The authors explore the compelling question of how to develop interpretable machine learning methods using prototypes and criticisms. The paper was well written and clear, even for a non-expert in the field like myself. The mathematical results appear to be sound. It is hard for me to assess the originality of the work in the field of machine learning, but I imagine that there is work on training with both positive and negative examples. At the very least, within the human category learning literature the issue of learning a concept through examples of the concept and non-examples has been explored.

Recent advancements in machine learning (ML) are transforming the field of structural biology. For example, AlphaFold, a groundbreaking neural network for protein structure prediction, has been widely adopted by researchers. The availability of easy-to-use interfaces and interpretable outcomes from the neural network architecture, such as the confidence scores used to color the predicted structures, have made AlphaFold accessible even to non-ML experts. In this paper, we present various methods for representing protein 3D structures from low- to high-resolution, and show how interpretable ML methods can support tasks such as predicting protein structures, protein function, and protein-protein interactions. This survey also emphasizes the significance of interpreting and visualizing ML-based inference for structure-based protein representations that enhance interpretability and knowledge discovery. Developing such interpretable approaches promises to further accelerate fields including drug development and protein design.

Manipulating the dispersive characteristics of vibrational waves is beneficial for many applications, e.g., high-precision instruments. architected hierarchical phononic materials have sparked promise tunability of elastodynamic waves and vibrations over multiple frequency ranges. In this article, hierarchical unit-cells are obtained, where features at each length scale result in a band gap within a targeted frequency range. Our novel approach, the ``hierarchical unit-cell template method,'' is an interpretable machine-learning approach that uncovers global unit-cell shape/topology patterns corresponding to predefined band-gap objectives. A scale-separation effect is observed where the coarse-scale band-gap objective is mostly unaffected by the fine-scale features despite the closeness of their length scales, thus enabling an efficient hierarchical algorithm. Moreover, the hierarchical patterns revealed are not predefined or self-similar hierarchies as common in current hierarchical phononic materials. Thus, our approach offers a flexible and efficient method for the exploration of new regions in the hierarchical design space, extracting minimal effective patterns for inverse design in applications targeting multiple frequency ranges.

In response to the COVID-19 pandemic, the integration of interpretable machine learning techniques has garnered significant attention, offering transparent and understandable insights crucial for informed clinical decision making. This literature review delves into the applications of interpretable machine learning in predicting the prognosis of respiratory diseases, particularly focusing on COVID-19 and its implications for future research and clinical practice. We reviewed various machine learning models that are not only capable of incorporating existing clinical domain knowledge but also have the learning capability to explore new information from the data. These models and experiences not only aid in managing the current crisis but also hold promise for addressing future disease outbreaks. By harnessing interpretable machine learning, healthcare systems can enhance their preparedness and response capabilities, thereby improving patient outcomes and mitigating the impact of respiratory diseases in the years to come.

The interpretability of model has become one of the obstacles to its wide application in the high-stake fields. The usual way to obtain interpretability is to build a black-box first and then explain it using the post-hoc methods. However, the explanations provided by the post-hoc method are not always reliable. Instead, we design an intrinsically interpretable model based on RRL(Rule Representation Learner) for the Lending Club dataset. Specifically, features can be divided into three categories according to their characteristics of themselves and build three sub-networks respectively, each of which is similar to a neural network with a single hidden layer but can be equivalently converted into a set of rules. During the training, we learned tricks from previous research to effectively train binary weights. Finally, our model is compared with the tree-based model. The results show that our model is much better than the interpretable decision tree in performance and close to other black-box, which is of practical significance to both financial institutions and borrowers. More importantly, our model is used to test the correctness of the explanations generated by the post-hoc method, the results show that the post-hoc method is not always reliable.

The aggravating effects of climate change and the growing population in hurricane-prone areas escalate the challenges in large-scale hurricane evacuations. While hurricane preparedness and response strategies vastly rely on the accuracy and timeliness of the predicted households' evacuation decisions, current studies featuring psychological-driven linear models leave some significant limitations in practice. Hence, the present study proposes a new methodology for predicting households' evacuation decisions constructed by easily accessible demographic and resource-related predictors compared to current models with a high reliance on psychological factors. Meanwhile, an enhanced logistic regression (ELR) model that could automatically account for nonlinearities (i.e., univariate and bivariate threshold effects) by an interpretable machine learning approach is developed to secure the accuracy of the results. Specifically, low-depth decision trees are selected for nonlinearity detection to identify the critical thresholds, build a transparent model structure, and solidify the robustness. Then, an empirical dataset collected after Hurricanes Katrina and Rita is hired to examine the practicability of the new methodology. The results indicate that the enhanced logistic regression (ELR) model has the most convincing performance in explaining the variation of the households' evacuation decision in model fit and prediction capability compared to previous linear models. It suggests that the proposed methodology could provide a new tool and framework for the emergency management authorities to improve the estimation of evacuation traffic demands in a timely and accurate manner.

Superalloys are a special class of heavy-duty materials with excellent strength retention and chemical stability at very high temperatures. Nickel-based superalloys are used commercially in aircraft turbines, power plants, and space launch vehicles. The optimization of mechanical properties of alloys has been traditionally carried out using experimental approaches, which demand massive costs in terms of time and infrastructure for testing. In this paper, we propose a method for mechanical property prediction of Ni-based superalloys by learning from past experimental results using machine learning (ML). Five highly accurate ML models are developed to predict yield strength (YS), ultimate tensile strength (UTS), creep rupture life, fatigue life with stress, and strain values. We have developed an extensive database containing mechanical properties of over 1500 Ni-based superalloys. Basic material parameters such as the composition of the alloy, annealing conditions, and testing conditions are also collected and used as features for developing the ML models. The prediction root mean squared errors for the YS, UTS, creep, and fatigue life models are 0.11, 0.06, 0.19, 0.22, which are minimal, leading to a highly accurate estimation of the target values. These ML models are highly transferable and require a minimum number of input features. In addition, feature analysis performed by SHapley Additive exPlanations (SHAP) for individual properties reveals the relative significance of each descriptor in deciding the target property. We demonstrate that a unified and highly accurate ML framework can be developed using common features for all mechanical properties. The models are developed on experimental data, making them directly applicable for industries.

The use of machine learning (ML) with metabolomics provides opportunities for the early diagnosis of disease. However, the accuracy and extent of information obtained from ML and metabolomics can be limited owing to challenges associated with interpreting disease prediction models and analysing many chemical features with abundances that are correlated and'noisy'. Here, we report an interpretable neural network (NN) framework to accurately predict disease and identify significant biomarkers using whole metabolomics datasets without feature selection. The performance of the NN approach for predicting Parkinson's disease (PD) from blood plasma metabolomics data was significantly higher than classical ML methods with a mean area under the curve of 0.995. PD-specific markers that contribute significantly to early disease prediction were identified including an exogenous polyfluoroalkyl substance. It is anticipated that this accurate and interpretable NN-based approach can improve diagnostic performance for many other diseases using metabolomics and other untargeted'omics methods.

Interpretability provides a means for humans to verify aspects of machine learning (ML) models and empower human+ML teaming in situations where the task cannot be fully automated. Different contexts require explanations with different properties. For example, the kind of explanation required to determine if an early cardiac arrest warning system is ready to be integrated into a care setting is very different from the type of explanation required for a loan applicant to help determine the actions they might need to take to make their application successful. Unfortunately, there is a lack of standardization when it comes to properties of explanations: different papers may use the same term to mean different quantities, and different terms to mean the same quantity. This lack of a standardized terminology and categorization of the properties of ML explanations prevents us from both rigorously comparing interpretable machine learning methods and identifying what properties are needed in what contexts. In this work, we survey properties defined in interpretable machine learning papers, synthesize them based on what they actually measure, and describe the trade-offs between different formulations of these properties. In doing so, we enable more informed selection of task-appropriate formulations of explanation properties as well as standardization for future work in interpretable machine learning.

Interpretable machine learning has been focusing on explaining final models that optimize performance. The current state-of-the-art is the Shapley additive explanations (SHAP) that locally explains variable impact on individual predictions, and it is recently extended for a global assessment across the dataset. Recently, Dong and Rudin proposed to extend the investigation to models from the same class as the final model that are "good enough", and identified a previous overclaim of variable importance based on a single model. However, this method does not directly integrate with existing Shapley-based interpretations. We close this gap by proposing a Shapley variable importance cloud that pools information across good models to avoid biased assessments in SHAP analyses of final models, and communicate the findings via novel visualizations.