Add Ver_1_0 iBOL and UniReps SSEL checkpoints and test DNA embeddings

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README.md

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+---
+language:
+- en
+tags:
+- biology
+- dna
+- biodiversity
+- hyperbolic-embeddings
+- pytorch
+---
+
+# Model Card for SSEL
+
+Checkpoints and extracted DNA embeddings for **Hierarchical Embedding of DNA Barcode Taxonomy with Hyperbolic Entailment Cones**. This repository contains the nine 768D experiments presented in the iBOL poster; eight also appear in the UniReps submission.
+
+## Model Details
+
+### Model Description
+
+**Structured Stacked Entailment Loss (SSEL)** extends **Stacked Entailment Loss (SEL)** with minimum-distance, full-cone nesting, sibling-cone separation and descendant-based cone allocation constraints. DNA barcodes and taxonomic labels are embedded in a shared hyperbolic space.
+
+The DNA branch starts from [BarcodeBERT](https://huggingface.co/bioscan-ml/clibd/tree/main/ckpt/BarcodeBERT), followed by a 768 → 1536 → 768 MLP without a residual connection. Taxonomic labels use learned embedding tables. These runs use DNA and four taxonomic ranks, without an image branch.
+
+### Model Sources
+
+- [Project page](https://bioscan-ml.org/ssel/)
+- [Code preparation repository](https://github.com/zmgong/SSEL_temp_release) (currently private)
+- [Paper](#)
+
+### Model Checkpoints
+
+| Method | Checkpoint (`last.pth`) | Test embeddings | Saved configuration | UniReps |
+| --- | --- | --- | --- | --- |
+| EL | [el](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_EL_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_EL_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_EL_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/config.yaml) | Yes |
+| SEL | [sel](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_SEL_basic_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/config.yaml) | Yes |
+| Positive EL + CL | [positive-el-cl](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_MERU_style_4rank_posEL02_CL1_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_MERU_style_4rank_posEL02_CL1_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_MERU_style_4rank_posEL02_CL1_768d_nonres_gap05_15epochs_seed42/config.yaml) | No |
+| SSEL | [ssel](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/SEL_structure_v2_768d_dna_nonres_margin05_gap05_weight10_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/SEL_structure_v2_768d_dna_nonres_margin05_gap05_weight10_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/SEL_structure_v2_768d_dna_nonres_margin05_gap05_weight10_15epochs_seed42/config.yaml) | Yes |
+| No direct placement | [no-direct-placement](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_no_direct_placement_768d_nonres_gap05_15epochs_seed42_retry_20261008/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_SEL_full_no_direct_placement_768d_nonres_gap05_15epochs_seed42_retry_20261008/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_no_direct_placement_768d_nonres_gap05_15epochs_seed42_retry_20261008/config.yaml) | Yes |
+| Frozen labels | [frozen-labels](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_frozen_labels_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_SEL_full_frozen_labels_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_frozen_labels_768d_nonres_gap05_15epochs_seed42/config.yaml) | Yes |
+| SEL + nesting | [sel-nesting](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_nesting_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_SEL_basic_plus_nesting_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_nesting_768d_nonres_gap05_15epochs_seed42/config.yaml) | Yes |
+| SEL + separation | [sel-separation](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_sibling_separation_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_SEL_basic_plus_sibling_separation_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_sibling_separation_768d_nonres_gap05_15epochs_seed42/config.yaml) | Yes |
+| SEL + allocation | [sel-allocation](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_allocation_768d_nonres_gap05_15epochs_seed42/last.pth) | [DNA](Ver_1_0/extracted_embedding/bioscan_5m/UniReps_SEL_basic_plus_allocation_768d_nonres_gap05_15epochs_seed42/extracted_feature_from_test_split.hdf5) | [Config](Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_allocation_768d_nonres_gap05_15epochs_seed42/config.yaml) | Yes |
+
+Each selected checkpoint is the exact **last.pth** used for its reported result. All nine runs use 768 dimensions, 15 epochs and seed 42. EL and SEL omit minimum distance; the other listed variants include it. Positive EL + CL is our DNA–taxonomy adaptation, not an exact reproduction of image–text MERU.
+
+## Files and Usage
+
+All versioned artifacts are under **Ver_1_0/**. The layout follows CLIBD's `ckpt/` and `extracted_embedding/` structure, with the version directory placed at the outside:
+
+```text
+Ver_1_0/
+  ckpt/
+    bioscan_clip/bioscan_5m/<model_output_name>/
+      last.pth
+      config.yaml
+    BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+  extracted_embedding/
+    bioscan_5m/<model_output_name>/
+      extracted_feature_from_test_split.hdf5
+      labels_test.json
+      processed_id_test.json
+      dna_to_label.csv
+      species_detection.csv
+      evaluation_complete.json
+    training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/
+  data/BIOSCAN_5M/global_label_to_id_mapping.json
+  metadata/experiments.json
+  SHA256SUMS.txt
+```
+
+The checkpoints are native PyTorch state dictionaries and use the SSEL codebase's loader. They are not Transformers `AutoModel` packages. Configuration copies retain the scientific settings; local absolute roots become `${oc.env:SSEL_ARTIFACT_ROOT,.}`, and W&B is disabled by default. Set `SSEL_ARTIFACT_ROOT` to the downloaded `Ver_1_0` directory. The processed BIOSCAN-5M HDF5 is downloaded separately into `data/BIOSCAN_5M/` within that root. The current loader additionally uses `prajjwal1/bert-small` from Hugging Face or its local cache.
+
+### Embedding Format
+
+Each HDF5 contains **test DNA embeddings only**, in the saved checkpoint's hyperbolic space:
+
+| HDF5 dataset | Shape | Type |
+| --- | --- | --- |
+| `seen/encoded_dna_feature` | 39,373 × 768 | float32 |
+| `unseen/encoded_dna_feature` | 7,887 × 768 | float32 |
+
+The companion JSON files provide labels and process IDs in exactly the same row order. These are spatial coordinates of Lorentz-model hyperbolic embeddings; they are not unit-normalized Euclidean vectors. Recover the time coordinate using the checkpoint curvature when needed.
+
+Final trained taxonomic label tables, learned scales and curvature are included **inside each checkpoint**. The shared placement artifact supplies initial coordinates, candidate labels, global IDs and parent relationships; **initial coordinates are not final trained label embeddings**. Separate final-label vector files, train/validation embeddings and specimen reference-key caches are not included in this version.
+
+Classification uses the nearest label by exterior angle at each rank. Unseen-species detection uses cone checks against the seen-species label candidates. These are separate measurements; the accompanying metric CSVs and evaluation records preserve that distinction.
+
+## Training Data
+
+The experiments use [BIOSCAN-5M](https://huggingface.co/datasets/bioscan-ml/BIOSCAN-5M). The [processed HDF5](https://huggingface.co/datasets/bioscan-ml/clibd) has 39,373 seen-species and 7,887 unseen-species test queries. Label candidates are training-derived: 55 orders, 929 families, 6,819 genera and 11,846 species. The raw dataset is not stored in this model repository.
+
+## Acknowledgement
+
+This work was supported by the Government of Canada's New Frontiers in Research Fund (NFRF) [NFRFT-2020-00073] and the Canada CIFAR AI Chairs Program. We acknowledge BIOSCAN-5M, BarcodeBERT and the CLIBD codebase. This model card and artifact layout follow [CLIBD](https://huggingface.co/bioscan-ml/clibd).

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+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: true
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 1.0
+    sel_inter_entailment_weight: 0.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: true
+        child_only_containment: false
+        nesting_weight: 1.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 10.0
+        allocation_weight: 1.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 1.0
+        inter_entailment: 0.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: true
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 1.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 10.0
+    sel_structured_allocation_weight: 1.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: SEL_structure_v2_768d_dna_nonres_margin05_gap05_weight10_15epochs_seed42
+  port: 29931
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/SEL_structure_v2_768d_dna_nonres_margin05_gap05_weight10_15epochs_seed42/last.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:cd98e1d8088524594719f3a45186950a2b7fac779708408c2577b42db33f71bc
+size 452784372

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_EL_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,489 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: true
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 128
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: false
+        child_only_containment: false
+        nesting_weight: 0.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 0.0
+        allocation_weight: 0.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: false
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 0.0
+        safety_ratio: 0.1
+        active_in_stage1: false
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 0.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: false
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: false
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 0.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 0.0
+    sel_structured_allocation_weight: 0.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_EL_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42
+  port: 29955
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_EL_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/last.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:b867680474bf7e1a77b48c580bc630e53d78526637c35be7434c09774e12c4df
+size 452784372

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_MERU_style_4rank_posEL02_CL1_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,501 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: false
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 0.2
+    sel_contrastive_weight: 1.0
+    sel_contrastive_loss_mode: stable_pairwise_dist
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: false
+        child_only_containment: false
+        nesting_weight: 0.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 0.0
+        allocation_weight: 0.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: false
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 0.2
+        enable_negative_inter_entailment: false
+        contrastive_weight: 1.0
+        train_logit_scale: true
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 0.2
+        contrastive: 1.0
+      contrastive:
+        mode: stable_pairwise_dist
+        compute_image_dna: false
+        dna_label:
+          enabled: true
+          candidate_scope: global_batch_unique
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+        detach_label_geometry: false
+        positive_contrastive:
+          enabled: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 1.0
+        negative_weight: 0.0
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 1.0
+    sel_neg_pair_weight: 0.0
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_dna_label_contrastive_enabled: true
+    sel_dna_label_contrastive_candidate_scope: global_batch_unique
+    sel_inter_entailment_detach_label_geometry: false
+    sel_positive_contrastive_enabled: false
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: false
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 0.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 0.0
+    sel_structured_allocation_weight: 0.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 0.2
+    sel_stage2_train_logit_scale: true
+    sel_stage2_contrastive_weight: 1.0
+    sel_stage2_enable_negative_inter_entailment: false
+    sel_stage2_inter_negative_entailment_weight: 0.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: null
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_MERU_style_4rank_posEL02_CL1_768d_nonres_gap05_15epochs_seed42
+  port: 29964
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_MERU_style_4rank_posEL02_CL1_768d_nonres_gap05_15epochs_seed42/last.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d3feac60f8901d988ce3b2645077f33f6896c23a11c24c742f542e941829e1fd
+size 452784799

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,489 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: true
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 128
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: false
+        child_only_containment: false
+        nesting_weight: 0.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 0.0
+        allocation_weight: 0.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: true
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 0.0
+        safety_ratio: 0.1
+        active_in_stage1: false
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 0.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: false
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: false
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 0.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 0.0
+    sel_structured_allocation_weight: 0.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_SEL_basic_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42
+  port: 29956
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_no_radius_barrier_4rank_posneg_768d_nonres_gap05_15epochs_seed42/last.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:542478eb799eea14243c8b4606d926db51585fde5852a2d79c097c577f8a50c3
+size 452784372

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_allocation_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,489 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: false
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: true
+        child_only_containment: false
+        nesting_weight: 0.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 0.0
+        allocation_weight: 1.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: true
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: true
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 0.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 0.0
+    sel_structured_allocation_weight: 1.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_SEL_basic_plus_allocation_768d_nonres_gap05_15epochs_seed42
+  port: 29963
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_allocation_768d_nonres_gap05_15epochs_seed42/last.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:74064b88cb700e226975a78e9ae012bacbcf01763bbe69c22a5dac3a81f892d6
+size 452784799

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_nesting_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,489 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: true
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: true
+        child_only_containment: false
+        nesting_weight: 1.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 0.0
+        allocation_weight: 0.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: true
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: true
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 1.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 0.0
+    sel_structured_allocation_weight: 0.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_SEL_basic_plus_nesting_768d_nonres_gap05_15epochs_seed42
+  port: 29961
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_nesting_768d_nonres_gap05_15epochs_seed42/last.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:453a80378a8062c102040922aa3d1302d0a891f0e20b286b47a3f214b6a5fb44
+size 452784799

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_sibling_separation_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,489 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: false
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: true
+        child_only_containment: false
+        nesting_weight: 0.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 10.0
+        allocation_weight: 0.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: true
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: true
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 0.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 10.0
+    sel_structured_allocation_weight: 0.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_SEL_basic_plus_sibling_separation_768d_nonres_gap05_15epochs_seed42
+  port: 29962
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_basic_plus_sibling_separation_768d_nonres_gap05_15epochs_seed42/last.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2e4b3d82f94f5e8359f483875f58aac647c4b6c79c47890e864f648b999fda08
+size 452784799

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_frozen_labels_768d_nonres_gap05_15epochs_seed42/config.yaml

@@ -0,0 +1,492 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: false
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: true
+        child_only_containment: false
+        nesting_weight: 1.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 10.0
+        allocation_weight: 1.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: true
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: false
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+        train_dna_branch_only: true
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+        apply_initialization: true
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: true
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 1.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 10.0
+    sel_structured_allocation_weight: 1.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
+    sel_structured_child_cone_fill_ratio: 0.82
+    sel_structured_allocation_loss_type: huber
+    sel_structured_allocation_huber_delta_deg: 1.0
+    sel_structured_allocation_relative_huber_delta: 0.25
+    sel_structured_allocation_relative_half_width_floor_deg: 0.01
+    sel_structured_allocation_detach_target: false
+    sel_structured_subtree_weight_mode: terminal_descendants
+    sel_stage2_train_only_dna_projection: false
+    sel_stage2_train_dna_projection_and_taxonomy: false
+    sel_stage2_train_dna_branch_only: true
+    sel_stage2_train_dna_encoder: true
+    sel_stage2_preserve_initialized_dna_encoder: true
+    sel_stage2_intra_entailment_weight: 0.0
+    sel_stage2_inter_entailment_weight: 1.0
+    sel_stage2_contrastive_weight: 0.0
+    sel_stage2_enable_negative_inter_entailment: true
+    sel_stage2_inter_negative_entailment_weight: 1.0
+  sel_two_stage_training:
+    use_two_stage_training: false
+    eval_stage_one_only: false
+    train_stage_one_only: false
+    freeze_text_encoder_for_first_few_epochs: 0
+    freeze_text_encoder_for_whole_stage_2: false
+    inter_entailment_weight_warmup_epochs: 0
+    first_stage_setting:
+      mode: node_minibatch
+      max_epoch: 5
+      max_steps: null
+      checkpoint_every_steps: 0
+      geometry_snapshot_every_steps: 0
+      batch_size: 80
+      lr: 0.001
+      weight_decay: 0.01
+      num_workers_per_gpu: 16
+      max_lr: 0.1
+      min_lr: 1.0e-08
+      final_div_factor: 10000.0
+      lr_scheduler: one_cycle
+  train_with_train_seen_only: true
+  dataset: bioscan_5m
+  for_open_clip: false
+  fix_temperature: false
+  amp: true
+  eval_skip_epoch: 0
+  fast_retrieval_subset: true
+  load_ckpt: true
+  pretrained_ckpt_path: null
+  no_pretrained_weights: false
+  ckpt_trained_with_insect_image_dna_text_path: null
+  train_with_small_subset: false
+  bin_for_positive_and_negative_pairs: false
+  transform_with_resize: false
+  pre_train_for_barcode_bert: null
+  for_bio_clip: false
+  base_batch_size: 500
+  output_dim: 768
+  dna_output_pipeline: transformed_hidden_state_mean
+  split_used_for_training: no_split_and_seen_train
+  taxonomy_subset:
+    enabled: false
+    level: order
+    include_labels: []
+  training_sample_filter:
+    enabled: false
+    required_taxonomy_levels: []
+    valid_indices_path: null
+    chunk_size: 250000
+  training_sample_repeat:
+    enabled: false
+    target_num_samples: null
+  image:
+    input_type: image
+    model: vit
+    freeze: true
+  dna:
+    input_type: sequence
+    model: barcode_bert
+    freeze: false
+    preserve_pretrained_mlm_decoder: true
+  language:
+    input_type: sequence
+    model: bert_small
+    freeze: true
+  lr_config:
+    lr: 1.0e-06
+    max_lr: 5.0e-05
+    min_lr: 1.0e-09
+  lr_scheduler: one_cycle
+  lr_warm_up_ratio: null
+  bind_to: null
+  no_image_text_loss: false
+  num_workers: 8
+  debug_max_steps_per_epoch: null
+  debug_autograd_anomaly: false
+  disable_lora: true
+  using_imagenet_mean_and_std: false
+  epochs: 15
+  wandb_project_name: SEL_v3_2_23_direct_placement_joint_full_train
+  model_output_dir: ${project_root_path}/ckpt/bioscan_hyperbolic
+  evaluation_period: 15
+  eval_every_epoch: false
+  all_gather: true
+  loss_setup:
+    gather_with_grad: true
+    use_horovod: false
+    local_loss: false
+  random_seed: false
+  default_seed: 42
+  batch_size: 200
+  model_output_name: UniReps_SEL_full_frozen_labels_768d_nonres_gap05_15epochs_seed42
+  port: 29955
+  local_loss_log_every: 100
+  retain_epoch_checkpoints:
+  - 1
+  - 5
+  - 10
+  - 15
+resolved_seed: 42

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_frozen_labels_768d_nonres_gap05_15epochs_seed42/last.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:a4b717541a82994ab8733205676249c9660243fc43aa6666e1be3840953ed8b2
+size 452784799

Ver_1_0/ckpt/bioscan_clip/bioscan_5m/UniReps_SEL_full_no_direct_placement_768d_nonres_gap05_15epochs_seed42_retry_20261008/config.yaml

@@ -0,0 +1,490 @@
+debug_flag: false
+debug_dataloader: false
+debug_skip_training: false
+project_root_path: ${oc.env:SSEL_ARTIFACT_ROOT,.}
+data_dir: ${project_root_path}/data
+activate_wandb: false
+save_inference: true
+load_inference: false
+enable_early_stopping: false
+imagenet_mean:
+- 0.485
+- 0.456
+- 0.406
+imagenet_std:
+- 0.229
+- 0.224
+- 0.225
+bioscan_data:
+  dir: ${data_dir}/BIOSCAN_1M
+  path_to_hdf5_data: ${bioscan_data.dir}/split_data/BioScan_data_in_splits.hdf5
+  path_to_tsv_data: ${bioscan_data.dir}/BioScan_Insect_Dataset_metadata_2.tsv
+  path_to_small_species_list_json: ${bioscan_data.dir}/small_species_list.json
+  path_to_id_to_position_mapping: ${bioscan_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_data.dir}/label_to_id_mapping_for_four_levels_1m.json
+  image_mean:
+  - 0.7251
+  - 0.7289
+  - 0.7296
+  image_std:
+  - 0.1265
+  - 0.143
+  - 0.161
+bioscan_5m_data:
+  dir: ${data_dir}/BIOSCAN_5M
+  image_dir: ${bioscan_5m_data.dir}/images
+  path_to_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M.hdf5
+  path_to_smaller_hdf5_data: ${bioscan_5m_data.dir}/BIOSCAN_5M_with_small_pre_train.hdf5
+  path_to_tsv_data: ${bioscan_5m_data.dir}/BIOSCAN-5M_Dataset_v3.4.csv
+  path_to_id_to_position_mapping: ${bioscan_5m_data.dir}/id_to_position_mapping.json
+  label_to_id_mapping: ${bioscan_5m_data.dir}/label_to_id_mapping_for_four_levels_5m.json
+  image_mean:
+  - 0.7628
+  - 0.765
+  - 0.7637
+  image_std:
+  - 0.1421
+  - 0.1564
+  - 0.1731
+insect_data:
+  dir: ${data_dir}/INSECT
+  path_to_att_splits_mat: ${insect_data.dir}/att_splits.mat
+  path_to_res_101_mat: ${insect_data.dir}/res101.mat
+  path_to_feature_hdf5: ${insect_data.dir}/extracted_features/clip_barcodebert_extracted_features.hdf5
+  path_to_image_hdf5: ${insect_data.dir}/INSECT_images.hdf5
+  path_to_meta_csv: ${insect_data.dir}/INSECT_metadata.csv
+  image_dir: ${insect_data.dir}/images
+  species_to_other: ${insect_data.dir}/specie_to_other_labels.json
+save_ckpt: true
+bioscan_bert_checkpoint: ${project_root_path}/ckpt/BarcodeBERT/old_checkpoints/trained_with_canada_1_5M/model_41.pth
+bioscan_bert_checkpoint_trained_with_canada_1_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_5m/BIOSCAN-5M-BEST_k4_6_6_w1_m0_r0.pt
+bioscan_bert_checkpoint_trained_with_bioscan_5_m: ${project_root_path}/ckpt/BarcodeBERT/new_checkpoints/trained_with_canada_1_5M/CANADA-1.5M-BEST_k4_4_4_w1_m0_r0_wd.pt
+model_output_dir: ${project_root_path}/ckpt/bioscan_clip
+inference_and_eval_setting:
+  plot_embeddings: false
+  retrieve_images: false
+  k_list:
+  - 1
+  - 3
+  - 5
+  levels:
+  - order
+  - family
+  - genus
+  - species
+  embeddings_filters:
+    order: Diptera
+    family: Sciaridae
+    genus: Corynoptera
+  retrieve_settings:
+    num_queries: 5
+    max_k: 3
+    seed: 413
+    independent: false
+    load_cached_results: false
+  eval_on: val
+  compute_genus_top1_excl_same_species: true
+  cone_check_split: train
+  cone_check_val_subsplit: seen
+  eval_batch_size_for_nn_retrieval: 512
+  encode_embeddings_to_parquet:
+    eval_image: true
+    eval_dna: true
+  diagnostics:
+    effective_rank:
+      enabled: true
+      device: auto
+      chunk_size: 32768
+      normalize: false
+      max_samples: null
+      seed: 42
+      include_sample_language: true
+  cone_check:
+    enabled: true
+    taxonomy_label: true
+    instance_taxonomy: true
+    modalities:
+    - image
+    - dna
+    target_levels:
+    - order
+    - family
+    - genus
+    - species
+    aperture_scale: 1.0
+    query_batch_size: null
+    candidate_batch_size: null
+    max_queries_per_split: null
+    max_candidates_per_level: null
+    allow_missing_modalities: true
+    show_progress: false
+    class_scatter_plot: true
+    class_scatter_x_axis: sample_count
+    class_scatter_min_samples: 1
+visualization:
+  output_dir: ${project_root_path}/visualizations
+  key_feature_type: image
+  k: 10
+general_fine_tune_setting:
+  save_ckpt: true
+  epoch: 15
+  batch_size: 200
+hf_repo_id: bioscan-ml/clibd
+default_seed: 42
+barcodebert_setting:
+  old_model_setting:
+    k: 5
+    max_len: 660
+version: ver_1_0
+default_dna_output_pipeline: hidden_state_mean
+epsilon: 1.0e-08
+model_config:
+  resume_from_checkpoint: true
+  for_rcme: false
+  legacy_clibd_eval_behavior: false
+  l2_normalize_embeddings: true
+  rcme_contrastive_loss_weight: 0.1
+  rcme_eloss_weight: 1.0
+  rcme_mloss_weight: 1.0
+  rcme_using_vit_and_bert_small: false
+  rcme_using_open_clip_as_pretrain: false
+  hyperbolic_space:
+    train_hyperbolic: false
+    train_with_stacked_entailment_loss: true
+    entail_weight: 0.2
+    loss_type: A
+    adjust_alpha: false
+    margin: 0
+    relative_margin: 0
+    nearest_neighbor_metric_uni_modality: cosine_similarity_in_euclidean
+    nearest_neighbor_metric_cross_modality: angle
+    disable_entailment_loss: false
+    compute_contrastive_loss_between_image_and_dna: false
+    min_radius: 0.1
+    sel_load_concat_text: false
+    full_text_for_contrastive_loss: false
+    sel_intra_entailment_weight: 0.0
+    sel_inter_entailment_weight: 1.0
+    sel_contrastive_weight: 0.0
+    sel_contrastive_loss_mode: euclidean
+    sel_contrastive_pairing: instance
+    entailment_geometry: hyperbolic
+    sel_add_dna_bin: false
+    sel_use_emb_table_for_label_bin: true
+    sel_disable_image: true
+    use_dna_barcode_embed_for_dna_bin: false
+    dna_bin_memory_bank_momentum: 0.999
+    sel_use_dna_projection: true
+    sel_dna_projection_identity_init: false
+    sel_dna_projection_residual: false
+    sel_dna_projection_normalize: false
+    stacked_entailment:
+      embedding_dim: 768
+      dna_projection:
+        input_dim: 768
+        output_dim: 768
+        normalize: false
+        enabled: true
+        type: mlp
+        hidden_dim: 1536
+        activation: gelu
+        dropout: 0.0
+        identity_init: false
+        residual: false
+      text_projection:
+        input_dim: null
+        output_dim: null
+        enabled: false
+      rank_norm_ordering:
+        enabled: false
+        weight: 1.0
+        parent_mean_margin_ratio: 0.1
+        apply_in_stage2: false
+      structured_hierarchy:
+        enabled: true
+        child_only_containment: false
+        nesting_weight: 1.0
+        nesting_margin_deg: 0.25
+        sibling_gap_weight: 10.0
+        allocation_weight: 1.0
+        order_total_width_deg: 300.0
+        child_axis_span_ratio: 0.9
+        child_cone_fill_ratio: 0.82
+        allocation_loss_type: huber
+        allocation_huber_delta_deg: 1.0
+        allocation_relative_huber_delta: 0.25
+        allocation_relative_half_width_floor_deg: 0.01
+        allocation_detach_target: false
+        subtree_weight_mode: terminal_descendants
+        version: v2
+        allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+        relative_margin: 0.05
+        relative_gap: 0.05
+        ratio_huber_delta: 0.25
+      stage2:
+        full_graph_taxonomy_loss:
+          enabled: true
+          weight: 1.0
+          source_split: no_split_and_seen_train
+          point_entailment_enabled: true
+        max_steps: 0
+        checkpoint_every_epochs: 1
+        geometry_snapshot_every_steps: 0
+        geometry_snapshot_probe_size: 64
+        geometry_snapshot_probe_strategy: first_batch
+        frozen_dna_feature_cache:
+          enabled: false
+          path: null
+          build_batch_size: 512
+          num_workers: 4
+        inter_entailment_rank_curriculum:
+          enabled: false
+          levels_by_epoch: []
+          save_phase_checkpoints: false
+        train_only_dna_projection: false
+        train_dna_projection_and_taxonomy: true
+        train_dna_encoder: true
+        preserve_initialized_dna_encoder: true
+        weight_decay: 0.01
+        intra_entailment_weight: 0.0
+        inter_entailment_weight: 1.0
+        enable_negative_inter_entailment: true
+        contrastive_weight: 0.0
+      geometry: hyperbolic
+      loss_type: A
+      disable_image: true
+      clamp_feature_alpha_max: true
+      full_text_for_contrastive_loss: false
+      load_concat_text: false
+      min_radius: 0.1
+      margin:
+        absolute: 0
+        relative: 0
+      label_table:
+        enabled: true
+        add_dna_bin_level: false
+        candidate_source_split: no_split_and_seen_train
+        initialization_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/seen_taxonomy_placement.pt
+        reset_label_alpha: true
+        reset_curvature: true
+        zero_unplaced_rows: true
+        require_candidate_match: true
+        apply_initialization: false
+      loss_weights:
+        intra_entailment: 0.0
+        inter_entailment: 1.0
+        contrastive: 0.0
+      contrastive:
+        mode: euclidean
+        compute_image_dna: false
+      inter_entailment:
+        stage2_mode: all_rank_dna_label
+        all_rank_levels:
+        - order
+        - family
+        - genus
+        - species
+        loss_mode: cone_hinge
+        ignore_non_candidate_positives: false
+      pos_neg_reduce:
+        mode: weighted_mean
+        positive_weight: 0.5
+        negative_weight: 0.5
+      radius_barrier:
+        weight: 1.0
+        safety_ratio: 0.1
+        active_in_stage1: true
+        reduction: sum_within_rank_mean_across_ranks
+    sel_clamp_feature_alpha_max: true
+    sel_use_text_projection: false
+    sel_text_projection_identity_init: true
+    sel_text_projection_residual: true
+    sel_text_projection_type: linear
+    sel_text_projection_hidden_dim: null
+    sel_text_projection_activation: gelu
+    sel_text_projection_dropout: 0.0
+    use_species_retrieval: true
+    use_full_text_for_retrieval: false
+    retrieve_each_level_separately: false
+    curv_init: 1.0
+    learn_curv: true
+    using_avg_norm_dict: false
+    inference_project_to_hyperbolic_space: true
+    sel_apply_margin_to_positive_and_negative_el: false
+    eval_instance_taxonomy_cone_check: true
+    log_in_cone_rate: true
+    log_wrong_cone_rate: true
+    sel_inter_entailment_pos_neg_pair_strategy: instance
+    sel_inter_entailment_loss_mode: cone_hinge
+    sel_inter_entailment_missing_level_negative_strategy: none
+    sel_stage2_inter_entailment_mode: all_rank_dna_label
+    sel_all_rank_dna_label_levels:
+    - order
+    - family
+    - genus
+    - species
+    sel_all_rank_ignore_non_candidate_positives: false
+    sel_inter_pairwise_chunk_rows: 0
+    sel_pos_pair_weight: 0.5
+    sel_neg_pair_weight: 0.5
+    sel_posneg_reduce_mode: weighted_mean
+    sel_posneg_max_mix_weight: 1.0
+    sel_radius_barrier_weight: 1.0
+    sel_radius_barrier_safety_ratio: 0.1
+    sel_radius_barrier_active_in_stage1: true
+    sel_radius_barrier_reduction: sum_within_rank_mean_across_ranks
+    eval_instance_taxonomy_during_training: false
+    eval_instance_taxonomy_modalities:
+    - dna
+    eval_instance_taxonomy_target_levels:
+    - order
+    - family
+    - genus
+    - species
+    eval_instance_taxonomy_query_splits:
+    - seen
+    eval_instance_taxonomy_candidate_source: training_seen
+    eval_instance_taxonomy_show_progress: true
+    sel_embedding_dim: 768
+    sel_dna_projection_input_dim: 768
+    sel_dna_projection_output_dim: 768
+    sel_dna_projection_type: mlp
+    sel_dna_projection_hidden_dim: 1536
+    sel_dna_projection_activation: gelu
+    sel_dna_projection_dropout: 0.0
+    sel_text_projection_input_dim: null
+    sel_text_projection_output_dim: null
+    sel_rank_norm_ordering_enabled: false
+    sel_rank_norm_ordering_weight: 1.0
+    sel_rank_norm_ordering_apply_in_stage2: false
+    sel_rank_norm_ordering_parent_mean_margin_ratio: 0.1
+    sel_structured_hierarchy_enabled: true
+    sel_structured_version: v2
+    sel_structured_allocation_targets_path: ${project_root_path}/extracted_embedding/training_seen_taxonomy_768d_weighted_simplex_beta025_margin05_gap05_placement/allocation_targets.json
+    sel_structured_relative_margin: 0.05
+    sel_structured_relative_gap: 0.05
+    sel_structured_ratio_huber_delta: 0.25
+    sel_structured_child_only_containment: false
+    sel_structured_nesting_weight: 1.0
+    sel_structured_nesting_margin_deg: 0.25
+    sel_structured_sibling_gap_weight: 10.0
+    sel_structured_allocation_weight: 1.0
+    sel_structured_order_total_width_deg: 300.0
+    sel_structured_child_axis_span_ratio: 0.9
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+  - 5
+  - 10
+  - 15
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+}

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