The growing adoption of machine learning models for biological sequences has intensified the need for interpretable predictions, with Shapley values emerging as a theoretically grounded standard for model explanation. While effective for local explanations of individual input sequences, scaling Shapley-based interpretability to extract global biological insights requires evaluating thousands of sequences--incurring exponential computational cost per query. We introduce SHAP zero, a novel algorithm that amortizes the cost of Shapley value computation across large-scale biological datasets. After a one-time model sketching step, SHAP zero enables near-zero marginal cost for future queries by uncovering an underexplored connection between Shapley values, high-order feature interactions, and the sparse Fourier transform of the model. Applied to models of guide RNA efficacy, DNA repair outcomes, and protein fitness, SHAP zero explains predictions orders of magnitude faster than existing methods, recovering rich combinatorial interactions previously inaccessible at scale. This work opens the door to principled, efficient, and scalable interpretability for black-box sequence models in biology.

SHAP (SHapley Additive exPlanations) values are a widely used method for local feature attribution in interpretable and explainable AI. We propose an efficient two-stage algorithm for computing SHAP values in both black-box setting and tree-based models. We assume the black-box predictor or tree model accepts binary (zero-one) features.

SHAP (SHapley Additive exPlanations) values are a widely used method for local feature attribution in interpretable and explainable AI. We propose an efficient two-stage algorithm for computing SHAP values in both black-box setting and tree-based models.

Explainable Artificial Intelligence (XAI) has become an increasingly important area of research, particularly as machine learning models are deployed in high-stakes domains. Among various XAI approaches, SHAP (SHapley Additive exPlanations) has gained prominence due to its ability to provide both global and local explanations across different machine learning models. While SHAP effectively visualizes feature importance, it often lacks contextual explanations that are meaningful for end-users, especially those without technical backgrounds. To address this gap, we propose a Python package that extends SHAP by integrating it with a large language model (LLM), specifically OpenAI's GPT, to generate contextualized textual explanations. This integration is guided by user-defined parameters (such as feature aliases, descriptions, and additional background) to tailor the explanation to both the model context and the user perspective. We hypothesize that this enhancement can improve the perceived understandability of SHAP explanations. To evaluate the effectiveness of the proposed package, we applied it in a healthcare-related case study and conducted user evaluations involving real end-users. The results, based on Likert-scale surveys and follow-up interviews, indicate that the generated explanations were perceived as more understandable and contextually appropriate compared to visual-only outputs. While the findings are preliminary, they suggest that combining visualization with contextualized text may support more user-friendly and trustworthy model explanations.

In this work, we propose a simple and computationally efficient framework for evaluating whether machine learning models align with the structure of the data they learn from; that is, whether the model says what the data says. Unlike existing interpretability methods that focus exclusively on explaining model behavior, our approach establishes a baseline derived directly from the data itself. Drawing inspiration from Rubin's Potential Outcomes Framework, we quantify how strongly each feature separates the two outcome groups in a binary classification task, moving beyond traditional descriptive statistics to estimate each feature's effect on the outcome. By comparing these data-derived feature rankings with model-based explanations, we provide practitioners with an interpretable and model-agnostic method for assessing model-data alignment.

Conventional Data Processing Workflow Conventional MD analysis, which has been used in previous data evaluation [2, 32, 33] and can serve labeling and validation purposes for ML model construction and preparation, employs a multi-tiered data distillation process to derive robust trends, see Figure 1. In the left column of this figure, we show representative examples of computational tomographs through the 3D MD model, with the atoms colored by (a) grain orientation in electron backscatter diffraction (EBSD) standard, (b) lattice type, grain boundaries, and defects, (c) advection (drift) velocity to visualize shearing, and (d) local stresses. As a first step in the data distillation process, these 3D data that are stored for each atom are averaged across the lateral system dimensions, revealing depth-resolved, time-dependent quantities of interest, as visualized in the heat map at the top of the middle column (e). Further elimination of the sample depth and time dimensions leads to time-resolved global quantities (f) and contact pressure dependent trends (g), which can be fitted with characteristic pressures that mark the transition between deformation patterns (h). As an outlook to the utility of such highly distilled data, we propose their incorporation into Ashby-style charts, as schematically shown in Figure 1 (i), which link material properties with tribological properties. This conventional approach 2 accommodates the complexities of polycrystalline materials under tribological loading conditions and is guided by the underlying physics, resulting in this time-consuming procedure. Thus, substituting this approach with a well-trained ML model is highly relevant. The conventional approach can serve as the ground truth for training this ML model or to refine and validate said model based on newly generated MD data.

Improving energy efficiency in residential buildings is critical to combating climate change and reducing greenhouse gas emissions. Retrofitting existing buildings, which contribute a significant share of energy use, is therefore a key priority, especially in regions with outdated building stock. Artificial Intelligence (AI) and Machine Learning (ML) can automate retrofit decision-making and find retrofit strategies. However, their use faces challenges of data availability, model transparency, and compliance with national and EU AI regulations including the AI act, ethics guidelines and the ALTAI. This paper presents a trustworthy-by-design ML-based decision support framework that recommends energy efficiency strategies for residential buildings using minimal user-accessible inputs. The framework merges Conditional Tabular Generative Adversarial Networks (CTGAN) to augment limited and imbalanced data with a neural network-based multi-label classifier that predicts potential combinations of retrofit actions. To support explanation and trustworthiness, an Explainable AI (XAI) layer using SHapley Additive exPlanations (SHAP) clarifies the rationale behind recommendations and guides feature engineering. Two case studies validate performance and generalization: the first leveraging a well-established, large EPC dataset for England and Wales; the second using a small, imbalanced post-retrofit dataset from Latvia (RETROFIT-LAT). Results show that the framework can handle diverse data conditions and improve performance up to 53% compared to the baseline. Overall, the proposed framework provides a feasible, interpretable, and trustworthy AI system for building retrofit decision support through assured performance, usability, and transparency to aid stakeholders in prioritizing effective energy investments and support regulation-compliant, data-driven innovation in sustainable energy transition.

Trustworthy machine learning in healthcare requires strong predictive performance, fairness, and explanations. While it is known that improving fairness can affect predictive performance, little is known about how fairness improvements influence explainability, an essential ingredient for clinical trust. Clinicians may hesitate to rely on a model whose explanations shift after fairness constraints are applied. In this study, we examine how enhancing fairness through bias mitigation techniques reshapes Shapley-based feature rankings. We quantify changes in feature importance rankings after applying fairness constraints across three datasets: pediatric urinary tract infection risk, direct anticoagulant bleeding risk, and recidivism risk. We also evaluate multiple model classes on the stability of Shapley-based rankings. We find that increasing model fairness across racial subgroups can significantly alter feature importance rankings, sometimes in different ways across groups. These results highlight the need to jointly consider accuracy, fairness, and explainability in model assessment rather than in isolation.

Large Language Models (LLMs) have attracted significant attention for classification tasks, offering a flexible alternative to trusted classical machine learning models like LightGBM through zero-shot prompting. However, their reliability for structured tabular data remains unclear, particularly in high-stakes applications like financial risk assessment. Our study systematically evaluates LLMs and generates their SHAP values on financial classification tasks. Our analysis shows a divergence between LLMs self-explanation of feature impact and their SHAP values, as well as notable differences between LLMs and LightGBM SHAP values. These findings highlight the limitations of LLMs as standalone classifiers for structured financial modeling, but also instill optimism that improved explainability mechanisms coupled with few-shot prompting will make LLMs usable in risk-sensitive domains.

Accurate multivariate time-series prediction of vital signs and laboratory results is crucial for early intervention and precision medicine in intensive care units (ICUs). However, vital signs are often noisy and exhibit rapid fluctuations, while laboratory tests suffer from missing values, measurement lags, and device-specific bias, making integrative forecasting highly challenging. To address these issues, we propose OmniTFT, a deep learning framework that jointly learns and forecasts high-frequency vital signs and sparsely sampled laboratory results based on the Temporal Fusion Transformer (TFT). Specifically, OmniTFT implements four novel strategies to enhance performance: sliding window equalized sampling to balance physiological states, frequency-aware embedding shrinkage to stabilize rare-class representations, hierarchical variable selection to guide model attention toward informative feature clusters, and influence-aligned attention calibration to enhance robustness during abrupt physiological changes. By reducing the reliance on target-specific architectures and extensive feature engineering, OmniTFT enables unified modeling of multiple heterogeneous clinical targets while preserving cross-institutional generalizability. Across forecasting tasks, OmniTFT achieves substantial performance improvement for both vital signs and laboratory results on the MIMIC-III, MIMIC-IV, and eICU datasets. Its attention patterns are interpretable and consistent with known pathophysiology, underscoring its potential utility for quantitative decision support in clinical care.