# Beyond Attention: Signed Integrated Gradients Attribution in a BiomeGPT-Style Microbiome Transformer

arXiv: https://arxiv.org/abs/2608.06486 · HTML: https://mlsanity.com/paper/2608.06486/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 17 references that are in the map.
- First posted on arXiv 6 Aug 2026.

## Builds on (most cited first, 9 of 9)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Attention is not Explanation](https://mlsanity.com/paper/1902.10186/) (2019)
- [Revisiting Deep Learning Models for Tabular Data](https://mlsanity.com/paper/2106.11959/) (2021)
- [Attention is not not Explanation](https://mlsanity.com/paper/1908.04626/) (2019)
- [Captum: A unified and generic model interpretability library for PyTorch](https://mlsanity.com/paper/2009.07896/) (2020)
- [Explaining Explanations: Axiomatic Feature Interactions for Deep Networks](https://mlsanity.com/paper/2002.04138/) (2020)
- [Rethinking Attention-Model Explainability through Faithfulness Violation Test](https://mlsanity.com/paper/2201.12114/) (2022)
- [Uniform Discretized Integrated Gradients: An effective attribution based method for explaining large language models](https://mlsanity.com/paper/2412.03886/) (2024)

## Abstract (arXiv)

In a feature-tokenized transformer (arXiv:2106.11959) such as BiomeGPT (doi:10.64898/2026.01.05.697599), each input token is built by fusing a fixed identity with a sample-specific measurement: a fixed species and a variable abundance, T = S + A. To interpret downstream classification in such models, prior work inspects the attention weights of the special [CLS] token (arXiv:2106.11959, arXiv:1810.04805, BiomeGPT) to rank sample tokens by importance. These weights have two critical limitations: they are nonnegative, so they cannot separate disease-supporting from health-supporting evidence (arXiv:2201.12114), and they act after token fusion, obscuring how the input sources S and A each affect the output. To address this we use Integrated Gradients (arXiv:1703.01365), a signed, fusion-aware attribution method, and propose a source-derived baseline T' = S + A_0 for feature-tokenized models such as BiomeGPT, which preserves species identity as a fixed biological coordinate while isolating the effect of abundance variation. Applied to a disease-versus-health decision margin, it yields polarity that explicitly separates pathogenic from protective microbial signals. We show that this gradient-based approach uncovers species-abundance directional relationships and sensitivity diagnostics entirely obscured by unsigned [CLS] attention weights. We further recommend second-order Integrated Hessians (arXiv:2002.04138) to expose microbiome community interaction rules: how a perturbation in one member alters the model's sensitivity to another, and which other species drive ambiguous cases toward disease or health at a given abundance level. This provides a principled approach to explainability in BiomeGPT that generalizes to other smooth and differentiable feature-tokenized transformers. Code is available at https://github.com/nohren/token-source-attribution