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Identifying and Mitigating Potential Biases in Predicting Drug Approvals

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Abstract

Introduction

Machine learning models are increasingly applied to predict the drug development outcomes based on intermediary clinical trial results. A key challenge to this task is to address various forms of bias in the historical drug approval data.

Objective

We aimed to identify and mitigate the bias in drug approval predictions and quantify the impacts of debiasing in terms of financial value and drug safety.

Methods

We instantiated the Debiasing Variational Autoencoder, the state-of-the-art model for automated debiasing. We trained and evaluated the model on the Citeline dataset provided by Informa Pharma Intelligence to predict the final drug development outcome from phase II trial results.

Results

The debiased Debiasing Variational Autoencoder model achieved better performance (measured by the \(F_{1}\) score 0.48) in predicting the drug development outcomes than its un-debiased baseline (\(F_{1}\) score 0.25). It had a much higher true-positive rate than baseline (60% vs 15%), while its true-negative rate was slightly lower (88% vs 99%). The Debiasing Variational Autoencoder distinguished between drugs developed by large pharmaceutical firms and those by small biotech companies. The model prediction is strongly influenced by multiple factors such as prior approval of the drug for another indication, whether the trial meets the positive/negative endpoints, and the year when the trial is completed. We estimate that the debiased model generates financial value for the drug developer in six major therapeutic areas, with a range of US$763–1,365 million.

Conclusions

Our analysis shows that debiasing improves the financial efficiency of late-stage drug development. From the pharmacovigilance perspective, the debiased model is more likely to identify drugs that are both safe and effective. Meanwhile, it may predict a higher probability of success for drugs with potential adverse effects (because of its lower true-negative rate), thus it must be used with caution to predict the development outcomes of drug candidates currently in the pipeline.

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Notes

  1. As of 5 December 2021. The Citeline data is continually updated to include new clinical trials.

  2. We use the notation of conditional probability, \(Q_{i} ( \cdot |X_{\text{train}})\), to emphasize that the latent space density is sensitive to the distribution of input features in the training dataset, \(X_{\text{train}}\).

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Acknowledgements

We thank Informa Pharma Intelligence for providing us access to their Citeline data. We thank Kate Lyons and Jillian Ternullo for logistics support, and Jayna Cummings for editorial assistance. Research support from the MIT Laboratory for Financial Engineering is gratefully acknowledged. The views and opinions expressed in this article are those of the authors only, and do not necessarily represent the views and opinions of any institution or agency, any of their affiliates or employees acknowledged above.

Author information

Authors and Affiliations

  1. MIT Laboratory for Financial Engineering, Cambridge, MA, USA

    Qingyang Xu & Andrew W. Lo

  2. MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA

    Elaheh Ahmadi, Alexander Amini, Daniela Rus & Andrew W. Lo

  3. MIT Department of Electrical Engineering and Computer Science, Cambridge, MA, USA

    Elaheh Ahmadi, Alexander Amini, Daniela Rus & Andrew W. Lo

  4. MIT Operations Research Center, Cambridge, MA, USA

    Qingyang Xu & Andrew W. Lo

  5. Sante Fe Institute, Santa Fe, NM, USA

    Andrew W. Lo

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  1. Qingyang Xu
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Corresponding author

Correspondence to Andrew W. Lo.

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Funding

Research support from MIT Laboratory for Financial Engineering is gratefully acknowledged. No direct funding was received for this study and no funding bodies had any role in the study design, data collection and analysis, decision to publish, or preparation of this article. The authors were personally salaried by their institutions during the period of writing (though no specific salary was set aside or given for the writing of this manuscript).

Conflict of interest

Q.X. reports personal investments in publicly traded pharmaceutical companies. E.A. and A.A. are co-founders of Themis AI. D.R. reports personal investments in technology companies and mutual funds. D.R. is co-founder of Venti Technologies, ThemisAI, and The Routing Company. She is a member of the technology advisory board of British Telecom, Hyundai Motor Company, RobGlobal, Knowledge AI, Ten63, Venti, and RIIID. She is a member of the board of trustees of MBZUAI, a senior visiting fellow at The MITRE Corporation, and a member of Accenture’s Luminary program. She was a member of PCAST and DIB and has given recent talks at GITEX, TransformAI, Stavros Niarchos Foundation, Purdue, Harvard Radcliff, UIUC, University of Pennsylvania, Johns Hopkins University, ETH, EPFL, KTH, and University of Cambridge. D.R.’s research is funded by the USA Air Force, NSF, ONR, DARPA, Toyota Research Institute, IBM, The Boeing Company, Amazon, JPMC, DSTA, DSO, GIST, the Israel Ministry of Defense, AMS, SMART, and a TED Audacious Prize. A.W.L. reports personal investments in private biotech companies, biotech venture capital funds, and mutual funds. A.W.L. is a co-founder and partner of QLS Advisors, a healthcare analytics and consulting company; an advisor to Apricity Health, Aracari Bio, BrightEdge Impact Fund, Enable Medicine, FINRA, Lazard, Quantile Health, SalioGen Therapeutics, the Swiss Finance Institute, Thalēs, and Think Therapeutics; a director of AbCellera, Atomwise, BridgeBio Pharma, Roivant Sciences, and Annual Reviews; and a member of the NIH’s National Center for Advancing Translational Sciences Advisory Council. During the most recent 6-year period, A.W.L. has received speaking/consulting fees, honoraria, or other forms of compensation from: AlphaSimplex Group, Annual Reviews, the Bernstein Fabozzi Jacobs Levy Award, BIS, BridgeBio Pharma, Cambridge Associates, Chicago Mercantile Exchange, Financial Times, Harvard Kennedy School, IMF, JOIM, National Bank of Belgium, New Frontiers Advisors (for 2020 Harry M. Markowitz Prize), Q Group, Research Affiliates, Roivant Sciences, and the Swiss Finance Institute.

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Availability of data and material

Citeline is a proprietary dataset provided by Informa Pharma Intelligence and can be accessed via commercial license. The probability of success estimates extracted from historical drug development data in Citeline can be accessed via Project ALPHA https://projectalpha.mit.edu/pos/.

Code availability

The code for this work is available from the corresponding author on reasonable request.

Authors’ contributions

The study was first conceived by D.R. and A.W.L. Data curation and preprocessing were performed by Q.X. The code for training the deep learning models, data visualization, and hyperparameter sensitivity analysis was written by E.A., with help from Q.X. and A.A. The deep learning models were trained by Q.X. on the MIT Engaging cluster. The code for formal analysis was primarily written by Q.X., with crucial inputs from E.A. and A.A. and supervision by D.R. and A.W.L. The first draft of the manuscript was written by Q.X. and E.A. All authors reviewed and commented on previous versions of the manuscript. All authors read and approved the final version of the manuscript.

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Xu, Q., Ahmadi, E., Amini, A. et al. Identifying and Mitigating Potential Biases in Predicting Drug Approvals. Drug Saf 45, 521–533 (2022). https://doi.org/10.1007/s40264-022-01160-9

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