Predicting Biomedical Interactions with Probabilistic Model Selection for Graph Neural Networks

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.

openFEAT: Improving Speaker Identification by Open-set Few-shot Embedding Adaptation with Transformer

Household speaker identification with few enrollment utterances is an important yet challenging problem, especially when household members share similar voice characteristics and room acoustics. A common embedding space learned from a large number of speakers is not universally applicable for the optimal identification of every speaker in a household. In this work, we first formulate household speaker identification as a few-shot open-set recognition task and then propose a novel embedding adaptation framework to adapt speaker representations from the given universal embedding space to a household-specific embedding space using a set-to-set function, yielding better household speaker identification performance. With our algorithm, Open-set Few-shot Embedding Adaptation with Transformer (openFEAT), we observe that the speaker identification equal error rate (IEER) on simulated households with 2 to 7 hard-to-discriminate speakers is reduced by 23% to 31% relative.