research paper on software reengineering

Automating Software Re-engineering

Introduction to the ISoLA 2020 Track

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• First Online: 27 October 2020
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• Serge Demeyer 10 ,
• Reiner Hähnle 11 &
• Heiko Mantel 11  

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12477))

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• International Symposium on Leveraging Applications of Formal Methods

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Software Engineering as a discipline and, in particular, as a research field within Computer Science, is still mainly focused on methods, techniques, processes, and tools to develop software from scratch. In reality, however, greenfield scenarios are not the most common ones. It is important to realize that dynamic evolution of software became a much more common and relevant issue in recent times, and its importance keeps growing. Software refactoring, parallelization, adaptation, therefore, become central activities in the value chain: automating them can realize huge gains. Formal approaches to software modeling and analysis are poised to make a substantial contribution to software re-engineering, because they are fundamentally concerned with automation and correctness. This potential, however, is far from being realized. Formal methods tend to aim at software development ab ovo or look at some piece of given software as a static object. This state of affairs motivated a track on Automating Software Re-Engineering, where we invited a group of leading researchers with an active interest in the automation of software re-engineering to discuss the state of the art.

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Automating Software Re-engineering: Introduction to the ISoLA 2022 Track

Maintaining Security in Software Evolution

Search-based detection of model level changes.

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Demeyer, S., Hähnle, R., Mantel, H. (2020). Automating Software Re-engineering. In: Margaria, T., Steffen, B. (eds) Leveraging Applications of Formal Methods, Verification and Validation: Engineering Principles. ISoLA 2020. Lecture Notes in Computer Science(), vol 12477. Springer, Cham. https://doi.org/10.1007/978-3-030-61470-6_1

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Title: no free lunch: research software testing in teaching.

Abstract: Software is at the core of most scientific discoveries today. Therefore, the quality of research results highly depends on the quality of the research software. Rigorous testing, as we know it from software engineering in the industry, could ensure the quality of the research software but it also requires a substantial effort that is often not rewarded in academia. Therefore, this research explores the effects of research software testing integrated into teaching on research software. In an in-vivo experiment, we integrated the engineering of a test suite for a large-scale network simulation as group projects into a course on software testing at the Blekinge Institute of Technology, Sweden, and qualitatively measured the effects of this integration on the research software. We found that the research software benefited from the integration through substantially improved documentation and fewer hardware and software dependencies. However, this integration was effortful and although the student teams developed elegant and thoughtful test suites, no code by students went directly into the research software since we were not able to make the integration back into the research software obligatory or even remunerative. Although we strongly believe that integrating research software engineering such as testing into teaching is not only valuable for the research software itself but also for students, the research of the next generation, as they get in touch with research software engineering and bleeding-edge research in their field as part of their education, the uncertainty about the intellectual properties of students' code substantially limits the potential of integrating research software testing into teaching.

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• Published: 08 May 2024

Accurate structure prediction of biomolecular interactions with AlphaFold 3

• Josh Abramson   ORCID: orcid.org/0009-0000-3496-6952 1   na1 ,
• Jonas Adler   ORCID: orcid.org/0000-0001-9928-3407 1   na1 ,
• Jack Dunger 1   na1 ,
• Richard Evans   ORCID: orcid.org/0000-0003-4675-8469 1   na1 ,
• Tim Green   ORCID: orcid.org/0000-0002-3227-1505 1   na1 ,
• Alexander Pritzel   ORCID: orcid.org/0000-0002-4233-9040 1   na1 ,
• Olaf Ronneberger   ORCID: orcid.org/0000-0002-4266-1515 1   na1 ,
• Lindsay Willmore   ORCID: orcid.org/0000-0003-4314-0778 1   na1 ,
• Andrew J. Ballard   ORCID: orcid.org/0000-0003-4956-5304 1 ,
• Joshua Bambrick   ORCID: orcid.org/0009-0003-3908-0722 2 ,
• Sebastian W. Bodenstein 1 ,
• David A. Evans 1 ,
• Chia-Chun Hung   ORCID: orcid.org/0000-0002-5264-9165 2 ,
• Michael O’Neill 1 ,
• David Reiman   ORCID: orcid.org/0000-0002-1605-7197 1 ,
• Kathryn Tunyasuvunakool   ORCID: orcid.org/0000-0002-8594-1074 1 ,
• Zachary Wu   ORCID: orcid.org/0000-0003-2429-9812 1 ,
• Akvilė Žemgulytė 1 ,
• Eirini Arvaniti 3 ,
• Charles Beattie   ORCID: orcid.org/0000-0003-1840-054X 3 ,
• Ottavia Bertolli   ORCID: orcid.org/0000-0001-8578-3216 3 ,
• Alex Bridgland 3 ,
• Alexey Cherepanov   ORCID: orcid.org/0000-0002-5227-0622 4 ,
• Miles Congreve 4 ,
• Alexander I. Cowen-Rivers 3 ,
• Andrew Cowie   ORCID: orcid.org/0000-0002-4491-1434 3 ,
• Michael Figurnov   ORCID: orcid.org/0000-0003-1386-8741 3 ,
• Fabian B. Fuchs 3 ,
• Hannah Gladman 3 ,
• Rishub Jain 3 ,
• Yousuf A. Khan   ORCID: orcid.org/0000-0003-0201-2796 3 ,
• Caroline M. R. Low 4 ,
• Kuba Perlin 3 ,
• Anna Potapenko 3 ,
• Pascal Savy 4 ,
• Sukhdeep Singh 3 ,
• Adrian Stecula   ORCID: orcid.org/0000-0001-6914-6743 4 ,
• Ashok Thillaisundaram 3 ,
• Catherine Tong   ORCID: orcid.org/0000-0001-7570-4801 4 ,
• Sergei Yakneen   ORCID: orcid.org/0000-0001-7827-9839 4 ,
• Ellen D. Zhong   ORCID: orcid.org/0000-0001-6345-1907 3 ,
• Michal Zielinski 3 ,
• Augustin Žídek   ORCID: orcid.org/0000-0002-0748-9684 3 ,
• Victor Bapst 1   na2 ,
• Pushmeet Kohli   ORCID: orcid.org/0000-0002-7466-7997 1   na2 ,
• Max Jaderberg   ORCID: orcid.org/0000-0002-9033-2695 2   na2 ,
• Demis Hassabis   ORCID: orcid.org/0000-0003-2812-9917 1 , 2   na2 &
• John M. Jumper   ORCID: orcid.org/0000-0001-6169-6580 1   na2  

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

• Drug discovery
• Machine learning
• Protein structure predictions
• Structural biology

The introduction of AlphaFold 2 1 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design 2–6 . In this paper, we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture, which is capable of joint structure prediction of complexes including proteins, nucleic acids, small molecules, ions, and modified residues. The new AlphaFold model demonstrates significantly improved accuracy over many previous specialised tools: far greater accuracy on protein-ligand interactions than state of the art docking tools, much higher accuracy on protein-nucleic acid interactions than nucleic-acid-specific predictors, and significantly higher antibody-antigen prediction accuracy than AlphaFold-Multimer v2.3 7,8 . Together these results show that high accuracy modelling across biomolecular space is possible within a single unified deep learning framework.

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Author information.

These authors contributed equally: Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore

These authors jointly supervised this work: Victor Bapst, Pushmeet Kohli, Max Jaderberg, Demis Hassabis, John M. Jumper

Authors and Affiliations

Core Contributor, Google DeepMind, London, UK

Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J. Ballard, Sebastian W. Bodenstein, David A. Evans, Michael O’Neill, David Reiman, Kathryn Tunyasuvunakool, Zachary Wu, Akvilė Žemgulytė, Victor Bapst, Pushmeet Kohli, Demis Hassabis & John M. Jumper

Core Contributor, Isomorphic Labs, London, UK

Joshua Bambrick, Chia-Chun Hung, Max Jaderberg & Demis Hassabis

Google DeepMind, London, UK

Eirini Arvaniti, Charles Beattie, Ottavia Bertolli, Alex Bridgland, Alexander I. Cowen-Rivers, Andrew Cowie, Michael Figurnov, Fabian B. Fuchs, Hannah Gladman, Rishub Jain, Yousuf A. Khan, Kuba Perlin, Anna Potapenko, Sukhdeep Singh, Ashok Thillaisundaram, Ellen D. Zhong, Michal Zielinski & Augustin Žídek

Isomorphic Labs, London, UK

Alexey Cherepanov, Miles Congreve, Caroline M. R. Low, Pascal Savy, Adrian Stecula, Catherine Tong & Sergei Yakneen

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Corresponding authors

Correspondence to Max Jaderberg , Demis Hassabis or John M. Jumper .

Supplementary information

Supplementary information.

This Supplementary Information file contains the following 9 sections: (1) Notation; (2) Data pipeline; (3) Model architecture; (4) Auxiliary heads; (5) Training and inference; (6) Evaluation; (7) Differences to AlphaFold2 and AlphaFold-Multimer; (8) Supplemental Results; and (9) Appendix: CCD Code and PDB ID tables.

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Abramson, J., Adler, J., Dunger, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature (2024). https://doi.org/10.1038/s41586-024-07487-w

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Received : 19 December 2023

Accepted : 29 April 2024

Published : 08 May 2024

DOI : https://doi.org/10.1038/s41586-024-07487-w

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