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| title: PanGramGraph | |
| emoji: 🧬 | |
| colorFrom: purple | |
| colorTo: yellow | |
| sdk: docker | |
| app_port: 7860 | |
| pinned: false | |
| short_description: E. coli pangenome graph read by a genomic LM | |
| # PanGramGraph | |
| The pangenome graph of *Escherichia coli* read with the grammar of gene order that a genomic | |
| language model learned. Every genome of PanGBank's pangenome 11587 (2,002 genomes) is walked | |
| gene by gene from `dnaA`; the graph shows what the genomes carry, and Bacformer, a causal | |
| genomic language model, what it expects next. Read in its own vocabulary it names the next | |
| gene 88.8 % of the time, and it hesitates where the pangenome is plastic. | |
| The page has five tabs: | |
| - **Graph**: the pangenome graph with the model's calls, from `dnaA` or anywhere along the | |
| chromosome. Hover a family for its card, click to pin it and have the model's exact call | |
| computed in any of the 2,002 genomes, with links to the genomes' pages on PanGBank. Draw | |
| paths through the graph to ask the model about any order of genes, including orders no | |
| genome carries. Move along the chromosome with the map of the 540 complete chromosomes, | |
| Previous and Next, or a search for any gene name. | |
| - **Attention**: the model's 96 heads and its attention matrix while it reads a path. | |
| - **Coupled regions**: accessory regions whose presence goes together within lineages, at | |
| long range (533 links) and close range (113 links), with the model's verdict on each link | |
| from in-silico knockouts. The model knows none of the long-range couplings, and the one | |
| close-range link it knows is explained by genomic background. Click an element to have it | |
| deleted live and see how far the model's expectations move downstream. | |
| - **Findings**: what the model gets right and where it doubts, for the window shown, with a | |
| reading of the window written by DeepSeek-V4.1-Flash from facts the server computes, every | |
| sentence checked against the facts it cites. | |
| - **About**: the data, the model, their credit, and how each part was computed. | |
| This Space runs the page and its model's server on a CPU (2 vCPU). Bacformer has 50.85 | |
| million parameters and the ESM-2 protein embeddings are precomputed: a drawn path is | |
| answered in about 0.1 s, a genome's call in 1 to 2 s, a window elsewhere on the chromosome in | |
| 1 to 3 s, and an element deleted and the model read again, against 8 control deletions, in | |
| under a minute. A reading written before comes back at once, a new one in 10 to 30 s, within | |
| daily limits. The Space sleeps after 48 hours without visits and takes a minute or two to | |
| wake up; several visitors at once wait their turn. | |
| **Code:** https://github.com/ggautreau/PanGramGraph | |
| **Data and model.** Genomes, gene families, partitions and regions of plasticity from | |
| PanGBank (pangenome 11587, GTDB_refseq v2.0.0, GTDB R232), built with PPanGGOLiN | |
| (Gautreau *et al.* 2020, PLOS Computational Biology 16(3):e1007732) and panRGP (Bazin *et | |
| al.* 2020, Bioinformatics 36(Suppl_2):i651); PanGBank data are CC BY-SA 4.0. Model: | |
| Bacformer (Wiatrak *et al.*, bioRxiv 2025.07.20.665723), `macwiatrak/bacformer-causal-complete-genomes`, | |
| Apache-2.0, on ESM-2 embeddings (Lin *et al.* 2023, Science 379:1123). Readings of the | |
| Findings tab by DeepSeek-V4.1-Flash through Hugging Face Inference Providers. | |