Anchen Sun

Anchen Sun, Elizabeth J. Franzmann, Zhibin Chen et al.

Recent advancements in image classification have demonstrated that contrastive learning (CL) can aid in further learning tasks by acquiring good feature representation from a limited number of data samples. In this paper, we applied CL to tumor transcriptomes and clinical data to learn feature representations in a low-dimensional space. We then utilized these learned features to train a classifier to categorize tumors into a high- or low-risk group of recurrence. Using data from The Cancer Genome Atlas (TCGA), we demonstrated that CL can significantly improve classification accuracy. Specifically, our CL-based classifiers achieved an area under the receiver operating characteristic curve (AUC) greater than 0.8 for 14 types of cancer, and an AUC greater than 0.9 for 2 types of cancer. We also developed CL-based Cox (CLCox) models for predicting cancer prognosis. Our CLCox models trained with the TCGA data outperformed existing methods significantly in predicting the prognosis of 19 types of cancer under consideration. The performance of CLCox models and CL-based classifiers trained with TCGA lung and prostate cancer data were validated using the data from two independent cohorts. We also show that the CLCox model trained with the whole transcriptome significantly outperforms the Cox model trained with the 21 genes of Oncotype DX that is in clinical use for breast cancer patients. CL-based classifiers and CLCox models for 19 types of cancer are publicly available and can be used to predict cancer prognosis using the RNA-seq transcriptome of an individual tumor. Python codes for model training and testing are also publicly accessible, and can be applied to train new CL-based models using gene expression data of tumors.

Anchen Sun, Juan J Londono, Batya Elbaum et al.

Young children spend substantial portions of their waking hours in noisy preschool classrooms. In these environments, children's vocal interactions with teachers are critical contributors to their language outcomes, but manually transcribing these interactions is prohibitive. Using audio from child- and teacher-worn recorders, we propose an automated framework that uses open source software both to classify speakers (ALICE) and to transcribe their utterances (Whisper). We compare results from our framework to those from a human expert for 110 minutes of classroom recordings, including 85 minutes from child-word microphones (n=4 children) and 25 minutes from teacher-worn microphones (n=2 teachers). The overall proportion of agreement, that is, the proportion of correctly classified teacher and child utterances, was .76, with an error-corrected kappa of .50 and a weighted F1 of .76. The word error rate for both teacher and child transcriptions was .15, meaning that 15% of words would need to be deleted, added, or changed to equate the Whisper and expert transcriptions. Moreover, speech features such as the mean length of utterances in words, the proportion of teacher and child utterances that were questions, and the proportion of utterances that were responded to within 2.5 seconds were similar when calculated separately from expert and automated transcriptions. The results suggest substantial progress in analyzing classroom speech that may support children's language development. Future research using natural language processing is under way to improve speaker classification and to analyze results from the application of the automated framework to a larger dataset containing classroom recordings from 13 children and 3 teachers observed on 17 occasions over one year.

Ziyuan Xia, Anchen Sun, Xiaodong Cai et al.

Environmental, social, and governance (ESG) reports are globally recognized as a keystone in sustainable enterprise development. However, current literature has not concluded the development of topics and trends in ESG contexts in the twenty-first century. Therefore, We selected 1114 ESG reports from firms in the technology industry to analyze the evolutionary trends of ESG topics by text mining. We discovered the homogenization effect towards low environmental, medium governance, and high social features in the evolution. We also designed a strategic framework to look closer into the dynamic changes of firms' within-industry scores and across-domain importances. We found that companies are gradually converging towards the third quadrant, which indicates that firms contribute less to industrial outstanding and professional distinctiveness in ESG reporting. Firms choose to imitate ESG reports from each other to mitigate uncertainty and enhance behavioral legitimacy.

Anchen Sun, Zhibin Chen, Xiaodong Cai

The Cox Proportional Hazards (PH) model is widely used in survival analysis. Recently, artificial neural network (ANN)-based Cox-PH models have been developed. However, training these Cox models with high-dimensional features typically requires a substantial number of labeled samples containing information about time-to-event. The limited availability of labeled data for training often constrains the performance of ANN-based Cox models. To address this issue, we employed a deep semi-supervised learning (DSSL) approach to develop single- and multi-modal ANN-based Cox models based on the Mean Teacher (MT) framework, which utilizes both labeled and unlabeled data for training. We applied our model, named Cox-MT, to predict the prognosis of several types of cancer using data from The Cancer Genome Atlas (TCGA). Our single-modal Cox-MT models, utilizing TCGA RNA-seq data or whole slide images, significantly outperformed the existing ANN-based Cox model, Cox-nnet, using the same data set across four types of cancer considered. As the number of unlabeled samples increased, the performance of Cox-MT significantly improved with a given set of labeled data. Furthermore, our multi-modal Cox-MT model demonstrated considerably better performance than the single-modal model. In summary, the Cox-MT model effectively leverages both labeled and unlabeled data to significantly enhance prediction accuracy compared to existing ANN-based Cox models trained solely on labeled data.

Anchen Sun, Tiantian Feng, Gabriela Gutierrez et al.

This paper introduces an automated framework WSW2.0 for analyzing vocal interactions in preschool classrooms, enhancing both accuracy and scalability through the integration of wav2vec2-based speaker classification and Whisper (large-v2 and large-v3) speech transcription. A total of 235 minutes of audio recordings (160 minutes from 12 children and 75 minutes from 5 teachers), were used to compare system outputs to expert human annotations. WSW2.0 achieves a weighted F1 score of .845, accuracy of .846, and an error-corrected kappa of .672 for speaker classification (child vs. teacher). Transcription quality is moderate to high with word error rates of .119 for teachers and .238 for children. WSW2.0 exhibits relatively high absolute agreement intraclass correlations (ICC) with expert transcriptions for a range of classroom language features. These include teacher and child mean utterance length, lexical diversity, question asking, and responses to questions and other utterances, which show absolute agreement intraclass correlations between .64 and .98. To establish scalability, we apply the framework to an extensive dataset spanning two years and over 1,592 hours of classroom audio recordings, demonstrating the framework's robustness for broad real-world applications. These findings highlight the potential of deep learning and natural language processing techniques to revolutionize educational research by providing accurate measures of key features of preschool classroom speech, ultimately guiding more effective intervention strategies and supporting early childhood language development.