Oceania
A Unified Framework for Inference with General Missingness Patterns and Machine Learning Imputation
Chen, Xingran, McCormick, Tyler, Mukherjee, Bhramar, Wu, Zhenke
Pre-trained machine learning (ML) predictions have been increasingly used to complement incomplete data to enable downstream scientific inquiries, but their naive integration risks biased inferences. Recently, multiple methods have been developed to provide valid inference with ML imputations regardless of prediction quality and to enhance efficiency relative to complete-case analyses. However, existing approaches are often limited to missing outcomes under a missing-completely-at-random (MCAR) assumption, failing to handle general missingness patterns under the more realistic missing-at-random (MAR) assumption. This paper develops a novel method which delivers valid statistical inference framework for general Z-estimation problems using ML imputations under the MAR assumption and for general missingness patterns. The core technical idea is to stratify observations by distinct missingness patterns and construct an estimator by appropriately weighting and aggregating pattern-specific information through a masking-and-imputation procedure on the complete cases. We provide theoretical guarantees of asymptotic normality of the proposed estimator and efficiency dominance over weighted complete-case analyses. Practically, the method affords simple implementations by leveraging existing weighted complete-case analysis software. Extensive simulations are carried out to validate theoretical results. The paper concludes with a brief discussion on practical implications, limitations, and potential future directions.
Classification errors distort findings in automated speech processing: examples and solutions from child-development research
Gautheron, Lucas, Kidd, Evan, Malko, Anton, Lavechin, Marvin, Cristia, Alejandrina
With the advent of wearable recorders, scientists are increasingly turning to automated methods of analysis of audio and video data in order to measure children's experience, behavior, and outcomes, with a sizable literature employing long-form audio-recordings to study language acquisition. While numerous articles report on the accuracy and reliability of the most popular automated classifiers, less has been written on the downstream effects of classification errors on measurements and statistical inferences (e.g., the estimate of correlations and effect sizes in regressions). This paper proposes a Bayesian approach to study the effects of algorithmic errors on key scientific questions, including the effect of siblings on children's language experience and the association between children's production and their input. In both the most commonly used \gls{lena}, and an open-source alternative (the Voice Type Classifier from the ACLEW system), we find that classification errors can significantly distort estimates. For instance, automated annotations underestimated the negative effect of siblings on adult input by 20--80\%, potentially placing it below statistical significance thresholds. We further show that a Bayesian calibration approach for recovering unbiased estimates of effect sizes can be effective and insightful, but does not provide a fool-proof solution. Both the issue reported and our solution may apply to any classifier involving event detection and classification with non-zero error rates.
A Robust BERT-Based Deep Learning Model for Automated Cancer Type Extraction from Unstructured Pathology Reports
Tran, Minh, Chan, Jeffery C., Huang, Min Li, Kansara, Maya, Grady, John P., Napier, Christine E., Thavaneswaran, Subotheni, Ballinger, Mandy L., Thomas, David M., Lin, Frank P.
The accurate extraction of clinical information from electronic medical records is particularly critical to clinical research but require much trained expertise and manual labor. In this study we developed a robust system for automated extraction of the specific cancer types for the purpose of supporting precision oncology research. from pathology reports using a fine-tuned RoBERTa model. This model significantly outperformed the baseline model and a Large Language Model, Mistral 7B, achieving F1_Bertscore 0.98 and overall exact match of 80.61%. This fine-tuning approach demonstrates the potential for scalability that can integrate seamlessly into the molecular tumour board process. Fine-tuning domain-specific models for precision tasks in oncology, may pave the way for more efficient and accurate clinical information extraction.
ITL-LIME: Instance-Based Transfer Learning for Enhancing Local Explanations in Low-Resource Data Settings
Raza, Rehan, Wang, Guanjin, Wong, Kok Wai, Laga, Hamid, Fisichella, Marco
Explainable Artificial Intelligence (XAI) methods, such as Local Interpretable Model-Agnostic Explanations (LIME), have advanced the interpretability of black-box machine learning models by approximating their behavior locally using interpretable surrogate models. However, LIME's inherent randomness in perturbation and sampling can lead to locality and instability issues, especially in scenarios with limited training data. In such cases, data scarcity can result in the generation of unrealistic variations and samples that deviate from the true data manifold. Consequently, the surrogate model may fail to accurately approximate the complex decision boundary of the original model. To address these challenges, we propose a novel Instance-based Transfer Learning LIME framework (ITL-LIME) that enhances explanation fidelity and stability in data-constrained environments. ITL-LIME introduces instance transfer learning into the LIME framework by leveraging relevant real instances from a related source domain to aid the explanation process in the target domain. Specifically, we employ clustering to partition the source domain into clusters with representative prototypes. Instead of generating random perturbations, our method retrieves pertinent real source instances from the source cluster whose prototype is most similar to the target instance. These are then combined with the target instance's neighboring real instances. To define a compact locality, we further construct a contrastive learning-based encoder as a weighting mechanism to assign weights to the instances from the combined set based on their proximity to the target instance. Finally, these weighted source and target instances are used to train the surrogate model for explanation purposes.
RadReason: Radiology Report Evaluation Metric with Reasons and Sub-Scores
Li, Yingshu, Liu, Yunyi, Liu, Lingqiao, Wang, Lei, Zhou, Luping
Evaluating automatically generated radiology reports remains a fundamental challenge due to the lack of clinically grounded, interpretable, and fine-grained metrics. Existing methods either produce coarse overall scores or rely on opaque black-box models, limiting their usefulness in real-world clinical workflows. We introduce RadReason, a novel evaluation framework for radiology reports that not only outputs fine-grained sub-scores across six clinically defined error types, but also produces human-readable justifications that explain the rationale behind each score. Our method builds on Group Relative Policy Optimization and incorporates two key innovations: (1) Sub-score Dynamic Weighting, which adaptively prioritizes clinically challenging error types based on live F1 statistics; and (2) Majority-Guided Advantage Scaling, which adjusts policy gradient updates based on prompt difficulty derived from sub-score agreement. Together, these components enable more stable optimization and better alignment with expert clinical judgment. Experiments on the ReXVal benchmark show that RadReason surpasses all prior offline metrics and achieves parity with GPT-4-based evaluations, while remaining explainable, cost-efficient, and suitable for clinical deployment. Code will be released upon publication.
A Solvable Molecular Switch Model for Stable Temporal Information Processing
This paper studies an input-driven one-state differential equation model initially developed for an experimentally demonstrated dynamic molecular switch that switches like synapses in the brain do. The linear-in-the-state and nonlinear-in-the-input model is exactly solvable, and it is shown that it also possesses mathematical properties of convergence and fading memory that enable stable processing of time-varying inputs by nonlinear dynamical systems. Thus, the model exhibits the co-existence of biologically-inspired behavior and desirable mathematical properties for stable learning on sequential data. The results give theoretical support for the use of the dynamic molecular switches as computational units in deep cascaded/layered feedforward and recurrent architectures as well as other more general structures for neuromorphic computing. They could also inspire more general exactly solvable models that can be fitted to emulate arbitrary physical devices which can mimic brain-inspired behaviour and perform stable computation on input signals.