Automated mining

PURPOSE: The expansion of research across various disciplines has led to a substantial increase in published papers and journals, highlighting the necessity for reliable text mining platforms for database construction and knowledge acquisition. This abstract introduces GPDMiner(Gene, Protein, and Disease Miner), a platform designed for the biomedical domain, addressing the challenges posed by the growing volume of academic papers. METHODS: GPDMiner is a text mining platform that utilizes advanced information retrieval techniques...

Incident reports of medication errors are valuable learning resources for improving patient safety. However, pertinent information is often contained within unstructured free text, which prevents automated analysis and limits the usefulness of these data. Natural language processing can structure this free text automatically and retrieve relevant past incidents and learning materials, but to be able to do so requires a large, fully annotated and validated corpus of incident reports. We present a corpus of 58,658 machine-annotated incident reports of medication errors that can be used to advance the development of information extraction models and subsequent incident learning...

Coal pillar retention plays a crucial role in ensuring safety and minimizing ground deformation in coal mining operations. However, accurately and efficiently determining the optimal size of protective pillars, reducing coal pillar pressure, and addressing challenges such as limited access to retention parameters, lengthy observation times, and high labor costs are challenges that must be addressed. In this paper, we presented a methodology using Huainan mine as a case study to address these challenges. The solution involves deriving the formula for coal pillar retention parameters based on the Three Regulations definition and requirements...

Negative sampling has swiftly risen to prominence as a focal point of research, with wide-ranging applications spanning machine learning, computer vision, natural language processing, data mining, and recommender systems. This growing interest raises several critical questions: Does negative sampling really matter? Is there a general framework that can incorporate all existing negative sampling methods? In what fields is it applied? Addressing these questions, we propose a general framework that leverages negative sampling...

Low-power and smart sensing systems for iron detection are necessary for in situ monitoring of water quality. Here, a potentiometric Fe2+ -selective electrode (ISE) was fabricated based on cyanomethyl N -methyl- N -phenyl dithiocarbamate for the first time as an ionophore. Under optimal conditions, the ISE showed a Nernstian slope of 29.76 ± 0.6 mV per decade for Fe2+ ions over a wide concentration range from 1.0 × 10-1 to 1.0 × 10-5 M with a lower detection limit (LOD) of 1.0 × 10-6 M. The ISE interference of various cations on the potentiometric response was also investigated...

Stomata are microscopic pores found in the plant leaf epidermis. Regulation of stomatal aperture is pivotal not only for balancing carbon dioxide uptake for photosynthesis and transpirational water loss but also for restricting bacterial invasion. While plants close stomata upon recognition of microbes, pathogenic bacteria, such as Pseudomonas syringae pv. tomato DC3000 (Pto), reopen the closed stomata to gain access into the leaf interior. In conventional assays for assessing stomatal responses to bacterial invasion, leaf epidermal peels, leaf discs, or detached leaves are floated on bacterial suspension, and then stomata are observed under a microscope followed by manual measurement of stomatal aperture...

This work studies the problem of image semantic segmentation. Current approaches focus mainly on mining "local" context, i.e., dependencies between pixels within individual images, by specifically-designed, context aggregation modules (e.g., dilated convolution, neural attention) or structure-aware optimization objectives (e.g., IoU-like loss). However, they ignore "global" context of the training data, i.e., rich semantic relations between pixels across different images. Inspired by recent advance in unsupervised contrastive representation learning, we propose a pixel-wise contrastive algorithm, dubbed as PiCo, for semantic segmentation in the fully supervised learning setting...

Unmanned vehicles have become increasingly popular in the underwater domain in the last decade, as they provide better operation reliability by minimizing human involvement in most tasks. Perception of the environment is crucial for safety and other tasks, such as guidance and trajectory control, mainly when operating underwater. Mine detection is one of the riskiest operations since it involves systems that can easily damage vehicles and endanger human lives if manned. Automating mine detection from side-scan sonar images enhances safety while reducing false negatives...

Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation...

The present work explores a data mining approach to study the fabrication of prednisolone-loaded chitosan nanoparticles and their properties. Eight PLC formulations were prepared using an automated adaptation of the antisolvent precipitation method. The PLCs were characterized using dynamic light scattering, infrared spectroscopy, and drug release studies. Results showed that that the effective diameter, loading capacity, encapsulation efficiency, zeta potential, and polydispersity of the PLCs were influenced by the concentration and molecular weight of chitosan...

Cerebral cavernous malformation (CCM) is a polygenic disease with intricate genetic interactions contributing to quantitative pathogenesis across multiple factors. The principal pathogenic genes of CCM, specifically KRIT1, CCM2, and PDCD10, have been reported, accompanied by a growing wealth of genetic data related to mutations. Furthermore, numerous other molecules associated with CCM have been unearthed. However, tackling such massive volumes of unstructured data remains challenging until the advent of advanced large language models...

OBJECTIVE: Alignment between preoperative images (high-resolution magnetic resonance imaging, magnetic resonance angiography) and intraoperative medical images (digital subtraction angiography) is currently required in neurointerventional surgery. Treating a lesion is usually guided by a 2D DSA silhouette image. DSA silhouette images increase procedure time and radiation exposure time due to the lack of anatomical information, but information from MRA images can be utilized to compensate for this in order to improve procedure efficiency...

The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets...

Data standardization promotes a common framework through which researchers can utilize others' data and is one of the leading methods neuroimaging researchers use to share and replicate findings. As of today, standardizing datasets requires technical expertise such as coding and knowledge of file formats. We present ezBIDS, a tool for converting neuroimaging data and associated metadata to the Brain Imaging Data Structure (BIDS) standard. ezBIDS contains four major features: (1) No installation or programming requirements...

BACKGROUND: Understanding complex biological pathways, including gene-gene interactions and gene regulatory networks, is critical for exploring disease mechanisms and drug development. Manual literature curation of biological pathways is useful but cannot keep up with the exponential growth of the literature. Large-scale language models (LLMs), notable for their vast parameter sizes and comprehensive training on extensive text corpora, have great potential in automated text mining of biological pathways...

By observing a scene and listening to corresponding audio cues, humans can easily recognize where the sound is. To achieve such cross-modal perception on machines, existing methods take advantage of the maps obtained by interpolation operations to localize the sound source. As semantic object-level localization is more attractive for prospective practical applications, we argue that these map-based methods only offer a coarse-grained and indirect description of the sound source. Additionally, these methods utilize a single audio-visual tuple at a time during self-supervised learning, causing the model to lose the crucial chance to reason about the data distribution of large-scale audio-visual samples...

Large-scale, multi-site collaboration is becoming indispensable for a wide range of research and clinical activities in oncology. To facilitate the next generation of advances in cancer biology, precision oncology and the population sciences it will be necessary to develop and implement data management and analytic tools that empower investigators to reliably and objectively detect, characterize and chronicle the phenotypic and genomic changes that occur during the transformation from the benign to cancerous state and throughout the course of disease progression...

The development of natural language processing techniques for deriving useful information from unstructured clinical narratives is a fast-paced and rapidly evolving area of machine learning research. Large volumes of veterinary clinical narratives now exist curated by projects such as the Small Animal Veterinary Surveillance Network (SAVSNET) and VetCompass, and the application of such techniques to these datasets is already (and will continue to) improve our understanding of disease and disease patterns within veterinary medicine...

In contrast to fully supervised methods using pixel-wise mask labels, box-supervised instance segmentation takes advantage of simple box annotations, which has recently attracted increasing research attention. This paper presents a novel single-shot instance segmentation approach, namely Box2Mask, which integrates the classical level-set evolution model into deep neural network learning to achieve accurate mask prediction with only bounding box supervision. Specifically, both the input image and its deep features are employed to evolve the level-set curves implicitly, and a local consistency module based on a pixel affinity kernel is used to mine the local context and spatial relations...

Automated Vehicles (AVs) based on a collection of advanced technologies such as big data and artificial intelligence have opened an opportunity to reduce traffic accidents caused by human drivers. Nevertheless, traffic accidents of AVs continue to occur, which raises safety and reliability concerns about AVs. AVs are particularly vulnerable to accidents on urban roads than on highways due to various dynamic objects and more complex infrastructure. Several studies proposed a scenario-based approach of experimenting with the response of AVs to specific situations as a way to test their safety...