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In the era of quantum computing, the emergence of quantum computers and subsequent advancements have led to the development of various quantum algorithms capable of solving linear equations and eigenvalues, surpassing the pace of classical computers. Notably, the hybrid solver provided by the D-wave system can leverage up to two million variables. By exploiting this technology, quantum optimization models based on quadratic unconstrained binary optimization (QUBO) have been proposed for applications, such as linear systems, eigenvalue problems, RSA cryptosystems, and CT image reconstruction. The formulation of QUBO typically involves straightforward arithmetic operations, presenting significant potential for future advancements as quantum computers continue to evolve. A prevalent approach in these developments is the binarization of variables and their mapping to multiple qubits. These methods increase the required number of qubits as the range and precision of each variable increase. Determining the optimal value of a QUBO model becomes more challenging as the number of qubits increases. Furthermore, the accuracies of the existing Qiskit simulator, D-Wave system simulator, and hybrid solver are limited to two decimal places. Problems arise because the qubits yielding the optimal value for the QUBO model may not necessarily correspond to the solution of a given problem. To address these issues, we propose a new iterative algorithm. The novel algorithm sequentially progresses from the highest to the lowest exponent in binarizing each number, whereby each number is calculated using two variables, and the accuracy can be computed up to a maximum of 16 decimal places., Comment: 7 pages, 4 figures, 1 table

In this work, we share the insights for achieving state-of-the-art quality in our text-to-image anime image generative model, called Illustrious. To achieve high resolution, dynamic color range images, and high restoration ability, we focus on three critical approaches for model improvement. First, we delve into the significance of the batch size and dropout control, which enables faster learning of controllable token based concept activations. Second, we increase the training resolution of images, affecting the accurate depiction of character anatomy in much higher resolution, extending its generation capability over 20MP with proper methods. Finally, we propose the refined multi-level captions, covering all tags and various natural language captions as a critical factor for model development. Through extensive analysis and experiments, Illustrious demonstrates state-of-the-art performance in terms of animation style, outperforming widely-used models in illustration domains, propelling easier customization and personalization with nature of open source. We plan to publicly release updated Illustrious model series sequentially as well as sustainable plans for improvements.

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., Comment: 18 pages, 9 figures

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.

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., Comment: 10 pages, 5 figures

With the advent and development of quantum computers, various quantum algorithms that can solve linear equations and eigenvalues faster than classical computers have been developed. The Harrow-Hassidim-Lloyd algorithm is an algorithm that can solve linear equations in a gate model quantum computer. Still, it is constrained by the use of quantum RAM and the size limit of the matrix according to the total number of qubits in the quantum computer. Recently, Jun and Lee developed a QUBO model for solving linear systems and eigenvalue problems in the quantum computer. However, even though their model uses 2048 qubits, the number of qubits for variables that can be used for the problem is only 64. To solve this problem, we introduce an algorithm that can be used by dividing the size of the entire domain according to the number of qubits. We also form a QUBO model related to each subregion., Comment: 11 pages, 1 figure

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.

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, Comment: 8 pages, 3 figures

To improve deep-learning performance in low-resource settings, many researchers have redesigned model architectures or applied additional data (e.g., external resources, unlabeled samples). However, there have been relatively few discussions on how to make good use of small amounts of labeled samples, although it is potentially beneficial and should be done before applying additional data or redesigning models. In this study, we assume a low-resource setting in which only a few labeled samples (i.e., 30-100 per class) are available, and we discuss how to exploit them without additional data or model redesigns. We explore possible approaches in the following three aspects: training-validation splitting, early stopping, and weight initialization. Extensive experiments are conducted on six public sentence classification datasets. Performance on various evaluation metrics (e.g., accuracy, loss, and calibration error) significantly varied depending on the approaches that were combined in the three aspects. Based on the results, we propose an integrated method, which is to initialize the model with a weight averaging method and use a non-validation stop method to train all samples. This simple integrated method consistently outperforms the competitive methods; e.g., the average accuracy of six datasets of this method was 1.8% higher than those of conventional validation-based methods. In addition, the integrated method further improves the performance when adapted to several state-of-the-art models that use additional data or redesign the network architecture (e.g., self-training and enhanced structural models). Our results highlight the importance of the training strategy and suggest that the integrated method can be the first step in the low-resource setting. This study provides empirical knowledge that will be helpful when dealing with low-resource data in future efforts., Comment: 15 pages, 8 figures, published in IEEE Access

Recent studies on quantum computing algorithms focus on excavating features of quantum computers which have potential for contributing to computational model enhancements. Among various approaches, quantum annealing methods effectively parallelize quadratic unconstrained binary optimization (QUBO) formulations of systems of linear equations. In this paper, we simplify these formulations by exploiting congruence of real symmetric matrices to diagonal matrices. We further exhibit computational merits of the proposed QUBO models, which can outperform classical algorithms such as QR and SVD decomposition.

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., Comment: 10 pages, 4 figures, accepted for the Findings of EMNLP

Automatic diagnosis of malignant melanoma highly depends on the segmentation methods used for the suspicious lesion. We suggest the parameter selection method (PSM) and maximum area method (MAM) for the segmentation of the lesion to be diagnosed. Herein, these segmentation methods are compared to a skin cancer expert's segmentation and three other conventional algorithms. The diagnosis of malignant melanoma based on the two suggested, three conventional, and expert's segmentation are compared with respect to sensitivity, specificity, and accuracy.