Deep Metric Loss for Multimodal Learning

Multimodal learning often outperforms its unimodal counterparts by exploiting unimodal contributions and cross-modal interactions. However, focusing only on integrating multimodal features into a unified comprehensive representation overlooks the unimodal characteristics. In real data, the contributions of modalities can vary from instance to instance, and they often reinforce or conflict with each other. In this study, we introduce a novel \text{MultiModal} loss paradigm for multimodal learning, which subgroups instances according to their unimodal contributions. \text{MultiModal} loss can prevent inefficient learning caused by overfitting and efficiently optimize multimodal models. On synthetic data, \text{MultiModal} loss demonstrates improved classification performance by subgrouping difficult instances within certain modalities. On four real multimodal datasets, our loss is empirically shown to improve the performance of recent models. Ablation studies verify the effectiveness of our loss. Additionally, we show that our loss generates a reliable prediction score for each modality, which is essential for subgrouping. Our \text{MultiModal} loss is a novel loss function to subgroup instances according to the contribution of modalities in multimodal learning and is applicable to a variety of multimodal models with unimodal decisions. Our code is available at https://github.com/SehwanMoon/MultiModalLoss.

PINNet: a deep neural network with pathway prior knowledge for Alzheimer's disease

Identification of Alzheimer's Disease (AD)-related transcriptomic signatures from blood is important for early diagnosis of the disease. Deep learning techniques are potent classifiers for AD diagnosis, but most have been unable to identify biomarkers because of their lack of interpretability. To address these challenges, we propose a pathway information-based neural network (PINNet) to predict AD patients and analyze blood and brain transcriptomic signatures using an interpretable deep learning model. PINNet is a deep neural network (DNN) model with pathway prior knowledge from either the Gene Ontology or Kyoto Encyclopedia of Genes and Genomes databases. Then, a backpropagation-based model interpretation method was applied to reveal essential pathways and genes for predicting AD. We compared the performance of PINNet with a DNN model without a pathway. Performances of PINNet outperformed or were similar to those of DNN without a pathway using blood and brain gene expressions, respectively. Moreover, PINNet considers more AD-related genes as essential features than DNN without a pathway in the learning process. Pathway analysis of protein-protein interaction modules of highly contributed genes showed that AD-related genes in blood were enriched with cell migration, PI3K-Akt, MAPK signaling, and apoptosis in blood. The pathways enriched in the brain module included cell migration, PI3K-Akt, MAPK signaling, apoptosis, protein ubiquitination, and t-cell activation. Collectively, with prior knowledge about pathways, PINNet reveals essential pathways related to AD.

SDGCCA: Supervised Deep Generalized Canonical Correlation Analysis for Multi-omics Integration

Integration of multi-omics data provides opportunities for revealing biological mechanisms related to certain phenotypes. We propose a novel method of multi-omics integration called supervised deep generalized canonical correlation analysis (SDGCCA) for modeling correlation structures between nonlinear multi-omics manifolds, aiming for improving classification of phenotypes and revealing biomarkers related to phenotypes. SDGCCA addresses the limitations of other canonical correlation analysis (CCA)-based models (e.g., deep CCA, deep generalized CCA) by considering complex/nonlinear cross-data correlations and discriminating phenotype groups. Although there are a few methods for nonlinear CCA projections for discriminant purposes of phenotypes, they only consider two views. On the other hand, SDGCCA is the nonlinear multiview CCA projection method for discrimination. When we applied SDGCCA to prediction of patients of Alzheimer's disease (AD) and discrimination of early- and late-stage cancers, it outperformed other CCA-based methods and other supervised methods. In addition, we demonstrate that SDGCCA can be used for feature selection to identify important multi-omics biomarkers. In the application on AD data, SDGCCA identified clusters of genes in multi-omics data, which are well known to be associated with AD.

A molecular generative model with genetic algorithm and tree search for cancer samples

Personalized medicine is expected to maximize the intended drug effects and minimize side effects by treating patients based on their genetic profiles. Thus, it is important to generate drugs based on the genetic profiles of diseases, especially in anticancer drug discovery. However, this is challenging because the vast chemical space and variations in cancer properties require a huge time resource to search for proper molecules. Therefore, an efficient and fast search method considering genetic profiles is required for de novo molecular design of anticancer drugs. Here, we propose a faster molecular generative model with genetic algorithm and tree search for cancer samples (FasterGTS). FasterGTS is constructed with a genetic algorithm and a Monte Carlo tree search with three deep neural networks: supervised learning, self-trained, and value networks, and it generates anticancer molecules based on the genetic profiles of a cancer sample. When compared to other methods, FasterGTS generated cancer sample-specific molecules with general chemical properties required for cancer drugs within the limited numbers of samplings. We expect that FasterGTS contributes to the anticancer drug generation.

Noise-resistant reconstruction algorithm based on the sinogram pattern

We introduce a new CT image reconstruction algorithm that is less affected by various artifacts. The new reconstruction algorithm is a method of minimizing the difference between synchrotron X-ray tomography data and sinograms generated using Radon transform of CT images. The CT image is iteratively updated to reduce the difference from the sinogram of the data. This method can obtain clean CT images from the projection data, which can create ring artifacts or metal artifacts. Also, even if the sample size is larger than the CCD and/or the projection image does not satisfy the Beer-Lambert law, a clean CT image can be reconstructed. Our new reconstruction algorithm can also be applied to fan beam CT or cone beam CT

Exploiting all samples in low-resource sentence classification: early stopping and initialization parameters

In low resource settings, deep neural models have often shown lower performance due to overfitting. The primary method to solve the overfitting problem is to generalize model parameters. To this end, many researchers have depended on large external resources with various manipulation techniques. In this study, we discuss how to exploit all available samples in low resource settings, without external datasets and model manipulation. This study focuses on natural language processing task. We propose a simple algorithm to find out good initialization parameters that improve robustness to a small sample set. We apply early stopping techniques that enable the use of all samples for training. Finally, the proposed learning strategy is to train all samples with the good initialization parameters and stop the model with the early stopping techniques. Extensive experiments are conducted on seven public sentence classification datasets, and the results demonstrate that the proposed learning strategy achieves better performance than several state-of-the-art works across the seven datasets.

Extracting Chemical-Protein Interactions via Calibrated Deep Neural Network and Self-training

The extraction of interactions between chemicals and proteins from several biomedical articles is important in many fields of biomedical research such as drug development and prediction of drug side effects. Several natural language processing methods, including deep neural network (DNN) models, have been applied to address this problem. However, these methods were trained with hard-labeled data, which tend to become over-confident, leading to degradation of the model reliability. To estimate the data uncertainty and improve the reliability, "calibration" techniques have been applied to deep learning models. In this study, to extract chemical--protein interactions, we propose a DNN-based approach incorporating uncertainty information and calibration techniques. Our model first encodes the input sequence using a pre-trained language-understanding model, following which it is trained using two calibration methods: mixup training and addition of a confidence penalty loss. Finally, the model is re-trained with augmented data that are extracted using the estimated uncertainties. Our approach has achieved state-of-the-art performance with regard to the Biocreative VI ChemProt task, while preserving higher calibration abilities than those of previous approaches. Furthermore, our approach also presents the possibilities of using uncertainty estimation for performance improvement.