Interpretable prediction of drug-drug interactions via text embedding in biomedical literature.

Polypharmacy is a promising approach for treating diseases, especially those with complex symptoms. However, it can lead to unexpected drug-drug interactions (DDIs), potentially reducing efficacy and triggering adverse drug reactions (ADRs). Predicting the risk of DDIs is crucial for ensuring safe drug use, particularly by identifying the types of DDIs and the mechanisms involved.

FetoML: Interpretable predictions of the fetotoxicity of drugs based on machine learning approaches.

Pregnant females may use medications to manage health problems that develop during pregnancy or that they had prior to pregnancy. However, using medications during pregnancy has a potential risk to the fetus. Assessing the fetotoxicity of drugs is essential to ensure safe treatments, but the current process is challenged by ethical issues, time, and cost.

Interpretable Prediction of SARS-CoV-2 Epitope-Specific TCR Recognition Using a Pre-Trained Protein Language Model.

The emergence of the novel coronavirus, designated as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has posed a significant threat to public health worldwide. There has been progress in reducing hospitalizations and deaths due to SARS-CoV-2. However, challenges stem from the emergence of SARS-CoV-2 variants, which exhibit high transmission rates, increased disease severity, and the ability to evade humoral immunity.

InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism.

Safety is one of the important factors constraining the distribution of clinical drugs on the market. Drug-induced liver injury (DILI) is the leading cause of safety problems produced by drug side effects. Therefore, the DILI risk of approved drugs and potential drug candidates should be assessed.

Identification of Breast Cancer Metastasis Markers from Gene Expression Profiles Using Machine Learning Approaches.

Cancer metastasis accounts for approximately 90% of cancer deaths, and elucidating markers in metastasis is the first step in its prevention. To characterize metastasis marker genes (MGs) of breast cancer, XGBoost models that classify metastasis status were trained with gene expression profiles from TCGA. Then, a metastasis score (MS) was assigned to each gene by calculating the inner product between the feature importance and the AUC performance of the models.

Medical service utilization by children with physical or brain disabilities in South Korea.

Background: Children with physical or brain disabilities experience several functional impairments and declining health complications that must be considered for adequate medical support. This study investigated the current medical service utilization of children expressing physical or brain disabilities in South Korea by analyzing medical visits, expenses, and comorbidities.

Methods: We used a database linked to the National Rehabilitation Center of South Korea to extract information on medical services utilized by children with physical or brain disabilities, the number of children with a disability, medical visits for each child, medical expenses per visit, total medical treatment cost, copayments by age group, condition severity, and disability type.

The Relationship between Nutrient Intake and Cataracts in the Older Adult Population of Korea.

Cataracts are a prevalent ophthalmic disease worldwide, and research on the risk factors for cataracts occurrence is actively being conducted. This study aimed to investigate the relationship between nutrient intake and cataracts in the older adult population in Korea. We analyzed data from Korean adults over the age of 60 years (cataract: 2137, non-cataract: 3497) using the Korean National Health and Nutrition Examination Survey.

Predicting Ischemic Stroke in Patients with Atrial Fibrillation Using Machine Learning.

Background: Atrial fibrillation (AF) is a well-known risk factor for stroke. Predicting the risk is important to prevent the first and secondary attacks of cerebrovascular diseases by determining early treatment. This study aimed to predict the ischemic stroke in AF patients based on the massive and complex Korean National Health Insurance (KNHIS) data through a machine learning approach.

Precise Characterization of Genetic Interactions in Cancer via Molecular Network Refining Processes.

Genetic interactions (GIs), such as the synthetic lethal interaction, are promising therapeutic targets in precision medicine. However, despite extensive efforts to characterize GIs by large-scale perturbation screening, considerable false positives have been reported in multiple studies. We propose a new computational approach for improved precision in GI identification by applying constraints that consider actual biological phenomena.

Analysis of the Effects of Nutrient Intake and Dietary Habits on Depression in Korean Adults.

While several studies have explored nutrient intake and dietary habits associated with depression, few studies have reflected recent trends and demographic factors. Therefore, we examined how nutrient intake and eating habits are associated with depression, according to gender and age. We performed simple and multiple regressions using nationally representative samples of 10,106 subjects from the Korea National Health and Nutrition Examination Survey.

A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds.

Medicinal plants and their extracts have been used as important sources for drug discovery. In particular, plant-derived natural compounds, including phytochemicals, antioxidants, vitamins, and minerals, are gaining attention as they promote health and prevent disease. Although several methods have been developed to confirm the biological activities of natural compounds, there is still considerable room to reduce time and cost.

Data resource profile: the allergic disease database of the Korean National Health Insurance Service.

Researchers have been interested in probing how the environmental factors associated with allergic diseases affect the use of medical services. Considering this demand, we have constructed a database, named the Allergic Disease Database, based on the National Health Insurance Database (NHID). The NHID contains information on demographic and medical service utilization for approximately 99% of the Korean population.

An interactive retrieval system for clinical trial studies with context-dependent protocol elements.

A well-defined protocol for a clinical trial guarantees a successful outcome report. When designing the protocol, most researchers refer to electronic databases and extract protocol elements using a keyword search. However, state-of-the-art database systems only offer text-based searches for user-entered keywords.

Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence.

Identifying the health benefits of phytochemicals is an essential step in drug and functional food development. While many in vitro screening methods have been developed to identify the health effects of phytochemicals, there is still room for improvement because of high cost and low productivity. Therefore, researchers have alternatively proposed in silico methods, primarily based on three types of approaches; utilizing molecular, chemical or ethnopharmacological information.

Phenotype-oriented network analysis for discovering pharmacological effects of natural compounds.

Although natural compounds have provided a wealth of leads and clues in drug development, the process of identifying their pharmacological effects is still a challenging task. Over the last decade, many in vitro screening methods have been developed to identify the pharmacological effects of natural compounds, but they are still costly processes with low productivity. Therefore, in silico methods, primarily based on molecular information, have been proposed.

A systematic approach to identify therapeutic effects of natural products based on human metabolite information.

Background: Natural products have been widely investigated in the drug development field. Their traditional use cases as medicinal agents and their resemblance of our endogenous compounds show the possibility of new drug development. Many researchers have focused on identifying therapeutic effects of natural products, yet the resemblance of natural products and human metabolites has been rarely touched.

In silico profiling of systemic effects of drugs to predict unexpected interactions.

Identifying unexpected drug interactions is an essential step in drug development. Most studies focus on predicting whether a drug pair interacts or is effective on a certain disease without considering the mechanism of action (MoA). Here, we introduce a novel method to infer effects and interactions of drug pairs with MoA based on the profiling of systemic effects of drugs.

Prediction of compound-target interactions of natural products using large-scale drug and protein information.

Background: Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates. However, this entails a great deal of effort to clarify the interaction throughout in vitro or in vivo experiments. In this light, in silico prediction of the interactions between compounds and target proteins can help ease the efforts.

An Approach to Reducing Information Loss and Achieving Diversity of Sensitive Attributes in k-anonymity Methods.

Electronic Health Records (EHRs) enable the sharing of patients' medical data. Since EHRs include patients' private data, access by researchers is restricted. Therefore k-anonymity is necessary to keep patients' private data safe without damaging useful medical information.