Naive implementation of gradient flow (in refactored code)

[stefan-apollo]

Description: Naive implementation of the gradient flow method, based on looping rib_build a few times. Approximately slows down the code by num_node_layers/2.

Tested: Did comparison plots below. They look much closer to NNIB than expected (from #141 plots) but we can't see anything broken. Also implemented tests

• to just run naive gradient flow on mod add, MNIST, and Pythia making and running the usual checks
• to test in Pythia that last two layers are same as NNIB, and 3rd-last layer is different.

No breaking changes. Doesn't work on MLP because our MLP implementation requires the node_layers to be a strict sub-sequence of model layers, which cannot be done in naive gradient flow. Added validation for this.

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Mod add example:

With naive gradient flow: With nearest neighbour:

[stefan-apollo]

Graphs look very similar (bug?) and ablation curve look sus compared to old ones

[stefan-apollo]

The code is definitely running the gradient-flow fashion, always computing [current_node_layer, final_node_layer]. Thus there cannot be any nearest neighbour computation going on. I'd rule out simple bugs.

[stefan-apollo]

Hmm ablation curves look sus as well, and unlike those in #141

[stefan-apollo]

Still happens even if I use the old (1-alpha)^2 basis

[stefan-apollo]

Lambdas do seem to shift differently between normal and NGF though

[stefan-apollo]

Cosine similarity of bases:

[stefan-apollo]

Run with lots of neighbouring node layers:

[stefan-apollo]

I've cleaned up the code a bit and removed all the lies. Changes since review:

• Create a temp dir if running NGF (naive gradient flow) without out_dir
• Add check_outfile_overwrite logic to _get_out_file_path and use the new function in NGF
• Don't lie about config.naive_gradient_flow = True even if config.interaction_matrices_path is not None
• Rather than setting results.config from results.config set it from config (requires less changes) results.config = replace_pydantic_model(config, {"calculate_edges": False})
• Don't lie if config.calculate_edges, run rib_build without save file and then add edges to existing results and save manually