arXiv subjects

Xinru Wei

Publications and source records attributed to Xinru Wei.

6 recordsLinked to original sources

arXiv2024

AC-EVAL: Evaluating Ancient Chinese Language Understanding in Large Language Models

Given the importance of ancient Chinese in capturing the essence of rich historical and cultural heritage, the rapid advancements in Large Language Models (LLMs) necessitate benchmarks that can effectively evaluate their understanding of ancient contexts. To meet this need, we present AC-EVAL, an innovative benchmark designed to assess the advanced knowledge and reasoning capabilities of LLMs within the context of ancient Chinese. AC-EVAL is structured across three levels of difficulty reflecting different facets of language comprehension: general historical knowledge, short text understanding, and long text comprehension. The benchmark comprises 13 tasks, spanning historical facts, geography, social customs, art, philosophy, classical poetry and prose, providing a comprehensive assessment framework. Our extensive evaluation of top-performing LLMs, tailored for both English and Chinese, reveals a substantial potential for enhancing ancient text comprehension. By highlighting the strengths and weaknesses of LLMs, AC-EVAL aims to promote their development and application forward in the realms of ancient Chinese language education and scholarly research. The AC-EVAL data and evaluation code are available at https://github.com/yuting-wei/AC-EVAL.

cs.CL↗

arXiv2023

Exploring the relationship between response time sequence in scale answering process and severity of insomnia: a machine learning approach

Objectives: The study aims to investigate the relationship between insomnia and response time. Additionally, it aims to develop a machine learning model to predict the presence of insomnia in participants using response time data. Methods: A mobile application was designed to administer scale tests and collect response time data from 2729 participants. The relationship between symptom severity and response time was explored, and a machine learning model was developed to predict the presence of insomnia. Results: The result revealed a statistically significant difference (p<.001) in the total response time between participants with or without insomnia symptoms. A correlation was observed between the severity of specific insomnia aspects and response times at the individual questions level. The machine learning model demonstrated a high predictive accuracy of 0.743 in predicting insomnia symptoms based on response time data. Conclusions: These findings highlight the potential utility of response time data to evaluate cognitive and psychological measures, demonstrating the effectiveness of using response time as a diagnostic tool in the assessment of insomnia.

cs.LG↗

arXiv2023

Attention-Based Acoustic Feature Fusion Network for Depression Detection

Depression, a common mental disorder, significantly influences individuals and imposes considerable societal impacts. The complexity and heterogeneity of the disorder necessitate prompt and effective detection, which nonetheless, poses a difficult challenge. This situation highlights an urgent requirement for improved detection methods. Exploiting auditory data through advanced machine learning paradigms presents promising research directions. Yet, existing techniques mainly rely on single-dimensional feature models, potentially neglecting the abundance of information hidden in various speech characteristics. To rectify this, we present the novel Attention-Based Acoustic Feature Fusion Network (ABAFnet) for depression detection. ABAFnet combines four different acoustic features into a comprehensive deep learning model, thereby effectively integrating and blending multi-tiered features. We present a novel weight adjustment module for late fusion that boosts performance by efficaciously synthesizing these features. The effectiveness of our approach is confirmed via extensive validation on two clinical speech databases, CNRAC and CS-NRAC, thereby outperforming previous methods in depression detection and subtype classification. Further in-depth analysis confirms the key role of each feature and highlights the importance of MFCCrelated features in speech-based depression detection.

cs.SD↗

arXiv2023

Total controllability analysis discovers explainable drugs for Covid-19 treatment

Network medicine has been pursued for Covid-19 drug repurposing. One such approach adopts structural controllability, a theory for controlling a network (the cell). Motivated to protect the cell from viral infections, we extended this theory to total controllability and introduced a new concept of control hubs. Perturbation to any control hub renders the cell uncontrollable by exogenous stimuli, e.g., viral infections, so control hubs are ideal drug targets. We developed an efficient algorithm for finding all control hubs and applied it to the largest homogenous human protein-protein interaction network. Our new method outperforms several popular gene-selection methods, including that based on structural controllability. The final 65 druggable control hubs are enriched with functions of cell proliferation, regulation of apoptosis, and responses to cellular stress and nutrient levels, revealing critical pathways induced by SARS-CoV-2. These druggable control hubs led to drugs in 4 major categories: antiviral and anti-inflammatory agents, drugs on central nerve systems, and dietary supplements and hormones that boost immunity. Their functions also provided deep insights into the therapeutic mechanisms of the drugs for Covid-19 therapy, making the new approach an explainable drug repurposing method. A remarkable example is Fostamatinib that has been shown to lower mortality, shorten the length of ICU stay, and reduce disease severity of hospitalized Covid-19 patients. The drug targets 10 control hubs, 9 of which are kinases that play key roles in cell differentiation and programmed death. One such kinase is RIPK1 that directly interacts with viral protein nsp12, the RdRp of the virus. The study produced many control hubs that were not targets of existing drugs but were enriched with proteins on membranes and the NF-$κ$B pathway, so are excellent candidate targets for new drugs.

q-bio.MN↗

arXiv2023

NetMoST: A network-based machine learning approach for subtyping schizophrenia using polygenic SNP allele biomarkers

Subtyping neuropsychiatric disorders like schizophrenia is essential for improving the diagnosis and treatment of complex diseases. Subtyping schizophrenia is challenging because it is polygenic and genetically heterogeneous, rendering the standard symptom-based diagnosis often unreliable and unrepeatable. We developed a novel network-based machine-learning approach, netMoST, to subtyping psychiatric disorders. NetMoST identifies polygenic risk SNP-allele modules from genome-wide genotyping data as polygenic haplotype biomarkers (PHBs) for disease subtyping. We applied netMoST to subtype a cohort of schizophrenia subjects into three distinct biotypes with differentiable genetic, neuroimaging and functional characteristics. The PHBs of the first biotype (36.9% of all patients) were related to neurodevelopment and cognition, the PHBs of the second biotype (28.4%) were enriched for neuroimmune functions, and the PHBs of the third biotype (34.7%) were associated with the transport of calcium ions and neurotransmitters. Neuroimaging patterns provided additional support to the new biotypes, with unique regional homogeneity (ReHo) patterns observed in the brains of each biotype compared with healthy controls. Our findings demonstrated netMoST's capability for uncovering novel biotypes of complex diseases such as schizophrenia. The results also showed the power of exploring polygenic allelic patterns that transcend the conventional GWAS approaches.

q-bio.MN↗

arXiv2022

Identification of cancer-keeping genes as therapeutic targets by finding network control hubs

Finding cancer driver genes has been a focal theme of cancer research and clinical studies. One of the recent approaches is based on network structural controllability that focuses on finding a control scheme and driver genes that can steer the cell from an arbitrary state to a designated state. While theoretically sound, this approach is impractical for many reasons, e.g., the control scheme is often not unique and half of the nodes may be driver genes for the cell. We developed a novel approach that transcends structural controllability. Instead of considering driver genes for one control scheme, we considered control hub genes that reside in the middle of a control path of every control scheme. Control hubs are the most vulnerable spots for controlling the cell and exogenous stimuli on them may render the cell uncontrollable. We adopted control hubs as cancer-keep genes (CKGs) and applied them to a gene regulatory network of bladder cancer (BLCA). All the genes on the cell cycle and p53 singling pathways in BLCA are CKGs, confirming the importance of these genes and the two pathways in cancer. A smaller set of 35 sensitive CKGs (sCKGs) for BLCA was identified by removing network links. Six sCKGs (RPS6KA3, FGFR3, N-cadherin (CDH2), EP300, caspase-1, and FN1) were subjected to small-interferencing-RNA knockdown in four cell lines to validate their effects on the proliferation or migration of cancer cells. Knocking down RPS6KA3 in a mouse model of BLCA significantly inhibited the growth of tumor xenografts in the mouse model. Combined, our results demonstrated the value of CKGs as therapeutic targets for cancer therapy and the potential of CKGs as an effective means for studying and characterizing cancer etiology.

q-bio.MN↗