Small Code Refactor (#73)

* update amplify model

* update Cargo

Cargo.toml

@@ -10,7 +10,7 @@ members = [
     "ferritin-molviewspec",
     "ferritin-pymol",
     "ferritin-test-data",
-    "ferritin-wasm-examples/*",
+    "ferritin-wasm-examples/amplify",
 ]
 resolver = "2"
 

ferritin-amplify/src/amplify/amplify.rs

@@ -12,6 +12,7 @@
 use super::config::AMPLIFYConfig;
 use super::encoder::EncoderBlock;
 use super::rotary::precompute_freqs_cis;
+use super::outputs::ModelOutput;
 use candle_core::{Device, Module, Result, Tensor, D};
 use candle_nn::{embedding, linear, rms_norm, Embedding, Linear, RmsNorm, VarBuilder};
 use tokenizers::Tokenizer;
@@ -133,66 +134,3 @@ impl AMPLIFY {
             .map_err(|e| candle_core::Error::Msg(format!("Failed to load tokenizer: {}", e)))
     }
 }
-
-// Helper structs and enums
-#[derive(Debug)]
-/// Amplify Model Output
-///
-/// logits, hidden states, and attentions.
-///
-///  logits -> distribution of the sequences.
-///  attentions -> contact map
-pub struct ModelOutput {
-    pub logits: Tensor,
-    pub hidden_states: Option<Vec<Tensor>>,
-    pub attentions: Option<Vec<Tensor>>,
-}
-
-impl ModelOutput {
-    /// "Perform average product correct, used for contact prediction."
-    /// https://github.com/chandar-lab/AMPLIFY/blob/rc-0.1/examples/utils.py#L83
-    /// "Perform average product correct, used for contact prediction."
-    fn apc(&self, x: &Tensor) -> Result<Tensor> {
-        let a1 = x.sum_keepdim(D::Minus1)?;
-        let a2 = x.sum_keepdim(D::Minus2)?;
-        let a12 = x.sum_keepdim((D::Minus1, D::Minus2))?;
-        let avg = a1.matmul(&a2)?;
-        // Divide by a12 (equivalent to pytorch's div_)
-        // println!("IN the APC: avg, a12 {:?}, {:?}", avg, a12);
-        // let avg = avg.div(&a12)?;
-        let a12_broadcast = a12.broadcast_as(avg.shape())?;
-        let avg = avg.div(&a12_broadcast)?;
-        x.sub(&avg)
-    }
-    // From https://github.com/facebookresearch/esm/blob/main/esm/modules.py
-    // https://github.com/chandar-lab/AMPLIFY/blob/rc-0.1/examples/utils.py#L77
-    // "Make layer symmetric in final two dimensions, used for contact prediction."
-    fn symmetrize(&self, x: &Tensor) -> Result<Tensor> {
-        let x_transpose = x.transpose(D::Minus1, D::Minus2)?;
-        x.add(&x_transpose)
-    }
-    /// Contact maps can be obtained from the self-attentions
-    pub fn get_contact_map(&self) -> Result<Option<Tensor>> {
-        let Some(attentions) = &self.attentions else {
-            return Ok(None);
-        };
-        // we need the dimensions to reshape below.
-        // the attention blocks have the following shape
-        let (_1, _n_head, _seq_length, seq_length) = attentions.first().unwrap().dims4()?;
-        let last_dim = seq_length;
-        let attn_stacked = Tensor::stack(attentions, 0)?;
-        let total_elements = attn_stacked.dims().iter().product::<usize>();
-        let first_dim = total_elements / (last_dim * last_dim);
-        let attn_map_combined2 = attn_stacked.reshape(&[first_dim, last_dim, last_dim])?;
-
-        // In PyTorch: attn_map = attn_map[:, 1:-1, 1:-1]
-        let attn_map_combined2 = attn_map_combined2
-            .narrow(1, 1, attn_map_combined2.dim(1)? - 2)? // second dim
-            .narrow(2, 1, attn_map_combined2.dim(2)? - 2)?; // third dim
-        let symmetric = self.symmetrize(&attn_map_combined2)?;
-        let normalized = self.apc(&symmetric)?;
-        let proximity_map = normalized.permute((1, 2, 0))?; //  # (residues, residues, map)
-
-        Ok(Some(proximity_map))
-    }
-}

ferritin-amplify/src/amplify/mod.rs

@@ -9,5 +9,6 @@
 pub mod amplify;
 pub mod config;
 pub mod encoder;
+pub mod outputs;
 pub mod rotary;
 // pub mod loss;

ferritin-amplify/src/amplify/outputs.rs

@@ -0,0 +1,64 @@
+use candle_core::{Result, Tensor, D};
+
+// Helper structs and enums
+#[derive(Debug)]
+/// Amplify Model Output
+///
+/// logits, hidden states, and attentions.
+///
+///  logits -> distribution of the sequences.
+///  attentions -> contact map
+pub struct ModelOutput {
+    pub logits: Tensor,
+    pub hidden_states: Option<Vec<Tensor>>,
+    pub attentions: Option<Vec<Tensor>>,
+}
+
+impl ModelOutput {
+    /// "Perform average product correct, used for contact prediction."
+    /// https://github.com/chandar-lab/AMPLIFY/blob/rc-0.1/examples/utils.py#L83
+    /// "Perform average product correct, used for contact prediction."
+    fn apc(&self, x: &Tensor) -> Result<Tensor> {
+        let a1 = x.sum_keepdim(D::Minus1)?;
+        let a2 = x.sum_keepdim(D::Minus2)?;
+        let a12 = x.sum_keepdim((D::Minus1, D::Minus2))?;
+        let avg = a1.matmul(&a2)?;
+        // Divide by a12 (equivalent to pytorch's div_)
+        // println!("IN the APC: avg, a12 {:?}, {:?}", avg, a12);
+        // let avg = avg.div(&a12)?;
+        let a12_broadcast = a12.broadcast_as(avg.shape())?;
+        let avg = avg.div(&a12_broadcast)?;
+        x.sub(&avg)
+    }
+    // From https://github.com/facebookresearch/esm/blob/main/esm/modules.py
+    // https://github.com/chandar-lab/AMPLIFY/blob/rc-0.1/examples/utils.py#L77
+    // "Make layer symmetric in final two dimensions, used for contact prediction."
+    fn symmetrize(&self, x: &Tensor) -> Result<Tensor> {
+        let x_transpose = x.transpose(D::Minus1, D::Minus2)?;
+        x.add(&x_transpose)
+    }
+    /// Contact maps can be obtained from the self-attentions
+    pub fn get_contact_map(&self) -> Result<Option<Tensor>> {
+        let Some(attentions) = &self.attentions else {
+            return Ok(None);
+        };
+        // we need the dimensions to reshape below.
+        // the attention blocks have the following shape
+        let (_1, _n_head, _seq_length, seq_length) = attentions.first().unwrap().dims4()?;
+        let last_dim = seq_length;
+        let attn_stacked = Tensor::stack(attentions, 0)?;
+        let total_elements = attn_stacked.dims().iter().product::<usize>();
+        let first_dim = total_elements / (last_dim * last_dim);
+        let attn_map_combined2 = attn_stacked.reshape(&[first_dim, last_dim, last_dim])?;
+
+        // In PyTorch: attn_map = attn_map[:, 1:-1, 1:-1]
+        let attn_map_combined2 = attn_map_combined2
+            .narrow(1, 1, attn_map_combined2.dim(1)? - 2)? // second dim
+            .narrow(2, 1, attn_map_combined2.dim(2)? - 2)?; // third dim
+        let symmetric = self.symmetrize(&attn_map_combined2)?;
+        let normalized = self.apc(&symmetric)?;
+        let proximity_map = normalized.permute((1, 2, 0))?; //  # (residues, residues, map)
+
+        Ok(Some(proximity_map))
+    }
+}