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In recent years, many incidents have been reported where machine learning models exhibited discrimination among people based on race, sex, age, etc. Research has been conducted to measure and mitigate unfairness in machine learning models. For a machine learning task, it is a common practice to build a pipeline that includes an ordered set of data preprocessing stages followed by a classifier. However, most of the research on fairness has considered a single classifier based prediction task. What are the fairness impacts of the preprocessing stages in machine learning pipeline? Furthermore, studies showed that often the root cause of unfairness is ingrained in the data itself, rather than the model. But no research has been conducted to measure the unfairness caused by a specific transformation made in the data preprocessing stage. In this paper, we introduced the causal method of fairness to reason about the fairness impact of data preprocessing stages in ML pipeline. We leveraged existing metrics to define the fairness measures of the stages. Then we conducted a detailed fairness evaluation of the preprocessing stages in 37 pipelines collected from three different sources. Our results show that certain data transformers are causing the model to exhibit unfairness. We identified a number of fairness patterns in several categories of data transformers. Finally, we showed how the local fairness of a preprocessing stage composes in the global fairness of the pipeline. We used the fairness composition to choose appropriate downstream transformer that mitigates unfairness in the machine learning pipeline. 

Machine learning models are increasingly being used in important decision-making software such as approving bank loans, recommending criminal sentencing, hiring employees, and so on. It is important to ensure the fairness of these models so that no discrimination is made between different groups in a protected attribute (e.g., race, sex, age) while decision making. Algorithms have been developed to measure unfairness and mitigate them to a certain extent. In this paper, we have focused on the empirical evaluation of fairness and mitigations on real-world machine learning models. We have created a benchmark of 40 top-rated models from Kaggle used for 5 different tasks, and then using a comprehensive set of fairness metrics evaluated their fairness. Then, we have applied 7 mitigation techniques on these models and analyzed the fairness, mitigation results, and impacts on performance. We have found that some model optimization techniques result in inducing unfairness in the models. On the other hand, although there are some fairness control mechanisms in machine learning libraries, they are not documented. The mitigation algorithm also exhibit common patterns such as mitigation in the post-processing is often costly (in terms of performance) and mitigation in the pre-processing stage is preferred in most cases. We have also presented different trade-off choices of fairness mitigation decisions. Our study suggests future research directions to reduce the gap between theoretical fairness aware algorithms and the software engineering methods to leverage them in practice. 

Deep learning is being incorporated in many modern software systems. Deep learning approaches train a deep neural network (DNN) model using training examples, and then use the DNN model for prediction. While the structure of a DNN model as layers is observable, the model is treated in its entirety as a monolithic component. To change the logic implemented by the model, e.g. to add/remove logic that recognizes inputs belonging to a certain class, or to replace the logic with an alternative, the training examples need to be changed and the DNN needs to be retrained using the new set of examples. We argue that decomposing a DNN into DNN modules-akin to decomposing a monolithic software code into modules-can bring the benefits of modularity to deep learning. In this work, we develop a methodology for decomposing DNNs for multi-class problems into DNN modules. For four canonical problems, namely MNIST, EMNIST, FMNIST, and KMNIST, we demonstrate that such decomposition enables reuse of DNN modules to create different DNNs, enables replacement of one DNN module in a DNN with another without needing to retrain. The DNN models formed by composing DNN modules are at least as good as traditional monolithic DNNs in terms of test accuracy for our problems. 

Machine learning models are increasingly being used in important decision-making software such as approving bank loans, recommending criminal sentencing, hiring employees, and so on. It is important to ensure the fairness of these models so that no discrimination is made based on protected attribute (e.g., race, sex, age) while decision making. Algorithms have been developed to measure unfairness and mitigate them to a certain extent. In this paper, we have focused on the empirical evaluation of fairness and mitigations on real-world machine learning models. We have created a benchmark of 40 top-rated models from Kaggle used for 5 different tasks, and then using a comprehensive set of fairness metrics, evaluated their fairness. Then, we have applied 7 mitigation techniques on these models and analyzed the fairness, mitigation results, and impacts on performance. We have found that some model optimization techniques result in inducing unfairness in the models. On the other hand, although there are some fairness control mechanisms in machine learning libraries, they are not documented. The mitigation algorithm also exhibit common patterns such as mitigation in the post-processing is often costly (in terms of performance) and mitigation in the pre-processing stage is preferred in most cases. We have also presented different trade-off choices of fairness mitigation decisions. Our study suggests future research directions to reduce the gap between theoretical fairness aware algorithms and the software engineering methods to leverage them in practice. 

Significant interest in applying Deep Neural Network (DNN) has fueled the need to support engineering of software that uses DNNs. Repairing software that uses DNNs is one such unmistakable SE need where automated tools could be very helpful; however, we do not fully understand challenges to repairing and patterns that are utilized when manually repairing them. What challenges should automated repair tools address? What are the repair patterns whose automation could help developers? Which repair patterns should be assigned a higher priority for automation? This work presents a comprehensive study of bug fix patterns to address these questions. We have studied 415 repairs from Stack Overflow and 555 repairs from GitHub for five popular deep learning libraries Caffe, Keras, Tensorflow, Theano, and Torch to understand challenges in repairs and bug repair patterns. Our key findings reveal that DNN bug fix patterns are distinctive compared to traditional bug fix patterns; the most common bug fix patterns are fixing data dimension and neural network connectivity; DNN bug fixes have the potential to introduce adversarial vulnerabilities; DNN bug fixes frequently introduce new bugs; and DNN bug localization, reuse of trained model, and coping with frequent releases are major challenges faced by developers when fixing bugs. We also contribute a benchmark of 667 DNN (bug, repair) instances. 

Abstract Motivation As the cost of sequencing decreases, the amount of data being deposited into public repositories is increasing rapidly. Public databases rely on the user to provide metadata for each submission that is prone to user error. Unfortunately, most public databases, such as non-redundant (NR), rely on user input and do not have methods for identifying errors in the provided metadata, leading to the potential for error propagation. Previous research on a small subset of the non-redundant (NR) database analyzed misclassification based on sequence similarity. To the best of our knowledge, the amount of misclassification in the entire database has not been quantified. We propose a heuristic method to detect potentially misclassified taxonomic assignments in the NR database. We applied a curation technique and quality control to find the most probable taxonomic assignment. Our method incorporates provenance and frequency of each annotation from manually and computationally created databases and clustering information at 95% similarity. Results We found more than 2 million potentially taxonomically misclassified proteins in the NR database. Using simulated data, we show a high precision of 97% and a recall of 87% for detecting taxonomically misclassified proteins. The proposed approach and findings could also be applied to other databases. Availability Source code, dataset, documentation, Jupyter notebooks, and Docker container are available at https://github.com/boalang/nr. Supplementary information Supplementary data are available at Bioinformatics online. 

Deep learning has gained substantial popularity in recent years. Developers mainly rely on libraries and tools to add deep learning capabilities to their software. What kinds of bugs are frequently found in such software? What are the root causes of such bugs? What impacts do such bugs have? Which stages of deep learning pipeline are more bug prone? Are there any antipatterns? Understanding such characteristics of bugs in deep learning software has the potential to foster the development of better deep learning platforms, debugging mechanisms, development practices, and encourage the development of analysis and verification frameworks. Therefore, we study 2716 high-quality posts from Stack Overflow and 500 bug fix commits from Github about five popular deep learning libraries Caffe, Keras, Tensorflow, Theano, and Torch to understand the types of bugs, root causes of bugs, impacts of bugs, bug-prone stage of deep learning pipeline as well as whether there are some common antipatterns found in this buggy software. The key findings of our study include: data bug and logic bug are the most severe bug types in deep learning software appearing more than 48% of the times, major root causes of these bugs are Incorrect Model Parameter (IPS) and Structural Inefficiency (SI) showing up more than 43% of the times.We have also found that the bugs in the usage of deep learning libraries have some common antipatterns.