caixudong2001 commited on May 19

Commit

bd6a9bf

1 Parent(s): 528ef77

Replace checkpoints with inference weights

Files changed (40) hide show

checkpoints/checkpoints7/config.json +0 -92
checkpoints/checkpoints7/pytorch_model.bin +0 -3
checkpoints/checkpoints8/special_tokens_map.json +0 -20
checkpoints/checkpoints8/tokenizer_config.json +0 -62
checkpoints/checkpoints8/vocab.txt +0 -15
checkpoints/{checkpoints1 → oriongeno_arthropods}/config.json +0 -0
checkpoints/{checkpoints5 → oriongeno_arthropods}/pytorch_model.bin +0 -0
checkpoints/{checkpoints1 → oriongeno_arthropods}/special_tokens_map.json +0 -0
checkpoints/{checkpoints1 → oriongeno_arthropods}/tokenizer_config.json +0 -0
checkpoints/{checkpoints1 → oriongeno_arthropods}/vocab.txt +0 -0
checkpoints/{checkpoints2 → oriongeno_birds}/config.json +0 -0
checkpoints/{checkpoints3 → oriongeno_birds}/pytorch_model.bin +0 -0
checkpoints/{checkpoints2 → oriongeno_birds}/special_tokens_map.json +0 -0
checkpoints/{checkpoints2 → oriongeno_birds}/tokenizer_config.json +0 -0
checkpoints/{checkpoints2 → oriongeno_birds}/vocab.txt +0 -0
checkpoints/{checkpoints3 → oriongeno_fish}/config.json +0 -0
checkpoints/{checkpoints2 → oriongeno_fish}/pytorch_model.bin +0 -0
checkpoints/{checkpoints3 → oriongeno_fish}/special_tokens_map.json +0 -0
checkpoints/{checkpoints3 → oriongeno_fish}/tokenizer_config.json +0 -0
checkpoints/{checkpoints3 → oriongeno_fish}/vocab.txt +0 -0
checkpoints/{checkpoints5 → oriongeno_fungi}/config.json +0 -0
checkpoints/{checkpoints6 → oriongeno_fungi}/pytorch_model.bin +1 -1
checkpoints/{checkpoints4 → oriongeno_fungi}/special_tokens_map.json +0 -0
checkpoints/{checkpoints4 → oriongeno_fungi}/tokenizer_config.json +0 -0
checkpoints/{checkpoints4 → oriongeno_fungi}/vocab.txt +0 -0
checkpoints/{checkpoints6 → oriongeno_mammals}/config.json +0 -0
checkpoints/{checkpoints1 → oriongeno_mammals}/pytorch_model.bin +0 -0
checkpoints/{checkpoints5 → oriongeno_mammals}/special_tokens_map.json +0 -0
checkpoints/{checkpoints5 → oriongeno_mammals}/tokenizer_config.json +0 -0
checkpoints/{checkpoints5 → oriongeno_mammals}/vocab.txt +0 -0
checkpoints/{checkpoints4 → oriongeno_other_vertebrates}/config.json +0 -0
checkpoints/{checkpoints4 → oriongeno_other_vertebrates}/pytorch_model.bin +0 -0
checkpoints/{checkpoints6 → oriongeno_other_vertebrates}/special_tokens_map.json +0 -0
checkpoints/{checkpoints6 → oriongeno_other_vertebrates}/tokenizer_config.json +0 -0
checkpoints/{checkpoints6 → oriongeno_other_vertebrates}/vocab.txt +0 -0
checkpoints/{checkpoints8 → oriongeno_plants}/config.json +0 -0
checkpoints/{checkpoints8 → oriongeno_plants}/pytorch_model.bin +0 -0
checkpoints/{checkpoints7 → oriongeno_plants}/special_tokens_map.json +0 -0
checkpoints/{checkpoints7 → oriongeno_plants}/tokenizer_config.json +0 -0
checkpoints/{checkpoints7 → oriongeno_plants}/vocab.txt +0 -0

checkpoints/checkpoints7/config.json DELETED Viewed

@@ -1,92 +0,0 @@
-{
-  "architectures": [
-    "OrionGenoForJointLabeling"
-  ],
-  "attention_type": "flash_attention_2",
-  "attn_cfg": {},
-  "attn_layer_idx": [],
-  "bidirectional": true,
-  "bidirectional_strategy": "add",
-  "bidirectional_weight_tie": true,
-  "bos_token_id": 14,
-  "d_intermediate": 0,
-  "d_model": 768,
-  "dtype": "bfloat16",
-  "eos_token_id": 13,
-  "fused_add_norm": true,
-  "initializer_cfg": null,
-  "keys_to_ignore_at_inference": [
-    "gene_logits",
-    "repeat_logits",
-    "boundary_logits",
-    "gene_cross_entropy",
-    "repeat_cross_entropy",
-    "boundary_focal_loss",
-    "hidden_states"
-  ],
-  "loss_weights": {
-    "boundary_focal_loss": 0.25,
-    "repeat_cross_entropy": 0.1,
-    "state_cross_entropy": 1.0
-  },
-  "mask_token_id": 10,
-  "model_type": "orion_geno",
-  "n_layer": 24,
-  "norm_epsilon": 1e-05,
-  "pad_token_id": 9,
-  "pad_vocab_size_multiple": 1,
-  "residual_in_fp32": true,
-  "rms_norm": true,
-  "settings": {
-    "channel_growth": 128,
-    "decoder_channel_sizes": [
-      768,
-      768,
-      640,
-      512,
-      384
-    ],
-    "encoder_output_channels": 384,
-    "feature_scales": [
-      1,
-      2,
-      4,
-      8
-    ],
-    "gene_label_count": 20,
-    "input_channels": 5,
-    "loss": {
-      "boundary_label_ids": [
-        7,
-        8,
-        9,
-        10,
-        11,
-        12,
-        13,
-        14,
-        17,
-        19
-      ],
-      "boundary_loss_gamma": 2.0,
-      "boundary_positive_weight": 4.0,
-      "intergenic_label_id": 0,
-      "state_boundary_weight": 1.6,
-      "state_default_weight": 1.0,
-      "state_intergenic_weight": 0.25,
-      "state_label_smoothing": 0.02,
-      "state_near_boundary_distance": 8,
-      "state_near_boundary_factor": 1.2
-    },
-    "pooling_kernel_size": 2,
-    "repeat_label_count": 2,
-    "use_decoder_skip_connection": false,
-    "use_repeat_head": true
-  },
-  "ssm_cfg": {
-    "layer": "Mamba2"
-  },
-  "transformers_version": "4.57.3",
-  "use_second_lm_head": false,
-  "vocab_size": 15
-}

checkpoints/checkpoints7/pytorch_model.bin DELETED Viewed

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:9701780388e4a4c06248d97c193821663b95c8a4c466332acee73174be2c86ec
-size 244045419

checkpoints/checkpoints8/special_tokens_map.json DELETED Viewed

@@ -1,20 +0,0 @@
-{
-  "bos_token": {
-    "content": "<bos>",
-    "lstrip": false,
-    "normalized": false,
-    "rstrip": false,
-    "single_word": false
-  },
-  "cls_token": "<cls>",
-  "eos_token": {
-    "content": "<eos>",
-    "lstrip": false,
-    "normalized": false,
-    "rstrip": false,
-    "single_word": false
-  },
-  "mask_token": "<mask>",
-  "pad_token": "<pad>",
-  "unk_token": "<unk>"
-}

checkpoints/checkpoints8/tokenizer_config.json DELETED Viewed

@@ -1,62 +0,0 @@
-{
-  "added_tokens_decoder": {
-    "9": {
-      "content": "<pad>",
-      "lstrip": false,
-      "normalized": false,
-      "rstrip": false,
-      "single_word": false,
-      "special": true
-    },
-    "10": {
-      "content": "<mask>",
-      "lstrip": false,
-      "normalized": false,
-      "rstrip": false,
-      "single_word": false,
-      "special": true
-    },
-    "11": {
-      "content": "<unk>",
-      "lstrip": false,
-      "normalized": false,
-      "rstrip": false,
-      "single_word": false,
-      "special": true
-    },
-    "12": {
-      "content": "<cls>",
-      "lstrip": false,
-      "normalized": false,
-      "rstrip": false,
-      "single_word": false,
-      "special": true
-    },
-    "13": {
-      "content": "<eos>",
-      "lstrip": false,
-      "normalized": false,
-      "rstrip": false,
-      "single_word": false,
-      "special": true
-    },
-    "14": {
-      "content": "<bos>",
-      "lstrip": false,
-      "normalized": false,
-      "rstrip": false,
-      "single_word": false,
-      "special": true
-    }
-  },
-  "bos_token": "<bos>",
-  "clean_up_tokenization_spaces": true,
-  "cls_token": "<cls>",
-  "eos_token": "<eos>",
-  "extra_special_tokens": {},
-  "mask_token": "<mask>",
-  "model_max_length": 51200,
-  "pad_token": "<pad>",
-  "tokenizer_class": "DnaTokenizer",
-  "unk_token": "<unk>"
-}

checkpoints/checkpoints8/vocab.txt DELETED Viewed

@@ -1,15 +0,0 @@
-A
-C
-G
-T
-N
-a
-c
-g
-t
-<pad>
-<mask>
-<unk>
-<cls>
-<eos>
-<bos>

checkpoints/{checkpoints1 → oriongeno_arthropods}/config.json RENAMED Viewed

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checkpoints/{checkpoints5 → oriongeno_arthropods}/pytorch_model.bin RENAMED Viewed

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checkpoints/{checkpoints1 → oriongeno_arthropods}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints1 → oriongeno_arthropods}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints1 → oriongeno_arthropods}/vocab.txt RENAMED Viewed

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checkpoints/{checkpoints2 → oriongeno_birds}/config.json RENAMED Viewed

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checkpoints/{checkpoints3 → oriongeno_birds}/pytorch_model.bin RENAMED Viewed

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checkpoints/{checkpoints2 → oriongeno_birds}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints2 → oriongeno_birds}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints2 → oriongeno_birds}/vocab.txt RENAMED Viewed

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checkpoints/{checkpoints3 → oriongeno_fish}/config.json RENAMED Viewed

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checkpoints/{checkpoints2 → oriongeno_fish}/pytorch_model.bin RENAMED Viewed

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checkpoints/{checkpoints3 → oriongeno_fish}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints3 → oriongeno_fish}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints3 → oriongeno_fish}/vocab.txt RENAMED Viewed

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checkpoints/{checkpoints5 → oriongeno_fungi}/config.json RENAMED Viewed

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checkpoints/{checkpoints6 → oriongeno_fungi}/pytorch_model.bin RENAMED Viewed

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:118a3fbbcb4a00459e5cd407d6061b1951d191d765e5638ad8d8e57f0483b4ee
 size 244045419

 version https://git-lfs.github.com/spec/v1
+oid sha256:c07455e26f50a21de82b1a27489350c2085d6f69f417bf441fbee098139f8a3e
 size 244045419

checkpoints/{checkpoints4 → oriongeno_fungi}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints4 → oriongeno_fungi}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints4 → oriongeno_fungi}/vocab.txt RENAMED Viewed

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checkpoints/{checkpoints6 → oriongeno_mammals}/config.json RENAMED Viewed

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checkpoints/{checkpoints1 → oriongeno_mammals}/pytorch_model.bin RENAMED Viewed

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checkpoints/{checkpoints5 → oriongeno_mammals}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints5 → oriongeno_mammals}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints5 → oriongeno_mammals}/vocab.txt RENAMED Viewed

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checkpoints/{checkpoints4 → oriongeno_other_vertebrates}/config.json RENAMED Viewed

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checkpoints/{checkpoints4 → oriongeno_other_vertebrates}/pytorch_model.bin RENAMED Viewed

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checkpoints/{checkpoints6 → oriongeno_other_vertebrates}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints6 → oriongeno_other_vertebrates}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints6 → oriongeno_other_vertebrates}/vocab.txt RENAMED Viewed

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checkpoints/{checkpoints8 → oriongeno_plants}/config.json RENAMED Viewed

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checkpoints/{checkpoints8 → oriongeno_plants}/pytorch_model.bin RENAMED Viewed

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checkpoints/{checkpoints7 → oriongeno_plants}/special_tokens_map.json RENAMED Viewed

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checkpoints/{checkpoints7 → oriongeno_plants}/tokenizer_config.json RENAMED Viewed

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checkpoints/{checkpoints7 → oriongeno_plants}/vocab.txt RENAMED Viewed

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