Interpretability is central for scientific machine learning, as understanding why models make predictions enables hypothesis generation and validation. While tabular foundation models show strong performance, existing explanation methods like SHAP are computationally expensive, limiting interactive exploration. We introduce ShapPFN, a foundation model that integrates Shapley value regression directly into its architecture, producing both predictions and explanations in a single forward pass. On standard benchmarks, ShapPFN achieves competitive performance while producing high-fidelity explanations (R2=0.96, cosine=0.99) over 1000\times faster than KernelSHAP (0.06s vs 610s). Our code is available at https://github.com/kunumi/ShapPFN
Figures & tables
Figure 1: ShapPFN architecture. The model encodes features and targets into embeddings, processes them through transformer layers with alternating attention over features and datapoints, then decodes into a global baseline and per-feature contributions. The final prediction is explicitly additive over features, enabling SHAP-like decomposition directly from the architecture.
Appendix figures & tables1 asset
Supplementary material from the paper’s appendix.
Appendix
Parameter Optimized
Loss Wt.
Warmup Steps
Num Subsets
Bkg Samples
SHAP Cos
ROC AUC
SHAP Loss Weight
1
2000
4
4
0.979
0.829
2
2000
4
4
0.977
0.826
10
2000
4
4
0.979
0.798
50
2000
4
4
0.890
0.777
Warmup Steps
1
0
4
4
0.977
0.830
1
400
4
4
0.979
0.828
Appendix
Table 3: Sequential hyperparameter optimization. Each block optimizes one parameter (highlighted in gray) while keeping others fixed. Best ROC AUC in each block shown in bold.
Neural network interpretability studies how models represent information and make predictions, and how to explain, test, or control their internal computations.
Existing post-hoc explainers for machine learning classifiers primarily focus on feature attribution, assigning importance scores to individual features. While valuable, this approach struggles to articulate the complex, combinatorial patterns that often drive a model's decision-making process. To overcome this limitation, we introduce ProToMEx, a new paradigm for explainability that leverages Probabilistic Topic Models (PTMs). Our model-agnostic framework learns latent ''topics'' that represent distinct, high-level reasons for a classification, moving beyond simple feature importance to reveal underlying semantic structures. ProToMEx naturally provides both global explanations of a model's overall behaviour and local explanations that can disentangle multiple co-existing reasons for a specific prediction. We demonstrate empirically that ProToMEx not only produces explanations of comparable fidelity to popular methods like SHAP and LIME but also drastically reduces the amortised computational cost of generating local explanations, making it highly suitable for real-time applications. Specifically, we show that ProToMEx is ~30-40x faster than SHAP and LIME over standardised tabular datasets and synthetic datasets.
Athina Georgara, Adarsh Valoor, Sarvapali D. Ramchurn
Large Language Models (LLMs) fine-tuned on serialized tabular data are emerging as powerful alternatives to traditional tree-based models, particularly for heterogeneous or context-rich datasets. However, their deployment in high-stakes domains is hindered by a lack of faithful interpretability; existing methods often rely on global linear proxies or scalar probability shifts that fail to capture the model's full probabilistic uncertainty. In this work, we introduce TabSHAP, a model-agnostic interpretability framework designed to directly attribute local query decision logic in LLM-based tabular classifiers. By adapting a Shapley-style sampled-coalition estimator with Jensen-Shannon divergence between full-input and masked-input class distributions, TabSHAP quantifies the distributional impact of each feature rather than simple prediction flips. To align with tabular semantics, we mask at the level of serialized key:value fields (atomic in the prompt string), not individual subword tokens. Experimental validation on the Adult Income and Heart Disease benchmarks demonstrates that TabSHAP isolates critical diagnostic features, achieving significantly higher faithfulness than random baselines and XGBoost proxies. We further run a distance-metric ablation on the same test instances and TabSHAP settings: attributions are recomputed with KL or L1 replacing JSD in the similarity step (results cached per metric), and we compare deletion faithfulness across all three.
Aryan Chaudhary, Prateek Agarwal, Tejasvi Alladi
Department of Computer Science Birla Institute of Technology and Science India
We introduce TabPFN-3.5, our new flagship Tabular Foundation Model. It significantly outperforms its predecessor, TabPFN-3, and all existing baselines across a broad range of tabular problems. TabPFN-3.5 sets a new state of the art on standard tabular prediction in TabArena, and extends it to the data practitioners encounter in practice: non-i.i.d. data with temporal or grouped splits, tables with strings, text and images, high-cardinality categorical features, and wide tables with many features. These gains carry over to our task-specific harnesses: state of the art on relational data and stronger time-series forecasting. For faster inference, our variant TabPFN-3.5-Fast runs up to 3x faster than TabPFN-3 while keeping most of the accuracy gains. In addition, we upgrade TabPFN-3.5-Plus, expanding our multimodal capabilities with advanced text and date handling alongside proprietary inference optimizations. Finally, we release a new version of our Thinking mode, TabPFN-3.5-Thinking, which scales inference-time computation to push the state of the art further. It benefits from our stronger base model and from inference-time improvements that make it up to 12x faster than TabPFN-3-Thinking.