rust/fused-plan7: Rust port of the fused Plan7+transducer kernel

rust/fused-plan7/.gitignore

@@ -0,0 +1 @@
+/target

rust/fused-plan7/Cargo.toml

@@ -0,0 +1,18 @@
+[package]
+name = "fused_plan7"
+version = "0.1.0"
+edition = "2021"
+description = "Fused Plan7 + transducer Forward/Viterbi kernel (Rust port of Machine Boss js/webgpu/cpu/fused-plan7.mjs). Native + wasm32."
+license = "MIT"
+
+[lib]
+name = "fused_plan7"
+path = "src/lib.rs"
+
+[dependencies]
+# serde_json + std only; the hot-path DP touches neither (wasm-safe).
+serde_json = "1"
+
+[profile.release]
+opt-level = 3
+lto = true

rust/fused-plan7/examples/score.rs

@@ -0,0 +1,68 @@
+//! Score one output sequence against a fused Plan7 + transducer model.
+//!
+//! Usage:
+//!   cargo run --release --example score -- \
+//!       <profile.hmm> <transducer.json> <params.json|-> <SEQ> [multihit] [L]
+//!
+//! `params.json` may be `-` for no params (empty map). Prints two lines:
+//!   FORWARD <value>
+//!   VITERBI <value>
+//!
+//! Used by the cross-implementation check against the JS CPU reference.
+
+use std::collections::HashMap;
+use std::process::exit;
+
+use fused_plan7::{
+    build_fused_plan7, fused_plan7_forward, fused_plan7_viterbi, parse_hmmer, prepare_machine,
+    tokenize, FusedOpts, Semiring,
+};
+
+fn die(msg: String) -> ! {
+    eprintln!("error: {msg}");
+    exit(1);
+}
+
+fn main() {
+    let args: Vec<String> = std::env::args().collect();
+    if args.len() < 5 {
+        die(format!(
+            "usage: {} <profile.hmm> <transducer.json> <params.json|-> <SEQ> [multihit] [L]",
+            args[0]
+        ));
+    }
+    let hmm_path = &args[1];
+    let td_path = &args[2];
+    let params_path = &args[3];
+    let seq = &args[4];
+    let multihit = args.get(5).map(|s| s == "true" || s == "1").unwrap_or(false);
+    let l: f64 = args.get(6).and_then(|s| s.parse().ok()).unwrap_or(400.0);
+
+    let hmm_text = std::fs::read_to_string(hmm_path).unwrap_or_else(|e| die(e.to_string()));
+    let model = parse_hmmer(&hmm_text).unwrap_or_else(|e| die(e));
+
+    let td_text = std::fs::read_to_string(td_path).unwrap_or_else(|e| die(e.to_string()));
+    let machine_json: serde_json::Value =
+        serde_json::from_str(&td_text).unwrap_or_else(|e| die(e.to_string()));
+
+    let params: HashMap<String, f64> = if params_path == "-" {
+        HashMap::new()
+    } else {
+        let pt = std::fs::read_to_string(params_path).unwrap_or_else(|e| die(e.to_string()));
+        serde_json::from_str(&pt).unwrap_or_else(|e| die(e.to_string()))
+    };
+
+    let transducer = prepare_machine(&machine_json, &params).unwrap_or_else(|e| die(e));
+    let fm = build_fused_plan7(&model, &transducer, FusedOpts { multihit, l });
+
+    let tokens = if seq == "-" || seq.is_empty() {
+        Vec::new()
+    } else {
+        tokenize(seq, &transducer.output_alphabet).unwrap_or_else(|e| die(e))
+    };
+
+    let fwd = fused_plan7_forward(&fm, &tokens, Semiring::LogSumExp);
+    let vit = fused_plan7_viterbi(&fm, &tokens);
+    println!("FORWARD {:.15}", fwd);
+    println!("VITERBI {:.15}", vit);
+}