Aida Tayebi

Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi et al.

Drug-Target Interaction (DTI) prediction is vital for drug discovery, yet challenges persist in achieving model interpretability and optimizing performance. We propose a novel transformer-based model, FragXsiteDTI, that aims to address these challenges in DTI prediction. Notably, FragXsiteDTI is the first DTI model to simultaneously leverage drug molecule fragments and protein pockets. Our information-rich representations for both proteins and drugs offer a detailed perspective on their interaction. Inspired by the Perceiver IO framework, our model features a learnable latent array, initially interacting with protein binding site embeddings using cross-attention and later refined through self-attention and used as a query to the drug fragments in the drug's cross-attention transformer block. This learnable query array serves as a mediator and enables seamless information translation, preserving critical nuances in drug-protein interactions. Our computational results on three benchmarking datasets demonstrate the superior predictive power of our model over several state-of-the-art models. We also show the interpretability of our model in terms of the critical components of both target proteins and drug molecules within drug-target pairs.

Mehdi Yazdani-Jahromi, AmirArsalan Rajabi, Ali Khodabandeh Yalabadi et al.

Bias in training datasets must be managed for various groups in classification tasks to ensure parity or equal treatment. With the recent growth in artificial intelligence models and their expanding role in automated decision-making, ensuring that these models are not biased is vital. There is an abundance of evidence suggesting that these models could contain or even amplify the bias present in the data on which they are trained, inherent to their objective function and learning algorithms; Many researchers direct their attention to this issue in different directions, namely, changing data to be statistically independent, adversarial training for restricting the capabilities of a particular competitor who aims to maximize parity, etc. These methods result in information loss and do not provide a suitable balance between accuracy and fairness or do not ensure limiting the biases in training. To this end, we propose a powerful strategy for training deep learning models called the Distraction module, which can be theoretically proven effective in controlling bias from affecting the classification results. This method can be utilized with different data types (e.g., Tabular, images, graphs, etc.). We demonstrate the potency of the proposed method by testing it on UCI Adult and Heritage Health datasets (tabular), POKEC-Z, POKEC-N and NBA datasets (graph), and CelebA dataset (vision). Using state-of-the-art methods proposed in the fairness literature for each dataset, we exhibit our model is superior to these proposed methods in minimizing bias and maintaining accuracy.

Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, AmirArsalan Rajabi et al.

The persistent challenge of bias in machine learning models necessitates robust solutions to ensure parity and equal treatment across diverse groups, particularly in classification tasks. Current methods for mitigating bias often result in information loss and an inadequate balance between accuracy and fairness. To address this, we propose a novel methodology grounded in bilevel optimization principles. Our deep learning-based approach concurrently optimizes for both accuracy and fairness objectives, and under certain assumptions, achieving proven Pareto optimal solutions while mitigating bias in the trained model. Theoretical analysis indicates that the upper bound on the loss incurred by this method is less than or equal to the loss of the Lagrangian approach, which involves adding a regularization term to the loss function. We demonstrate the efficacy of our model primarily on tabular datasets such as UCI Adult and Heritage Health. When benchmarked against state-of-the-art fairness methods, our model exhibits superior performance, advancing fairness-aware machine learning solutions and bridging the accuracy-fairness gap. The implementation of FairBiNN is available on https://github.com/yazdanimehdi/FairBiNN.

Aida Tayebi, Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi et al.

As AI systems become more embedded in everyday life, the development of fair and unbiased models becomes more critical. Considering the social impact of AI systems is not merely a technical challenge but a moral imperative. As evidenced in numerous research studies, learning fair and robust representations has proven to be a powerful approach to effectively debiasing algorithms and improving fairness while maintaining essential information for prediction tasks. Representation learning frameworks, particularly those that utilize self-supervised and contrastive learning, have demonstrated superior robustness and generalizability across various domains. Despite the growing interest in applying these approaches to tabular data, the issue of fairness in these learned representations remains underexplored. In this study, we introduce a contrastive learning framework specifically designed to address bias and learn fair representations in tabular datasets. By strategically selecting positive pair samples and employing supervised and self-supervised contrastive learning, we significantly reduce bias compared to existing state-of-the-art contrastive learning models for tabular data. Our results demonstrate the efficacy of our approach in mitigating bias with minimum trade-off in accuracy and leveraging the learned fair representations in various downstream tasks.

Ece Çiğdem Mutlu, Toktam A. Oghaz, Jasser Jasser et al.

At the time of this study, the SARS-CoV-2 virus that caused the COVID-19 pandemic has spread significantly across the world. Considering the uncertainty about policies, health risks, financial difficulties, etc. the online media, specially the Twitter platform, is experiencing a high volume of activity related to this pandemic. Among the hot topics, the polarized debates about unconfirmed medicines for the treatment and prevention of the disease have attracted significant attention from online media users. In this work, we present a stance data set, COVID-CQ, of user-generated content on Twitter in the context of COVID-19. We investigated more than 14 thousand tweets and manually annotated the opinions of the tweet initiators regarding the use of "chloroquine" and "hydroxychloroquine" for the treatment or prevention of COVID-19. To the best of our knowledge, COVID-CQ is the first data set of Twitter users' stances in the context of the COVID-19 pandemic, and the largest Twitter data set on users' stances towards a claim, in any domain. We have made this data set available to the research community via GitHub. We expect this data set to be useful for many research purposes, including stance detection, evolution and dynamics of opinions regarding this outbreak, and changes in opinions in response to the exogenous shocks such as policy decisions and events.