate the inferred classification model on unseen execution traces from the program. We evaluate our approach using case studies from different application domains: 1. Module from Ethereum Blockchain, 2. Module from PyTorch deep learning framework, 3. Microsoft SEAL encryption library components, 4. Sed stream editor, 5. Value pointer library and 6. Nine network protocols from Linux packet identifier, L7-Filter. We found the classification models for all subject programs resulted in high precision, recall and specificity, over 95%, while only training with an average 9% of the total traces. Our experiments show that the proposed neural network model is highly effective as a test oracle and is able to learn runtime patterns to distinguish passing and failing test executions for systems and tests from different application domains.

Semantic code search is the task of retrieving relevant code given a natural language query. While related to other information retrieval tasks, it requires bridging the gap between the language used in code (often abbreviated and highly technical) and natural language more suitable to describe vague concepts and ideas. To enable evaluation of progress on code search, we are releasing the CodeSearchNet Corpus and are presenting the CodeSearchNet Challenge, which consists of 99 natural language queries with about 4k expert relevance annotations of likely results from CodeSearchNet Corpus. The corpus contains about 6 million functions from open-source code spanning six programming languages (Go, Java, JavaScript, PHP, Python, and Ruby). The CodeSearchNet Corpus also contains automatically generated query-like natural language for 2 million functions, obtained from mechanically scraping and preprocessing associated function documentation. In this article, we describe the methodology used to obtain the corpus and expert labels, as well as a number of simple baseline solutions for the task. We hope that CodeSearchNet Challenge encourages researchers and practitioners to study this interesting task further and will host a competition and leaderboard to track the progress on the challenge. We are also keen on extending CodeSearchNet Challenge to more queries and programming languages in the future., Updated evaluation numbers after fixing indexing bug

Program synthesis of general-purpose source code from natural language specifications is challenging due to the need to reason about high-level patterns in the target program and low-level implementation details at the same time. In this work, we present PATOIS, a system that allows a neural program synthesizer to explicitly interleave high-level and low-level reasoning at every generation step. It accomplishes this by automatically mining common code idioms from a given corpus, incorporating them into the underlying language for neural synthesis, and training a tree-based neural synthesizer to use these idioms during code generation. We evaluate PATOIS on two complex semantic parsing datasets and show that using learned code idioms improves the synthesizer's accuracy., Comment: 33rd Conference on Neural Information Processing Systems (NeurIPS) 2019. 13 pages total, 9 pages of main text

Summarization of long sequences into a concise statement is a core problem in natural language processing, requiring non-trivial understanding of the input. Based on the promising results of graph neural networks on highly structured data, we develop a framework to extend existing sequence encoders with a graph component that can reason about long-distance relationships in weakly structured data such as text. In an extensive evaluation, we show that the resulting hybrid sequence-graph models outperform both pure sequence models as well as pure graph models on a range of summarization tasks., Published in ICLR 2019 https://openreview.net/forum?id=H1ersoRqtm

We introduce the problem of learning distributed representations of edits. By combining a "neural editor" with an "edit encoder", our models learn to represent the salient information of an edit and can be used to apply edits to new inputs. We experiment on natural language and source code edit data. Our evaluation yields promising results that suggest that our neural network models learn to capture the structure and semantics of edits. We hope that this interesting task and data source will inspire other researchers to work further on this problem., ICLR 2019

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution observed in training data. We propose a variational autoencoder model in which both encoder and decoder are graph-structured. Our decoder assumes a sequential ordering of graph extension steps and we discuss and analyze design choices that mitigate the potential downsides of this linearization. Experiments compare our approach with a wide range of baselines on the molecule generation task and show that our method is more successful at matching the statistics of the original dataset on semantically important metrics. Furthermore, we show that by using appropriate shaping of the latent space, our model allows us to design molecules that are (locally) optimal in desired properties., 8 pages, 5 figures

Generative models for source code are an interesting structured prediction problem, requiring to reason about both hard syntactic and semantic constraints as well as about natural, likely programs. We present a novel model for this problem that uses a graph to represent the intermediate state of the generated output. The generative procedure interleaves grammar-driven expansion steps with graph augmentation and neural message passing steps. An experimental evaluation shows that our new model can generate semantically meaningful expressions, outperforming a range of strong baselines.

Learning tasks on source code (i.e., formal languages) have been considered recently, but most work has tried to transfer natural language methods and does not capitalize on the unique opportunities offered by code's known syntax. For example, long-range dependencies induced by using the same variable or function in distant locations are often not considered. We propose to use graphs to represent both the syntactic and semantic structure of code and use graph-based deep learning methods to learn to reason over program structures. In this work, we present how to construct graphs from source code and how to scale Gated Graph Neural Networks training to such large graphs. We evaluate our method on two tasks: VarNaming, in which a network attempts to predict the name of a variable given its usage, and VarMisuse, in which the network learns to reason about selecting the correct variable that should be used at a given program location. Our comparison to methods that use less structured program representations shows the advantages of modeling known structure, and suggests that our models learn to infer meaningful names and to solve the VarMisuse task in many cases. Additionally, our testing showed that VarMisuse identifies a number of bugs in mature open-source projects., Comment: Published in ICLR 2018. arXiv admin note: text overlap with arXiv:1705.07867

Deep Neural Networks have been shown to succeed at a range of natural language tasks such as machine translation and text summarization. While tasks on source code (ie, formal languages) have been considered recently, most work in this area does not attempt to capitalize on the unique opportunities offered by its known syntax and structure. In this work, we introduce SmartPaste, a first task that requires to use such information. The task is a variant of the program repair problem that requires to adapt a given (pasted) snippet of code to surrounding, existing source code. As first solutions, we design a set of deep neural models that learn to represent the context of each variable location and variable usage in a data flow-sensitive way. Our evaluation suggests that our models can learn to solve the SmartPaste task in many cases, achieving 58.6% accuracy, while learning meaningful representation of variable usages.

Combining abstract, symbolic reasoning with continuous neural reasoning is a grand challenge of representation learning. As a step in this direction, we propose a new architecture, called neural equivalence networks, for the problem of learning continuous semantic representations of algebraic and logical expressions. These networks are trained to represent semantic equivalence, even of expressions that are syntactically very different. The challenge is that semantic representations must be computed in a syntax-directed manner, because semantics is compositional, but at the same time, small changes in syntax can lead to very large changes in semantics, which can be difficult for continuous neural architectures. We perform an exhaustive evaluation on the task of checking equivalence on a highly diverse class of symbolic algebraic and boolean expression types, showing that our model significantly outperforms existing architectures., Comment: Accepted to ICML 2017

In recent years, multi-label classification has attracted a significant body of research, motivated by real-life applications, such as text classification and medical diagnoses. Although sparsely studied in this context, Learning Classifier Systems are naturally well-suited to multi-label classification problems, whose search space typically involves multiple highly specific niches. This is the motivation behind our current work that introduces a generalized multi-label rule format -- allowing for flexible label-dependency modeling, with no need for explicit knowledge of which correlations to search for -- and uses it as a guide for further adapting the general Michigan-style supervised Learning Classifier System framework. The integration of the aforementioned rule format and framework adaptations results in a novel algorithm for multi-label classification whose behavior is studied through a set of properly defined artificial problems. The proposed algorithm is also thoroughly evaluated on a set of multi-label datasets and found competitive to other state-of-the-art multi-label classification methods.