Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning

BACKGROUND: Medication and adverse drug event (ADE) information extracted from electronic health record (EHR) notes can be a rich resource for drug safety surveillance. Existing observational studies have mainly relied on structured EHR data to obtain ADE information; however, ADEs are often buried in the EHR narratives and not recorded in structured data. OBJECTIVE: To unlock ADE-related information from EHR narratives, there is a need to extract relevant entities and identify relations among them. In this study, we focus on relation identification. This study aimed to evaluate natural language processing and machine learning approaches using the expert-annotated medical entities and relations in the context of drug safety surveillance, and investigate how different learning approaches perform under different configurations. METHODS: We have manually annotated 791 EHR notes with 9 named entities (eg, medication, indication, severity, and ADEs) and 7 different types of relations (eg, medication-dosage, medication-ADE, and severity-ADE). Then, we explored 3 supervised machine learning systems for relation identification: (1) a support vector machines (SVM) system, (2) an end-to-end deep neural network system, and (3) a supervised descriptive rule induction baseline system. For the neural network system, we exploited the state-of-the-art recurrent neural network (RNN) and attention models. We report the performance by macro-averaged precision, recall, and F1-score across the relation types. RESULTS: Our results show that the SVM model achieved the best average F1-score of 89.1% on test data, outperforming the long short-term memory (LSTM) model with attention (F1-score of 65.72%) as well as the rule induction baseline system (F1-score of 7.47%) by a large margin. The bidirectional LSTM model with attention achieved the best performance among different RNN models. With the inclusion of additional features in the LSTM model, its performance can be boosted to an average F1-score of 77.35%. CONCLUSIONS: It shows that classical learning models (SVM) remains advantageous over deep learning models (RNN variants) for clinical relation identification, especially for long-distance intersentential relations. However, RNNs demonstrate a great potential of significant improvement if more training data become available. Our work is an important step toward mining EHRs to improve the efficacy of drug safety surveillance. Most importantly, the annotated data used in this study will be made publicly available, which will further promote drug safety research in the community

MedTxting: learning based and knowledge rich SMS-style medical text contraction

In mobile health (M-health), Short Message Service (SMS) has shown to improve disease related self-management and health service outcomes, leading to enhanced patient care. However, the hard limit on character size for each message limits the full value of exploring SMS communication in health care practices. To overcome this problem and improve the efficiency of clinical workflow, we developed an innovative system, MedTxting (available at http://medtxting.askhermes.org), which is a learning-based but knowledge-rich system that compresses medical texts in a SMS style. Evaluations on clinical questions and discharge summary narratives show that MedTxting can effectively compress medical texts with reasonable readability and noticeable size reduction. Findings in this work reveal potentials of MedTxting to the clinical settings, allowing for real-time and cost-effective communication, such as patient condition reporting, medication consulting, physicians connecting to share expertise to improve point of care

Harnessing LSTM for Nonlinear Ship Deck Motion Prediction in UAV Autonomous Landing amidst High Sea States

Autonomous landing of UAVs in high sea states requires the UAV to land exclusively during the ship deck's "rest period," coinciding with minimal movement. Given this scenario, determining the ship's "rest period" based on its movement patterns becomes a fundamental prerequisite for addressing this challenge. This study employs the Long Short-Term Memory (LSTM) neural network to predict the ship's motion across three dimensions: longi-tudinal, transverse, and vertical waves. In the absence of actual ship data under high sea states, this paper employs a composite sine wave model to simulate ship deck motion. Through this approach, a highly accurate model is established, exhibiting promising outcomes within various stochastic sine wave combination models.Comment: 11 pages, 7 figures, accept by ICANDVC202

Automatic Figure Ranking and User Interfacing for Intelligent Figure Search

Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of "figure ranking": figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.We empirically validated the hypothesis of figure ranking with over 100 bioscience researchers, and then developed unsupervised natural language processing (NLP) approaches to automatically rank figures. Evaluating on a collection of 202 full-text articles in which authors have ranked the figures based on importance, our best system achieved a weighted error rate of 0.2, which is significantly better than several other baseline systems we explored. We further explored a user interfacing application in which we built novel user interfaces (UIs) incorporating figure ranking, allowing bioscience researchers to efficiently access important figures. Our evaluation results show that 92% of the bioscience researchers prefer as the top two choices the user interfaces in which the most important figures are enlarged. With our automatic figure ranking NLP system, bioscience researchers preferred the UIs in which the most important figures were predicted by our NLP system than the UIs in which the most important figures were randomly assigned. In addition, our results show that there was no statistical difference in bioscience researchers' preference in the UIs generated by automatic figure ranking and UIs by human ranking annotation.The evaluation results conclude that automatic figure ranking and user interfacing as we reported in this study can be fully implemented in online publishing. The novel user interface integrated with the automatic figure ranking system provides a more efficient and robust way to access scientific information in the biomedical domain, which will further enhance our existing figure search engine to better facilitate accessing figures of interest for bioscientists

API-Bank: A Comprehensive Benchmark for Tool-Augmented LLMs

Recent research has demonstrated that Large Language Models (LLMs) can enhance their capabilities by utilizing external tools. However, three pivotal questions remain unanswered: (1) How effective are current LLMs in utilizing tools? (2) How can we enhance LLMs' ability to utilize tools? (3) What obstacles need to be overcome to leverage tools? To address these questions, we introduce API-Bank, a groundbreaking benchmark, specifically designed for tool-augmented LLMs. For the first question, we develop a runnable evaluation system consisting of 73 API tools. We annotate 314 tool-use dialogues with 753 API calls to assess the existing LLMs' capabilities in planning, retrieving, and calling APIs. For the second question, we construct a comprehensive training set containing 1,888 tool-use dialogues from 2,138 APIs spanning 1,000 distinct domains. Using this dataset, we train Lynx, a tool-augmented LLM initialized from Alpaca. Experimental results demonstrate that GPT-3.5 exhibits improved tool utilization compared to GPT-3, while GPT-4 excels in planning. However, there is still significant potential for further improvement. Moreover, Lynx surpasses Alpaca's tool utilization performance by more than 26 pts and approaches the effectiveness of GPT-3.5. Through error analysis, we highlight the key challenges for future research in this field to answer the third question.Comment: EMNLP 202

Detection of Bleeding Events in Electronic Health Record Notes Using Convolutional Neural Network Models Enhanced With Recurrent Neural Network Autoencoders: Deep Learning Approach

BACKGROUND: Bleeding events are common and critical and may cause significant morbidity and mortality. High incidences of bleeding events are associated with cardiovascular disease in patients on anticoagulant therapy. Prompt and accurate detection of bleeding events is essential to prevent serious consequences. As bleeding events are often described in clinical notes, automatic detection of bleeding events from electronic health record (EHR) notes may improve drug-safety surveillance and pharmacovigilance. OBJECTIVE: We aimed to develop a natural language processing (NLP) system to automatically classify whether an EHR note sentence contains a bleeding event. METHODS: We expert annotated 878 EHR notes (76,577 sentences and 562,630 word-tokens) to identify bleeding events at the sentence level. This annotated corpus was used to train and validate our NLP systems. We developed an innovative hybrid convolutional neural network (CNN) and long short-term memory (LSTM) autoencoder (HCLA) model that integrates a CNN architecture with a bidirectional LSTM (BiLSTM) autoencoder model to leverage large unlabeled EHR data. RESULTS: HCLA achieved the best area under the receiver operating characteristic curve (0.957) and F1 score (0.938) to identify whether a sentence contains a bleeding event, thereby surpassing the strong baseline support vector machines and other CNN and autoencoder models. CONCLUSIONS: By incorporating a supervised CNN model and a pretrained unsupervised BiLSTM autoencoder, the HCLA achieved high performance in detecting bleeding events

Degradable mesoporous semimetal antimony nanospheres for near-infrared II multimodal theranostics.

Metallic and semimetallic mesoporous frameworks are of great importance owing to their unique properties and broad applications. However, semimetallic mesoporous structures cannot be obtained by the traditional template-mediated strategies due to the inevitable hydrolytic reaction of semimetal compounds. Therefore, it is yet challenging to fabricate mesoporous semimetal nanostructures, not even mention controlling their pore sizes. Here we develop a facile and robust selective etching route to synthesize monodispersed mesoporous antimony nanospheres (MSbNSs). The pore sizes of MSbNSs are tunable by carefully controlling the partial oxidation of Sb nuclei and the selective etching of the as-formed Sb2O3. MSbNSs show a wide absorption from visible to second near-infrared (NIR-II) region. Moreover, PEGylated MSbNSs are degradable and the degradation mechanism is further explained. The NIR-II photothermal performance of MSbNSs is promising with a high photothermal conversion efficiency of ~44% and intensive NIR-II photoacoustic signal. MSbNSs show potential as multifunctional nanomedicines for NIR-II photoacoustic imaging guided synergistic photothermal/chemo therapy in vivo. Our selective etching process would contribute to the development of various semimetallic mesoporous structures and efficient multimodal nanoplatforms for theranostics

Multi-time-scale voltage control of the distribution network with energy storage equipped soft open points

The integration of distributed generation (DG) units into distribution networks (DNs) has brought about several operational challenges, including voltage issues and increased power loss. Energy storage equipped soft open points (E-SOPs) can accurately and flexibly control active and reactive power flows to address these problems. Additionally, the photovoltaic (PV) inverter and the network reconfiguration (NR) play a significant role in voltage control by adjusting the reactive power and the topology of the DN, respectively. However, due to differences in response times, there is a lack of systematic coordination between NR and the inverters of the E-SOP and PV. This paper proposes a multi-time-scale voltage control model that includes day-ahead NR scheduling, inter-day droop control optimization of the PV and E-SOP, and real-time local droop control. Considering the uncertainties of renewable DG outputs and loads, a robust optimization method is used in the day-ahead stage to obtain a reliable network structure. Then, with more accurate intra-day predictions, a stochastic optimization method is used to obtain the optimal state-of-charge interval, aiming to provide a flexible regulation range for battery energy storage to cope with the power fluctuations during the real-time stage. In addition, to address the intra-day voltage control model with bilinear constraints of the droop control function, a particle swarm optimization method is used. The results are verified on a 33-bus DN system through comparative analyses, showing effective performance