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Register a new userTowards Long-term and Archivable Reproducibility
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Added by
Mohammad Akhlaghi
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Analysis pipelines commonly use high-level technologies that are popular when created, but are unlikely to be readable, executable, or sustainable in the long term. A set of criteria is introduced to address this problem: Completeness (no execution requirement beyond a minimal Unix-like operating system, no administrator privileges, no network connection, and storage primarily in plain text); modular design; minimal complexity; scalability; verifiable inputs and outputs; version control; linking analysis with narrative; and free software. As a proof of concept, we introduce Maneage (Managing data lineage), enabling cheap archiving, provenance extraction, and peer verification that been tested in several research publications. We show that longevity is a realistic requirement that does not sacrifice immediate or short-term reproducibility. The caveats (with proposed solutions) are then discussed and we conclude with the benefits for the various stakeholders. This paper is itself written with Maneage (project commit eeff5de).
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Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results, but then loosely describe the steps taken to derive them. Not only can the methods and the implementation be complex, but also their configuration may require setting many parameters and/or depend on particular system configurations. While many researchers recognize the importance of reproducibility, the challenge of making it happen often outweigh the benefits. Fortunately, a plethora of reproducibility solutions have been recently designed and implemented by the community. In particular, packaging tools (e.g., ReproZip) and virtualization tools (e.g., Docker) are promising solutions towards facilitating reproducibility for both authors and reviewers. To address the incentive problem, we have implemented a new publication model for the Reproducibility Section of Information Systems Journal. In this section, authors submit a reproducibility paper that explains in detail the computational assets from a previous published manuscript in Information Systems.
As Recommender Systems (RS) influence more and more people in their daily life, the issue of fairness in recommendation is becoming more and more important. Most of the prior approaches to fairness-aware recommendation have been situated in a static or one-shot setting, where the protected groups of items are fixed, and the model provides a one-time fairness solution based on fairness-constrained optimization. This fails to consider the dynamic nature of the recommender systems, where attributes such as item popularity may change over time due to the recommendation policy and user engagement. For example, products that were once popular may become no longer popular, and vice versa. As a result, the system that aims to maintain long-term fairness on the item exposure in different popularity groups must accommodate this change in a timely fashion. Novel to this work, we explore the problem of long-term fairness in recommendation and accomplish the problem through dynamic fairness learning. We focus on the fairness of exposure of items in different groups, while the division of the groups is based on item popularity, which dynamically changes over time in the recommendation process. We tackle this problem by proposing a fairness-constrained reinforcement learning algorithm for recommendation, which models the recommendation problem as a Constrained Markov Decision Process (CMDP), so that the model can dynamically adjust its recommendation policy to make sure the fairness requirement is always satisfied when the environment changes. Experiments on several real-world datasets verify our frameworks superiority in terms of recommendation performance, short-term fairness, and long-term fairness.
Recent reproducibility case studies have raised concerns showing that much of the deposited research has not been reproducible. One of their conclusions was that the way data repositories store research data and code cannot fully facilitate reproducibility due to the absence of a runtime environment needed for the code execution. New specialized reproducibility tools provide cloud-based computational environments for code encapsulation, thus enabling research portability and reproducibility. However, they do not often enable research discoverability, standardized data citation, or long-term archival like data repositories do. This paper addresses the shortcomings of data repositories and reproducibility tools and how they could be overcome to improve the current lack of computational reproducibility in published and archived research outputs.
In recent years, significant effort has been invested verifying the reproducibility and robustness of research claims in social and behavioral sciences (SBS), much of which has involved resource-intensive replication projects. In this paper, we investigate prediction of the reproducibility of SBS papers using machine learning methods based on a set of features. We propose a framework that extracts five types of features from scholarly work that can be used to support assessments of reproducibility of published research claims. Bibliometric features, venue features, and author features are collected from public APIs or extracted using open source machine learning libraries with customized parsers. Statistical features, such as p-values, are extracted by recognizing patterns in the body text. Semantic features, such as funding information, are obtained from public APIs or are extracted using natural language processing models. We analyze pairwise correlations between individual features and their importance for predicting a set of human-assessed ground truth labels. In doing so, we identify a subset of 9 top features that play relatively more important roles in predicting the reproducibility of SBS papers in our corpus. Results are verified by comparing performances of 10 supervised predictive classifiers trained on different sets of features.
We present an overview of the recently funded Merging Science and Cyberinfrastructure Pathways: The Whole Tale project (NSF award #1541450). Our approach has two nested goals: 1) deliver an environment that enables researchers to create a complete narrative of the research process including exposure of the data-to-publication lifecycle, and 2) systematically and persistently link research publications to their associated digital scholarly objects such as the data, code, and workflows. To enable this, Whole Tale will create an environment where researchers can collaborate on data, workspaces, and workflows and then publish them for future adoption or modification. Published data and applications will be consumed either directly by users using the Whole Tale environment or can be integrated into existing or future domain Science Gateways.
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