Jian Du

Jian Du, Haitao Mi

When applied to large-scale learning problems, the conventional wisdom on privacy-preserving deep learning, known as Differential Private Stochastic Gradient Descent (DP-SGD), has met with limited success due to significant performance degradation and high memory overhead when compared to the non-privacy counterpart. We show how to mitigate the performance drop by replacing the DP-SGD with a novel DP Forward-Propagation (DP-FP) followed by an off-the-shelf non-DP optimizer. Our DP-FP employs novel (1) representation clipping followed by noise addition in the forward propagation stage, as well as (2) micro-batch construction via subsampling to achieve DP amplification and reduce noise power to $1/M$, where $M$ is the number of micro-batch in a step. When training a classification model, our DP-FP with all of the privacy-preserving operations on the representation is innately free of gradient bias, total noise proportionally to model size, and memory issues in DP-SGD. As a result, our DP-FP outperforms cutting-edge DP-SGD while retaining the same level of privacy, and it approaches non-private baselines and significantly outperforms state-of-the-art DP-SGD variants. When applied to RoBERTa-large on four downstream tasks, for example, DP-FP achieves an average accuracy of 91.34\% with privacy budgets less than 3, representing a 3.81\% performance improvement over the state-of-the-art DP-SGD and only a 0.9\% loss compared to the non-private baseline but with a significantly lower privacy leakage risk.

Xuanyu Shi, Jian Du

In clinical research and clinical decision-making, it is important to know if a study changes or only supports the current standards of care for specific disease management. We define such a change as transformative and a support as incremental research. It usually requires a huge amount of domain expertise and time for humans to finish such tasks. Faculty Opinions provides us with a well-annotated corpus on whether a research challenges or only confirms established research. In this study, a machine learning approach is proposed to distinguishing transformative from incremental clinical evidence. The texts from both abstract and a 2-year window of citing sentences are collected for a training set of clinical studies recommended and labeled by Faculty Opinions experts. We achieve the best performance with an average AUC of 0.755 (0.705-0.875) using Random Forest as the classifier and citing sentences as the feature. The results showed that transformative research has typical language patterns in citing sentences unlike abstract sentences. We provide an efficient tool for identifying those clinical evidence challenging or only confirming established claims for clinicians and researchers.

Xin Guo, Yuming Chen, Jian Du et al.

Purpose: This study aims to develop a novel approach to extracting and measuring uncertain biomedical knowledge from scientific statements. Design/methodology/approach: Taking cardiovascular research publications in China as a sample, we extracted the SPO triples as knowledge unit and the hedging/conflicting uncertainties as the knowledge context. We introduced Information Entropy and Uncertainty Rate as potential metrics to quantity the uncertainty of biomedical knowledge claims represented at different levels, such as the SPO triples (micro level), as well as the semantic type pairs (micro-level). Findings: The results indicated that while the number of scientific publications and total SPO triples showed a liner growth, the novel SPO triples occurring per year remained stable. After examining the frequency of uncertain cue words in different part of scientific statements, we found hedging words tend to appear in conclusive and purposeful sentences, whereas conflicting terms often appear in background and act as the premise (e.g., unsettled scientific issues) of the work to be investigated. Practical implications: Our approach identified major uncertain knowledge areas, such as diagnostic biomarkers, genetic characteristics, and pharmacologic therapies surrounding cardiovascular diseases in China. These areas are suggested to be prioritized in which new hypotheses need to be verified, and disputes, conflicts, as well as contradictions to be settled further.

Shuang Wang, Jian Du

Purpose: To explore whether comments could be used as an assistant tool for heuristic decision-making, especially in cases where missing, incomplete, uncertain, or even incorrect evidence is acquired. Methods: Six COVID-19 drug candidates were selected from WHO clinical guidelines. Evidence-comment networks (ECNs) were completed of these six drug candidates based on evidence-comment pairs from all PubMed indexed COVID-19 publications with formal published comments. WHO guidelines were utilized to validate the feasibility of comment-derived evidence assertions as a fast decision supporting tool. Results: Out of 6 drug candidates, comment-derived evidence assertions of leading subgraphs of 5 drugs were consistent with WHO guidelines, and the overall comment sentiment of 6 drugs was aligned with WHO clinical guidelines. Additionally, comment topics were in accordance with the concerns of guidelines and evidence appraisal criteria. Furthermore, half of the critical comments emerged 4.5 months earlier than the date guidelines were published. Conclusions: Comment-derived evidence assertions have the potential as an evidence appraisal tool for heuristic decisions based on the accuracy, sensitivity, and efficiency of evidence-comment networks. In essence, comments reflect that academic communities do have a self-screening evaluation and self-purification (argumentation) mechanism, thus providing a tool for decision makers to filter evidence.

Xiaoying Li, Suyuan Peng, Jian Du

In China, Prof. Hongzhou Zhao and Zeyuan Liu are the pioneers of the concept "knowledge unit" and "knowmetrics" for measuring knowledge. However, the definition of "computable knowledge object" remains controversial so far in different fields. For example, it is defined as 1) quantitative scientific concept in natural science and engineering, 2) knowledge point in the field of education research, and 3) semantic predications, i.e., Subject-Predicate-Object (SPO) triples in biomedical fields. The Semantic MEDLINE Database (SemMedDB), a high-quality public repository of SPO triples extracted from medical literature, provides a basic data infrastructure for measuring medical knowledge. In general, the study of extracting SPO triples as computable knowledge unit from unstructured scientific text has been overwhelmingly focusing on scientific knowledge per se. Since the SPO triples would be possibly extracted from hypothetical, speculative statements or even conflicting and contradictory assertions, the knowledge status (i.e., the uncertainty), which serves as an integral and critical part of scientific knowledge has been largely overlooked. This article aims to put forward a framework for Medical Knowmetrics using the SPO triples as the knowledge unit and the uncertainty as the knowledge context. The lung cancer publications dataset is used to validate the proposed framework. The uncertainty of medical knowledge and how its status evolves over time indirectly reflect the strength of competing knowledge claims, and the probability of certainty for a given SPO triple. We try to discuss the new insights using the uncertainty-centric approaches to detect research fronts, and identify knowledge claims with high certainty level, in order to improve the efficacy of knowledge-driven decision support.

Jian Du, Zhigang Hua, Shuang Yang

We examine the \emph{submodular maximum coverage problem} (SMCP), which is related to a wide range of applications. We provide the first variational approximation for this problem based on the Nemhauser divergence, and show that it can be solved efficiently using variational optimization. The algorithm alternates between two steps: (1) an E step that estimates a variational parameter to maximize a parameterized \emph{modular} lower bound; and (2) an M step that updates the solution by solving the local approximate problem. We provide theoretical analysis on the performance of the proposed approach and its curvature-dependent approximate factor, and empirically evaluate it on a number of public data sets and several application tasks.