HELM: Hierarchical Encoding for mRNA Language Modeling

Messenger RNA (mRNA) plays a crucial role in protein synthesis, with its codon structure directly impacting biological properties. While Language Models (LMs) have shown promise in analyzing biological sequences, existing approaches fail to account for the hierarchical nature of mRNA's codon structure. We introduce Hierarchical Encoding for mRNA Language Modeling (HELM), a novel pre-training strategy that incorporates codon-level hierarchical structure into language model training. HELM modulates the loss function based on codon synonymity, aligning the model's learning process with the biological reality of mRNA sequences. We evaluate HELM on diverse mRNA datasets and tasks, demonstrating that HELM outperforms standard language model pre-training as well as existing foundation model baselines on six diverse downstream property prediction tasks and an antibody region annotation tasks on average by around 8\%. Additionally, HELM enhances the generative capabilities of language model, producing diverse mRNA sequences that better align with the underlying true data distribution compared to non-hierarchical baselines.

FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation

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.

Through a fair looking-glass: mitigating bias in image datasets

With the recent growth in computer vision applications, the question of how fair and unbiased they are has yet to be explored. There is abundant evidence that the bias present in training data is reflected in the models, or even amplified. Many previous methods for image dataset de-biasing, including models based on augmenting datasets, are computationally expensive to implement. In this study, we present a fast and effective model to de-bias an image dataset through reconstruction and minimizing the statistical dependence between intended variables. Our architecture includes a U-net to reconstruct images, combined with a pre-trained classifier which penalizes the statistical dependence between target attribute and the protected attribute. We evaluate our proposed model on CelebA dataset, compare the results with a state-of-the-art de-biasing method, and show that the model achieves a promising fairness-accuracy combination.

Distraction is All You Need for Fairness

With the recent growth in artificial intelligence models and its expanding role in automated decision making, ensuring that these models are not biased is of vital importance. 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. In this paper, we propose a novel classification algorithm that improves fairness, while maintaining accuracy of the predictions. Utilizing the embedding layer of a pre-trained classifier for the protected attributes, the network uses an attention layer to distract the classification from depending on the protected attribute in its predictions. We compare our model with six state-of-the-art methodologies proposed in fairness literature, and show that the model is superior to those methods in terms of minimizing bias while maintaining accuracy.