Azam Shirali

Jimeng Shi, Azam Shirali, Giri Narasimhan

Extreme events are of great importance since they often represent impactive occurrences. For instance, in terms of climate and weather, extreme events might be major storms, floods, extreme heat or cold waves, and more. However, they are often located at the tail of the data distribution. Consequently, accurately predicting these extreme events is challenging due to their rarity and irregularity. Prior studies have also referred to this as the out-of-distribution (OOD) problem, which occurs when the distribution of the test data is substantially different from that used for training. In this work, we propose two strategies, reweighting and fine-tuning, to tackle the challenge. Reweighting is a strategy used to force machine learning models to focus on extreme events, which is achieved by a weighted loss function that assigns greater penalties to the prediction errors for the extreme samples relative to those on the remainder of the data. Unlike previous intuitive reweighting methods based on simple heuristics of data distribution, we employ meta-learning to dynamically optimize these penalty weights. To further boost the performance on extreme samples, we start from the reweighted models and fine-tune them using only rare extreme samples. Through extensive experiments on multiple data sets, we empirically validate that our meta-learning-based reweighting outperforms existing heuristic ones, and the fine-tuning strategy can further increase the model performance. More importantly, these two strategies are model-agnostic, which can be implemented on any type of neural network for time series forecasting. The open-sourced code is available at \url{https://github.com/JimengShi/ReFine}.

Azam Shirali, Giri Narasimhan

Protein-protein docking tools help in studying interactions between proteins, and are essential for drug, vaccine, and therapeutic development. However, the accuracy of a docking tool depends on a robust scoring function that can reliably differentiate between native and non-native complexes. PIsToN is a state-of-the-art deep learning-based scoring function that uses Vision Transformers in its architecture. Recently, the Mamba architecture has demonstrated exceptional performance in both natural language processing and computer vision, often outperforming Transformer-based models in their domains. In this study, we introduce PUMBA (Protein-protein interface evaluation with Vision Mamba), which improves PIsToN by replacing its Vision Transformer backbone with Vision Mamba. This change allows us to leverage Mamba's efficient long-range sequence modeling for sequences of image patches. As a result, the model's ability to capture both global and local patterns in protein-protein interface features is significantly improved. Evaluation on several widely-used, large-scale public datasets demonstrates that PUMBA consistently outperforms its original Transformer-based predecessor, PIsToN.

Jimeng Shi, Rukmangadh Myana, Vitalii Stebliankin et al.

Accurate time series forecasting is a fundamental challenge in data science. It is often affected by external covariates such as weather or human intervention, which in many applications, may be predicted with reasonable accuracy. We refer to them as predicted future covariates. However, existing methods that attempt to predict time series in an iterative manner with autoregressive models end up with exponential error accumulations. Other strategies hat consider the past and future in the encoder and decoder respectively limit themselves by dealing with the historical and future data separately. To address these limitations, a novel feature representation strategy -- shifting -- is proposed to fuse the past data and future covariates such that their interactions can be considered. To extract complex dynamics in time series, we develop a parallel deep learning framework composed of RNN and CNN, both of which are used hierarchically. We also utilize the skip connection technique to improve the model's performance. Extensive experiments on three datasets reveal the effectiveness of our method. Finally, we demonstrate the model interpretability using the Grad-CAM algorithm.