Goto

Collaborating Authors

 Qin, Peiwu


pLDDT-Predictor: High-speed Protein Screening Using Transformer and ESM2

arXiv.org Artificial Intelligence

Recent advancements in protein structure prediction, particularly AlphaFold2, have revolutionized structural biology by achieving near-experimental accuracy ($\text{average RMSD} < 1.5\text{\AA}$). However, the computational demands of these models (approximately 30 minutes per protein on an RTX 4090) significantly limit their application in high-throughput protein screening. While large language models like ESM (Evolutionary Scale Modeling) have shown promise in extracting structural information directly from protein sequences, rapid assessment of protein structure quality for large-scale analyses remains a major challenge. We introduce pLDDT-Predictor, a high-speed protein screening tool that achieves a $250,000\times$ speedup compared to AlphaFold2 by leveraging pre-trained ESM2 protein embeddings and a Transformer architecture. Our model predicts AlphaFold2's pLDDT (predicted Local Distance Difference Test) scores with a Pearson correlation of 0.7891 and processes proteins in just 0.007 seconds on average. Using a comprehensive dataset of 1.5 million diverse protein sequences (ranging from 50 to 2048 amino acids), we demonstrate that pLDDT-Predictor accurately classifies high-confidence structures (pLDDT $>$ 70) with 91.2\% accuracy and achieves an MSE of 84.8142 compared to AlphaFold2's predictions. The source code and pre-trained models are freely available at \url{https://github.com/jw-chae/pLDDT_Predictor}, enabling the research community to perform rapid, large-scale protein structure quality assessments.


COVID-19: post infection implications in different age groups, mechanism, diagnosis, effective prevention, treatment, and recommendations

arXiv.org Artificial Intelligence

SARS-CoV-2, the highly contagious pathogen responsible for the COVID-19 pandemic, has persistent effects that begin four weeks after initial infection and last for an undetermined duration. These chronic effects are more harmful than acute ones. This review explores the long-term impact of the virus on various human organs, including the pulmonary, cardiovascular, neurological, reproductive, gastrointestinal, musculoskeletal, endocrine, and lymphoid systems, particularly in older adults. Regarding diagnosis, RT-PCR is the gold standard for detecting COVID-19, though it requires specialized equipment, skilled personnel, and considerable time to produce results. To address these limitations, artificial intelligence in imaging and microfluidics technologies offers promising alternatives for diagnosing COVID-19 efficiently. Pharmacological and non-pharmacological strategies are effective in mitigating the persistent impacts of COVID-19. These strategies enhance immunity in post-COVID-19 patients by reducing cytokine release syndrome, improving T cell response, and increasing the circulation of activated natural killer and CD8 T cells in blood and tissues. This, in turn, alleviates symptoms such as fever, nausea, fatigue, muscle weakness, and pain. Vaccines, including inactivated viral, live attenuated viral, protein subunit, viral vectored, mRNA, DNA, and nanoparticle vaccines, significantly reduce the adverse long-term effects of the virus. However, no vaccine has been reported to provide lifetime protection against COVID-19. Consequently, protective measures such as physical distancing, mask usage, and hand hygiene remain essential strategies. This review offers a comprehensive understanding of the persistent effects of COVID-19 on individuals of varying ages, along with insights into diagnosis, treatment, vaccination, and future preventative measures against the spread of SARS-CoV-2.


LAMPER: LanguAge Model and Prompt EngineeRing for zero-shot time series classification

arXiv.org Artificial Intelligence

This study constructs the LanguAge Model with Prompt EngineeRing (LAMPER) framework, designed to systematically evaluate the adaptability of pre-trained language models (PLMs) in accommodating diverse prompts and their integration in zero-shot time series (TS) classification. Our findings indicate that the feature representation capacity of LAMPER is influenced by the maximum input token threshold imposed by PLMs. The exploration of time series (TS)-based tasks constitutes a research-intensive domain with significant implications with wide-ranging implications in diverse professional fields, including healthcare, finance, and energy (Zhang et al., 2022; Zheng et al., 2023; Santoro et al., 2023). Within the realms of natural language processing (NLP), the dynamic landscape witnesses the rapid evolution of pre-trained language models (PLMs) and prompt engineering (Min et al., 2023; Wei et al., 2022). These advancements underscore their commendable capacity to adeptly execute an extensive array of tasks, particularly under few-shot or even zero-shot conditions (Brown et al., 2020; Webson & Pavlick, 2022).


Cognitive resilience: Unraveling the proficiency of image-captioning models to interpret masked visual content

arXiv.org Artificial Intelligence

This study explores the ability of Image Captioning (IC) models to decode masked visual content sourced from diverse datasets. Our findings reveal the IC model's capability to generate captions from masked images, closely resembling the original content. Notably, even in the presence of masks, the model adeptly crafts descriptive textual information that goes beyond what is observable in the original image-generated captions. While the decoding performance of the IC model experiences a decline with an increase in the masked region's area, the model still performs well when important regions of the image are not masked at high coverage.


GAME: Generalized deep learning model towards multimodal data integration for early screening of adolescent mental disorders

arXiv.org Artificial Intelligence

The timely identification of mental disorders in adolescents is a global public health challenge.Single factor is difficult to detect the abnormality due to its complex and subtle nature. Additionally, the generalized multimodal Computer-Aided Screening (CAS) systems with interactive robots for adolescent mental disorders are not available. Here, we design an android application with mini-games and chat recording deployed in a portable robot to screen 3,783 middle school students and construct the multimodal screening dataset, including facial images, physiological signs, voice recordings, and textual transcripts.We develop a model called GAME (Generalized Model with Attention and Multimodal EmbraceNet) with novel attention mechanism that integrates cross-modal features into the model. GAME evaluates adolescent mental conditions with high accuracy (73.34%-92.77%) and F1-Score (71.32%-91.06%).We find each modality contributes dynamically to the mental disorders screening and comorbidities among various mental disorders, indicating the feasibility of explainable model. This study provides a system capable of acquiring multimodal information and constructs a generalized multimodal integration algorithm with novel attention mechanisms for the early screening of adolescent mental disorders.


Neuro-Symbolic Learning: Principles and Applications in Ophthalmology

arXiv.org Artificial Intelligence

Neural networks have been rapidly expanding in recent years, with novel strategies and applications. However, challenges such as interpretability, explainability, robustness, safety, trust, and sensibility remain unsolved in neural network technologies, despite the fact that they will unavoidably be addressed for critical applications. Attempts have been made to overcome the challenges in neural network computing by representing and embedding domain knowledge in terms of symbolic representations. Thus, the neuro-symbolic learning (NeSyL) notion emerged, which incorporates aspects of symbolic representation and bringing common sense into neural networks (NeSyL). In domains where interpretability, reasoning, and explainability are crucial, such as video and image captioning, question-answering and reasoning, health informatics, and genomics, NeSyL has shown promising outcomes. This review presents a comprehensive survey on the state-of-the-art NeSyL approaches, their principles, advances in machine and deep learning algorithms, applications such as opthalmology, and most importantly, future perspectives of this emerging field.