MicroConceptBERT: concept-relation based document information extraction framework.

Extracting information from documents is a crucial task in natural language processing research. Existing information extraction methodologies often focus on specific domains, such as medicine, education or finance, and are limited by language constraints. However, more comprehensive approaches that transcend document types, languages, contexts, and structures would significantly advance the field proposed in recent research. This study addresses this challenge by introducing microConceptBERT: a concept-relations-based framework for document information extraction, which offers flexibility for various document processing tasks while accounting for hierarchical, semantic, and heuristic features. The proposed framework has been applied to a question-answering task on benchmark datasets: SQUAD 2.0 and DOCVQA. Notably, the F1 evaluation metric attains an outperforming 87.01 performance rate on the SQUAD 2.0 dataset compared to baseline models: BERT-base and BERT-large models

Explainable weather forecasts through an LSTM-CBR twin system.

In this paper, we explore two methods for explaining LSTM-based temperature forecasts using previous 14 day progressions of humidity and pressure. First, we propose and evaluate an LSTM-CBR twin system that generates nearest-neighbors that can be visualised as explanations. Second, we use feature attributions from Integrated Gradients to generate textual explanations that summarise the key progressions in the past 14 days that led to the predicted value

Clinical dialogue transcription error correction using Seq2Seq models.

Good communication is critical to good healthcare. Clinical dialogue is a conversation between health practitioners and their patients, with the explicit goal of obtaining and sharing medical information. This information contributes to medical decision-making regarding the patient and plays a crucial role in their healthcare journey. The reliance on note taking and manual scribing processes are extremely inefficient and leads to manual transcription errors when digitizing notes. Automatic Speech Recognition (ASR) plays a significant role in speech-to-text applications, and can be directly used as a text generator in conversational applications. However, recording clinical dialogue presents a number of general and domain-specific challenges. In this paper, we present a seq2seq learning approach for ASR transcription error correction of clinical dialogues. We introduce a new Gastrointestinal Clinical Dialogue (GCD) Dataset which was gathered by health-care professionals from a NHS Inflammatory Bowel Disease clinic and use this in a comparative study with four commercial ASR systems. Using self-supervision strategies, we fine-tune a seq2seq model on a mask-filling task using a domain-specific PubMed dataset which we have shared publicly for future research. The BART model fine-tuned for mask-filling was able to correct transcription errors and achieve lower word error rates for three out of four commercial ASR outputs

Detection and tracking volumes of interest in 3D printed tissue engineering scaffolds using 4D imaging modalities.

Additive manufacturing (AM) platforms allow the production of patient tissue engineering scaffolds with desirable architectures. Although AM platforms offer exceptional control on architecture, post-processing methods such as sintering and freeze-drying often deform the printed scaffold structure. In-situ 4D imaging can be used to analyze changes that occur during post-processing. Visualization and analysis of changes in selected volumes of interests (VOIs) over time are essential to understand the underlining mechanisms of scaffold deformations. Yet, automated detection and tracking of VOIs in the 3D printed scaffold over time using 4D image data is currently an unsolved image processing task. This paper proposes a new image processing technique to segment, detect and track volumes of interest in 3D printed tissue engineering scaffolds. The method is validated using a 4D synchrotron sourced microCT image data captured during the sintering of bioactive glass scaffolds in-situ. The proposed method will contribute to the development of scaffolds with controllable designs and optimum properties for the development of patient-specific scaffolds

DNA Checkpoint and Repair Factors Are Nuclear Sensors for Intracellular Organelle Stresses-Inflammations and Cancers Can Have High Genomic Risks.

Under inflammatory conditions, inflammatory cells release reactive oxygen species (ROS) and reactive nitrogen species (RNS) which cause DNA damage. If not appropriately repaired, DNA damage leads to gene mutations and genomic instability. DNA damage checkpoint factors (DDCF) and DNA damage repair factors (DDRF) play a vital role in maintaining genomic integrity. However, how DDCFs and DDRFs are modulated under physiological and pathological conditions are not fully known. We took an experimental database analysis to determine the expression of 26 DNA D

Twenty Novel Disease Group-Specific and 12 New Shared Macrophage Pathways in Eight Groups of 34 Diseases Including 24 Inflammatory Organ Diseases and 10 Types of Tumors.

The mechanisms underlying pathophysiological regulation of tissue macrophage (Mφ) subsets remain poorly understood. From the expression of 207 Mφ genes comprising 31 markers for 10 subsets, 45 transcription factors (TFs), 56 immunometabolism enzymes, 23 trained immunity (innate immune memory) enzymes, and 52 other genes in microarray data, we made the following findings. (1) When 34 inflammation diseases and tumor types were grouped into eight categories, there was differential expression of the 31 Mφ markers and 45 Mφ TFs, highlighted by 12 shared and 20 group-specific disease pathways. (2) Mφ in lung, liver, spleen, and intestine (LLSI-Mφ) express higher M1 Mφ markers than lean adipose tissue Mφ (ATMφ) physiologically. (3) Pro-adipogenic TFs C/EBPα and PPARγ and proinflammatory adipokine leptin upregulate the expression of M1 Mφ markers. (4) Among 10 immune checkpoint receptors (ICRs), LLSI-Mφ and bone marrow (BM) Mφ express higher levels of CD274 (PDL-1) than ATMφ, presumably to counteract the M1 dominant status via its reverse signaling behavior. (5) Among 24 intercellular communication exosome mediators, LLSI- and BM- Mφ prefer to use RAB27A and STX3 than RAB31 and YKT6, suggesting new inflammatory exosome mediators for propagating inflammation. (6) Mφ in peritoneal tissue and LLSI-Mφ upregulate higher levels of immunometabolism enzymes than does ATMφ. (7) Mφ from peritoneum and LLSI-Mφ upregulate more trained immunity enzyme genes than does ATMφ. Our results suggest that multiple new mechanisms including the cell surface, intracellular immunometabolism, trained immunity, and TFs may be responsible for disease group-specific and shared pathways. Our findings have provided novel insights on the pathophysiological regulation of tissue Mφ, the disease group-specific and shared pathways of Mφ, and novel therapeutic targets for cancers and inflammations

Construction and demolition waste as a road construction material in rigid pavement design

This paper focus on investigation of properties of recycled aggregate and use of recycled concrete aggregates to partially or fully replaced natural aggregates in the production of lower grade concrete. Recycled products may reduce the demands for new materials. Among which recycled aggregate (RA) is one of the major construction waste capable of being reused in the production of concrete. To evaluate the viability of this process, an experimental campaign was implemented in order to monitor the mechanical behavior of such concrete. With aim of that, the recycled aggregate properties were evaluated at the beginning before utilizing them in concrete application. The obtained test results in assessing properties of aggregate are reported in terms of (i) particle size distribution; (ii) particle density; (iii) porosity and absorption; (IV) particle shape; (v) strength and toughness

Clinical dialogue transcription error correction with self-supervision.

A clinical dialogue is a conversation between a clinician and a patient to share medical information, which is critical in clinical decision-making. The reliance on manual note-taking is highly inefficient and leads to transcription errors when digitising notes. Speech-to-text applications designed using Automatic Speech Recognition (ASR) can potentially overcome these errors using post-ASR error correction. Pre-trained language models are increasingly used in this area. However, the performance suffers from the lack of domain-specific vocabulary and the mismatch between error correction and pre-training objectives. This research explores these challenges in gastrointestinal specialism by introducing self-supervision strategies to fine-tune pre-trained language models for clinical dialogue error correction. We show that our mask-filling objective specialised for the medical domain (med-mask-filling) outperforms the best performing commercial ASR system by 10.27%

Clinical dialogue transcription error correction using Seq2Seq models.

Good communication is critical to good healthcare. Clinical dialogue is a conversation between health practitioners and their patients, with the explicit goal of obtaining and sharing medical information. This information contributes to medical decision-making regarding the patient and plays a crucial role in their healthcare journey. The reliance on note taking and manual scribing processes are extremely inefficient and leads to manual transcription errors when digitizing notes. Automatic Speech Recognition (ASR) plays a significant role in speech-totext applications, and can be directly used as a text generator in conversational applications. However, recording clinical dialogue presents a number of general and domain-specific challenges. In this paper, we present a seq2seq learning approach for ASR transcription error correction of clinical dialogues. We introduce a new Gastrointestinal Clinical Dialogue (GCD) Dataset which was gathered by healthcare professionals from a NHS Inflammatory Bowel Disease clinic and use this in 7a comparative study with four commercial ASR systems. Using self-supervision strategies, we fine-tune a seq2seq model on a mask-filling task using a domainspecific PubMed dataset which we have shared publicly for future research. The BART model fine-tuned for mask-filling was able to correct transcription errors and achieve lower word error rates for three out of four commercial ASR outputs

Clinical Dialogue Transcription Error Correction using Seq2Seq Models

Good communication is critical to good healthcare. Clinical dialogue is a conversation between health practitioners and their patients, with the explicit goal of obtaining and sharing medical information. This information contributes to medical decision-making regarding the patient and plays a crucial role in their healthcare journey. The reliance on note taking and manual scribing processes are extremely inefficient and leads to manual transcription errors when digitizing notes. Automatic Speech Recognition (ASR) plays a significant role in speech-to-text applications, and can be directly used as a text generator in conversational applications. However, recording clinical dialogue presents a number of general and domain-specific challenges. In this paper, we present a seq2seq learning approach for ASR transcription error correction of clinical dialogues. We introduce a new Gastrointestinal Clinical Dialogue (GCD) Dataset which was gathered by healthcare professionals from a NHS Inflammatory Bowel Disease clinic and use this in a comparative study with four commercial ASR systems. Using self-supervision strategies, we fine-tune a seq2seq model on a mask-filling task using a domain-specific PubMed dataset which we have shared publicly for future research. The BART model fine-tuned for mask-filling was able to correct transcription errors and achieve lower word error rates for three out of four commercial ASR outputs.Comment: Pre-print of the paper accepted at the 6th International Workshop on Health Intelligence (W3PHIAI-22