Kishan KC

Minh Van Nguyen, Kishan KC, Toan Nguyen et al. · amazon-science

Answer sentence selection (AS2) in open-domain question answering finds answer for a question by ranking candidate sentences extracted from web documents. Recent work exploits answer context, i.e., sentences around a candidate, by incorporating them as additional input string to the Transformer models to improve the correctness scoring. In this paper, we propose to improve the candidate scoring by explicitly incorporating the dependencies between question-context and answer-context into the final representation of a candidate. Specifically, we use Optimal Transport to compute the question-based dependencies among sentences in the passage where the answer is extracted from. We then represent these dependencies as edges in a graph and use Graph Convolutional Network to derive the representation of a candidate, a node in the graph. Our proposed model achieves significant improvements on popular AS2 benchmarks, i.e., WikiQA and WDRASS, obtaining new state-of-the-art on all benchmarks.

Paribesh Regmi, Rui Li, Kishan KC

The neighborhood scope (i.e., number of hops) where graph neural networks (GNNs) aggregate information to characterize a node's statistical property is critical to GNNs' performance. Two-stage approaches, training and validating GNNs for every pre-specified neighborhood scope to search for the best setting, is a time-consuming task and tends to be biased due to the search space design. How to adaptively determine proper neighborhood scopes for the aggregation process for both homophilic and heterophilic graphs remains largely unexplored. We thus propose to model the GNNs' message-passing behavior on a graph as a stochastic process by treating the number of hops as a beta process. This Bayesian framework allows us to infer the most plausible neighborhood scope for message aggregation simultaneously with the optimization of GNN parameters. Our theoretical analysis shows that the scope inference improves the expressivity of a GNN. Experiments on benchmark homophilic and heterophilic datasets show that the proposed method is compatible with state-of-the-art GNN variants, achieving competitive or superior performance on the node classification task, and providing well-calibrated predictions. Implementation is available at : https://github.com/paribeshregmi/BNA-GNN

Kishan KC, Rui Li, Paribesh Regmi et al.

A biological system is a complex network of heterogeneous molecular entities and their interactions contributing to various biological characteristics of the system. However, current biological networks are noisy, sparse, and incomplete, limiting our ability to create a holistic view of the biological system and understand the biological phenomena. Experimental identification of such interactions is both time-consuming and expensive. With the recent advancements in high-throughput data generation and significant improvement in computational power, various computational methods have been developed to predict novel interactions in the noisy network. Recently, deep learning methods such as graph neural networks have shown their effectiveness in modeling graph-structured data and achieved good performance in biomedical interaction prediction. However, graph neural networks-based methods require human expertise and experimentation to design the appropriate complexity of the model and significantly impact the performance of the model. Furthermore, deep graph neural networks face overfitting problems and tend to be poorly calibrated with high confidence on incorrect predictions. To address these challenges, we propose Bayesian model selection for graph convolutional networks to jointly infer the most plausible number of graph convolution layers (depth) warranted by data and perform dropout regularization simultaneously. Experiments on four interaction datasets show that our proposed method achieves accurate and calibrated predictions. Our proposed method enables the graph convolutional networks to dynamically adapt their depths to accommodate an increasing number of interactions.

Kishan KC, Rui Li, Feng Cui et al.

Biomedical interaction networks have incredible potential to be useful in the prediction of biologically meaningful interactions, identification of network biomarkers of disease, and the discovery of putative drug targets. Recently, graph neural networks have been proposed to effectively learn representations for biomedical entities and achieved state-of-the-art results in biomedical interaction prediction. These methods only consider information from immediate neighbors but cannot learn a general mixing of features from neighbors at various distances. In this paper, we present a higher-order graph convolutional network (HOGCN) to aggregate information from the higher-order neighborhood for biomedical interaction prediction. Specifically, HOGCN collects feature representations of neighbors at various distances and learns their linear mixing to obtain informative representations of biomedical entities. Experiments on four interaction networks, including protein-protein, drug-drug, drug-target, and gene-disease interactions, show that HOGCN achieves more accurate and calibrated predictions. HOGCN performs well on noisy, sparse interaction networks when feature representations of neighbors at various distances are considered. Moreover, a set of novel interaction predictions are validated by literature-based case studies.

Kishan KC, Feng Cui, Anne Haake et al.

Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been proposed to model PPIs from sequences, these methods are computationally expensive for a large number of PPIs due to the pairwise encoding process. Furthermore, these methods are difficult to interpret because of non-intuitive mappings from protein sequences to their sequence representation. To address these challenges, we present a novel deep framework to model and predict PPIs from sequence alone. Our model incorporates a bidirectional gated recurrent unit to learn sequence representations by leveraging contextualized and sequential information from sequences. We further employ a sparse regularization to model long-range dependencies between amino acids and to select important amino acids (protein motifs), thus enhancing interpretability. Besides, the novel design of the encoding process makes our model computationally efficient and scalable to an increasing number of interactions. Experimental results on up-to-date interaction datasets demonstrate that our model achieves superior performance compared to other state-of-the-art methods. Literature-based case studies illustrate the ability of our model to provide biological insights to interpret the predictions.