update HNSW to use scale_modification

Add scale_modification in HNSW to have HubNSW

src/bin/annembed.rs

@@ -7,25 +7,22 @@
 //!
 //! hnsw is an optional subcommand to change default parameters of the Hnsw structure. See [hnsw_rs](https://crates.io/crates/hnsw_rs).  
 //!
-//! - Parameters for embedding.  
-//!  The options are optional and give access to some fields of the [EmbedderParams] structure.  
-//!
-//!     --batch    : optional, a integer giving the number of batch to run. Default to 15.  
-//!     --stepg    : optional, a float value , initial gradient step, default is 2.  
-//!     --scale    : optional, a float value, scale modification factor, default is 1.  
-//!     --nbsample : optional, a number of edge sampling , default is 10   
-//!     --layer    : optional, in case of hierarchical embedding num of the lower layer we consider to run preliminary step.
-//!               default is set to 0 meaning one pass embedding.  
-//!     --dim      : optional, dimension of the embedding , default to 2.  
-//!
-//!     --quality  : optional, asks for quality estimation.  
-//!     --sampling : optional, for large data defines the fraction of sampled data as 1./sampling
+//! - Parameters for embedding part are all optional The options give access to some fields of the [EmbedderParams] structure.  
+//!  --batch    : optional, a integer giving the number of batch to run. Default to 15.
+//!  --stepg    : optional, a float value , initial gradient step, default is 2.  
+//!  --scale    : optional, a float value, scale modification factor, default is 1.  
+//!  --nbsample : optional, a number of edge sampling , default is 10   
+//!  --layer    : optional, in case of hierarchical embedding num of the lower layer we consider to run preliminary step.
+//!               default is set to 0 meaning one pass embedding
+//!  --dim      : optional, dimension of the embedding , default to 2.  
+//!  --quality  : optional, asks for quality estimation
+//!  --sampling : optional, for large data defines the fraction of sampled data as 1./sampling
 //!
 //! - Parameters for the hnsw subcommand. For more details see [hnsw_rs](https://crates.io/crates/hnsw_rs).   
-//!     --nbconn  : defines the number of connections by node in a layer.   Can range from 4 to 64 or more if necessary and enough memory.  
-//!     --dist    : name of distance to use: "DistL1", "DistL2", "DistCosine", "DistJeyffreys".  
-//!     --ef      : controls the with of the search, a good guess is between 24 and 64 or more if necessary.  
-//!     --knbn    : the number of nodes to use in retrieval requests.  
+//! --nbconn  : defines the number of connections by node in a layer.   Can range from 4 to 64 or more if necessary and enough memory
+//! --dist    : name of distance to use: "DistL1", "DistL2", "DistCosine", "DistJeyffreys"
+//! --ef      : controls the with of the search, a good guess is between 24 and 64 or more if necessay
+//! --knbn    : the number of nodes to use in retrieval requests.  
 //!     
 //! The csv file must have one record by vector to embed. The default delimiter is ','.  
 //! The output is a csv file with embedded vectors.  
@@ -55,25 +52,29 @@ pub struct HnswParams {
     knbn: usize,
     /// distance to use in Hnsw. Default is "DistL2". Other choices are "DistL1", "DistCosine", DistJeffreys
     distance: String,
+    //scale_modification factor, must be [0.2, 1]
+    scale_modification : f64,
 } // end of struct HnswParams
 
 impl HnswParams {
-    pub fn my_default() -> Self {
+    pub fn default() -> Self {
         HnswParams {
             max_conn: 48,
             ef_c: 400,
             knbn: 10,
             distance: String::from("DistL2"),
+            scale_modification: 1.0,
         }
     }
 
     #[allow(unused)]
-    pub fn new(max_conn: usize, ef_c: usize, knbn: usize, distance: String) -> Self {
+    pub fn new(max_conn: usize, ef_c: usize, knbn: usize, distance: String, scale_modification: f64) -> Self {
         HnswParams {
             max_conn,
             ef_c,
             knbn,
             distance,
+            scale_modification,
         }
     }
 } // end impl block
@@ -98,10 +99,11 @@ impl Default for QualityParams {
 fn parse_hnsw_cmd(matches: &ArgMatches) -> Result<HnswParams, anyhow::Error> {
     log::debug!("in parse_hnsw_cmd");
 
-    let mut hnswparams = HnswParams::my_default();
+    let mut hnswparams = HnswParams::default();
     hnswparams.max_conn = *matches.get_one::<usize>("nbconn").unwrap();
     hnswparams.ef_c = *matches.get_one::<usize>("ef").unwrap();
     hnswparams.knbn = *matches.get_one::<usize>("knbn").unwrap();
+    hnswparams.scale_modification = *matches.get_one::<f64>("scale_modification").unwrap();
 
     match matches.get_one::<String>("dist") {
         Some(str) => match str.as_str() {
@@ -169,6 +171,7 @@ pub fn main() {
     let embedparams: EmbedderParams;
     //
     let hnswcmd = Command::new("hnsw")
+        .about("Build HNSW graph")
         .arg(Arg::new("dist")
             .long("dist")
             .short('d')
@@ -193,15 +196,25 @@ pub fn main() {
             .required(true)
             .action(ArgAction::Set)
             .value_parser(clap::value_parser!(usize))
-            .help("search factor"));
+            .help("search factor"))
+        .arg(Arg::new("scale_modification")
+            .long("scale_modify_f")
+            .help("scale modification factor in HNSW or HubNSW, must be in [0.2,1]")
+            .value_name("scale_modify")
+            .default_value("1.0")
+            .action(ArgAction::Set)
+            .value_parser(clap::value_parser!(f64))
+        );
 
     //
     // Now the command line
     // ===================
     //
     let matches = Command::new("annembed")
         //        .subcommand_required(true)
+        .version("0.1.7")
         .arg_required_else_help(true)
+        .about("Non-linear Dimension Reduction/Embedding via Approximate Nearest Neighbor Graph")
         .arg(
             Arg::new("csvfile")
                 .long("csv")
@@ -311,7 +324,7 @@ pub fn main() {
             }
         }
     } else {
-        hnswparams = HnswParams::my_default();
+        hnswparams = HnswParams::default();
     }
     log::debug!("hnswparams : {:?}", hnswparams);
 
@@ -433,13 +446,14 @@ where
 {
     //
     let nb_data = data_with_id.len();
-    let hnsw = Hnsw::<f64, Dist>::new(
+    let mut hnsw = Hnsw::<f64, Dist>::new(
         hnswparams.max_conn,
         nb_data,
         nb_layer,
         hnswparams.ef_c,
         Dist::default(),
     );
+    hnsw.modify_level_scale(hnswparams.scale_modification);
     hnsw.parallel_insert(data_with_id);
     hnsw.dump_layer_info();
     let kgraph = kgraph_from_hnsw_all(&hnsw, hnswparams.knbn).unwrap();
@@ -496,13 +510,14 @@ where
 {
     //
     let nb_data = data_with_id.len();
-    let hnsw = Hnsw::<f64, Dist>::new(
+    let mut hnsw = Hnsw::<f64, Dist>::new(
         hnswparams.max_conn,
         nb_data,
         nb_layer,
         hnswparams.ef_c,
         Dist::default(),
     );
+    hnsw.modify_level_scale(hnswparams.scale_modification);
     hnsw.parallel_insert(data_with_id);
     hnsw.dump_layer_info();
     KGraphProjection::<f64>::new(&hnsw, hnswparams.knbn, layer_proj)