Biology subjects

Kuru, H. I.

Publications and source records attributed to Kuru, H. I..

5 recordsLinked to original sources

bioRxiv2025

One-Hot News: Drug Synergy Models Take a Shortcut

Combinatorial drug therapy holds great promise for tackling complex diseases, but the vast number of possible drug combinations makes exhaustive experimental testing infeasible. Computational models have been developed to guide experimental screens by assigning synergy scores to drug pair-cell line combinations, where they take input structural and chemical information on drugs and molecular features of cell lines. The premise of these models is that they leverage this biological and chemical information to predict synergy measurements. In this study, we demonstrate that replacing drug and cell line representations with simple one-hot encodings results in comparable or even slightly improved performance across diverse published drug combination models. This unexpected finding suggests that current models use these representations primarily as identifiers and exploit covariation in the synergy labels. Our synthetic data experiments show that models can learn from the true features; however, when drugs and cell lines recur across drug-drug-cell triplets, this repeating structure impairs feature-based learning. While the current synergy prediction models can still aid in prioritizing drug pairs within a panel of tested drugs and cell lines, our results highlight the need for better strategies to learn from intended features and generalize to unseen drugs and cell lines.

bioinformatics↗

bioRxiv2025

DeepSynBa: Actionable Drug Combination Prediction with Complete Dose-Response Profiles

Many cancer monotherapies demonstrate limited clinical efficacy, making combination therapies a relevant treatment strategy. The extensive number of potential drug combinations and context-specific response profiles complicates the prediction of drug combination responses. Existing computational models are typically trained to predict a single aggregated synergy score, which summarises drug responses across different dosage combinations, such as Bliss or Loewe scores. This oversimplification of the drug-response surface leads to high prediction uncertainty and limited actionability, as these models fail to distinguish between potency and efficacy. We introduce DeepSynBa, an actionable model that predicts the complete dose-response matrix of drug pairs instead of relying on an aggregated synergy score. This is achieved by predicting parameters describing the response surface as an intermediate layer in the model. Evaluated on the NCI-ALMANAC and the ONeil datasets, DeepSynBa outperforms the state-of-the-art methods in the dose-response matrix prediction task across most evaluation scenarios, including testing on novel drug combinations, cell lines, and drugs, across nine different tissue types. We also show that DeepSynBa yields reliable synergy score predictions. More importantly, DeepSynBa can predict drug combination responses across different dosages for untested combinations. The intermediate dose-response parameter layer enables the separation of efficacy from potency, informing the selection of dosage ranges that optimise efficacy while limiting off-target toxicity in experimental screens. The predictive capability and the downstream actionability make DeepSynBa a powerful tool for advancing drug combination research beyond the limitations of the current approaches. The code and the dataset for DeepSynBa are available at https://github.com/hikuru/DeepSynBa.

bioinformatics↗

bioRxiv2023

From Cell-Lines to Cancer Patients: Personalized Drug Synergy Prediction

Combination drug therapies are effective treatments for cancer. However, the genetic heterogeneity of the patients and exponentially large space of drug pairings pose significant challenges for finding the right combination for a specific patient. Current in silico prediction methods can be instrumental in reducing the vast number of candidate drug combinations. However, existing powerful methods are trained with cancer cell line gene expression data, which limits their applicability in clinical settings. While synergy measurements on cell lines models are available at large scale, patient-derived samples are too few to train a complex model. On the other hand, patient-specific single-drug response data are relatively more available. In this work, we propose a deep learning framework, Personalized Deep Synergy Predictor (PDSP), that enables us to use the patient-specific single drug response data for customizing patient drug synergy predictions. PDSP is first trained to learn synergy scores of drug pairs and their single drug presonses for a given cell line using drug structures and large scale cell line gene expression data. Then, the model is fine-tuned for patients with their patient gene expression data and associated single drug response measured on the patient ex vivo samples. In this study, we evaluate PDSP on data from three leukemia patients and observe that it improves the prediction accuracy by 27% compared to models trained on cancer cell line data. PDSP is built and available at https://github.com/hikuru/PDSP

bioinformatics↗

bioRxiv2020

PRER: A Patient Representation with Pairwise Relative Expression of Proteins on Biological Networks

Changes in protein and gene expression levels are often used as features to predictive models such as survival prediction. A common strategy to aggregate information on individual proteins is to integrate the expression information with biological networks. We propose a novel patient representation in this work where we integrate proteins expression levels with the protein-protein interaction (PPI) networks. Patient representation with PRER (Pairwise Relative Expressions with Random walks) uses the neighborhood of a protein to capture the dysregulation patterns in protein abundance. Specifically, PRER computes a feature vector for a patient by comparing the source proteins protein expression level with other proteins levels in its neighborhood. This neighborhood of the source protein is derived using a biased random-walk strategy on the network. We test PRERs performance through a survival prediction task in 10 different cancers using random forest survival models. PRER representation yields a statistically significant predictive performance in 9 out of 10 cancer types when compared to a representation based on individual protein expression. We also identify important proteins that are not important in the models trained with the expression values but emerge as predictive in models trained with PRER features. The set of identified relations provides a valuable collection of biomarkers with high prognostic value. PRER representation can be used for other complex diseases and prediction tasks that use molecular expression profiles as input. PRER is freely available at: https://github.com/hikuru/PRER

systems biology↗

bioRxiv2020

MatchMaker: A Deep Learning Framework for Drug Synergy Prediction

Drug combination therapies have been a viable strategy for the treatment of complex diseases such as cancer due to increased efficacy and reduced side effects. However, experimentally validating all possible combinations for synergistic interaction even with high-throughout screens is intractable due to vast combinatorial search space. Computational techniques can reduce the number of combinations to be evaluated experimentally by prioritizing promising candidates. We present MatchMaker that predicts drug synergy scores using drug chemical structure information and gene expression profiles of cell lines in a deep learning framework. For the first time, our model utilizes the largest known drug combination dataset to date, DrugComb. We compare the performance of MatchMaker with the state-of-the-art models and observe up to ~ 20% correlation and ~ 40% mean squared error (MSE) improvements over the next best method. We investigate the cell types and drug pairs that are relatively harder to predict and present novel candidate pairs. MatchMaker is built and available at https://github.com/tastanlab/matchmaker

bioinformatics↗