Dongfang Xu

Yanjun Gao, Dmitriy Dligach, Timothy Miller et al. · harvard

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Hang Zhao, Hongru Li, Dongfang Xu et al.

Semantic communication is emerging as a key enabler for distributed edge intelligence due to its capability to convey task-relevant meaning. However, achieving communication-efficient training and robust inference over wireless links remains challenging. This challenge is further exacerbated for multi-modal edge inference (MMEI) by two factors: 1) prohibitive communication overhead for distributed learning over bandwidth-limited wireless links, due to the \emph{multi-modal} nature of the system; and 2) limited robustness under varying channels and noisy multi-modal inputs. In this paper, we propose a three-stage communication-aware distributed learning framework to improve training and inference efficiency while maintaining robustness over wireless channels. In Stage~I, devices perform local multi-modal self-supervised learning to obtain shared and modality-specific encoders without device--server exchange, thereby reducing the communication cost. In Stage~II, distributed fine-tuning with centralized evidential fusion calibrates per-modality uncertainty and reliably aggregates features distorted by noise or channel fading. In Stage~III, an uncertainty-guided feedback mechanism selectively requests additional features for uncertain samples, optimizing the communication--accuracy tradeoff in the distributed setting. Experiments on RGB--depth indoor scene classification show that the proposed framework attains higher accuracy with far fewer training communication rounds and remains robust to modality degradation or channel variation, outperforming existing self-supervised and fully supervised baselines.

Hang Zhao, Hongru Li, Dongfang Xu et al.

Semantic communication is emerging as a promising paradigm that focuses on the extraction and transmission of semantic meanings using deep learning techniques. While current research primarily addresses the reduction of semantic communication overhead, it often overlooks the training phase, which can incur significant communication costs in dynamic wireless environments. To address this challenge, we propose a multi-modal semantic communication system that leverages multi-modal self-supervised learning to enhance task-agnostic feature extraction. The proposed approach employs self-supervised learning during the pre-training phase to extract task-agnostic semantic features, followed by supervised fine-tuning for downstream tasks. This dual-phase strategy effectively captures both modality-invariant and modality-specific features while minimizing training-related communication overhead. Experimental results on the NYU Depth V2 dataset demonstrate that the proposed method significantly reduces training-related communication overhead while maintaining or exceeding the performance of existing supervised learning approaches. The findings underscore the advantages of multi-modal self-supervised learning in semantic communication, paving the way for more efficient and scalable edge inference systems.

Yanjun Gao, Dmitriy Dligach, Leslie Christensen et al.

Objective: to provide a scoping review of papers on clinical natural language processing (NLP) tasks that use publicly available electronic health record data from a cohort of patients. Materials and Methods: We searched six databases, including biomedical research and computer science literature database. A round of title/abstract screening and full-text screening were conducted by two reviewers. Our method followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Results: A total of 35 papers with 47 clinical NLP tasks met inclusion criteria between 2007 and 2021. We categorized the tasks by the type of NLP problems, including name entity recognition, summarization, and other NLP tasks. Some tasks were introduced with a topic of clinical decision support applications, such as substance abuse, phenotyping, cohort selection for clinical trial. We summarized the tasks by publication and dataset information. Discussion: The breadth of clinical NLP tasks keeps growing as the field of NLP evolves with advancements in language systems. However, gaps exist in divergent interests between general domain NLP community and clinical informatics community, and in generalizability of the data sources. We also identified issues in data selection and preparation including the lack of time-sensitive data, and invalidity of problem size and evaluation. Conclusions: The existing clinical NLP tasks cover a wide range of topics and the field will continue to grow and attract more attention from both general domain NLP and clinical informatics community. We encourage future work to incorporate multi-disciplinary collaboration, reporting transparency, and standardization in data preparation.

Dongfang Xu, Shan Chen, Timothy Miller

In this paper, we present our work participating in the BioCreative VII Track 3 - automatic extraction of medication names in tweets, where we implemented a multi-task learning model that is jointly trained on text classification and sequence labelling. Our best system run achieved a strict F1 of 80.4, ranking first and more than 10 points higher than the average score of all participants. Our analyses show that the ensemble technique, multi-task learning, and data augmentation are all beneficial for medication detection in tweets.

Dongfang Xu, Peter Jansen, Jaycie Martin et al.

Prior work has demonstrated that question classification (QC), recognizing the problem domain of a question, can help answer it more accurately. However, developing strong QC algorithms has been hindered by the limited size and complexity of annotated data available. To address this, we present the largest challenge dataset for QC, containing 7,787 science exam questions paired with detailed classification labels from a fine-grained hierarchical taxonomy of 406 problem domains. We then show that a BERT-based model trained on this dataset achieves a large (+0.12 MAP) gain compared with previous methods, while also achieving state-of-the-art performance on benchmark open-domain and biomedical QC datasets. Finally, we show that using this model's predictions of question topic significantly improves the accuracy of a question answering system by +1.7% P@1, with substantial future gains possible as QC performance improves.