Efficient differentially private learning improves drug sensitivity prediction

Antti Honkela, Mrinal Das, Arttu Nieminen, Onur Dikmen, Samuel Kaski

Research output: Contribution to journalArticleScientificpeer-review

17 Citations (Scopus)
198 Downloads (Pure)


Background: Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are based is also particularly sensitive, as it directly identifies the patients and hence cannot easily be anonymised. Differential privacy has emerged as a potentially promising solution: privacy is considered sufficient if presence of individual patients cannot be distinguished. However, differentially private learning with current methods does not improve predictions with feasible data sizes and dimensionalities. Results: We show that useful predictors can be learned under powerful differential privacy guarantees, and even from moderately-sized data sets, by demonstrating significant improvements in the accuracy of private drug sensitivity prediction with a new robust private regression method. Our method matches the predictive accuracy of the state-of-the-art non-private lasso regression using only 4x more samples under relatively strong differential privacy guarantees. Good performance with limited data is achieved by limiting the sharing of private information by decreasing the dimensionality and by projecting outliers to fit tighter bounds, therefore needing to add less noise for equal privacy. Conclusions: The proposed differentially private regression method combines theoretical appeal and asymptotic efficiency with good prediction accuracy even with moderate-sized data. As already the simple-to-implement method shows promise on the challenging genomic data, we anticipate rapid progress towards practical applications in many fields. Reviewers: This article was reviewed by Zoltan Gaspari and David Kreil.
Original languageEnglish
Pages (from-to)1-12
JournalBiology Direct
Issue number1
Publication statusPublished - 6 Feb 2018
MoE publication typeA1 Journal article-refereed


  • Differential privacy
  • Drug sensitivity prediction
  • Linear regression
  • Machine learning


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