johnnas12/e5-galaxy-finetuned

SentenceTransformer based on intfloat/e5-base-v2

This is a sentence-transformers model finetuned from intfloat/e5-base-v2. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.

Model Details

Model Description

• Model Type: Sentence Transformer
• Base model: intfloat/e5-base-v2
• Maximum Sequence Length: 512 tokens
• Output Dimensionality: 768 dimensions
• Similarity Function: Cosine Similarity

Model Sources

• Documentation: Sentence Transformers Documentation
• Repository: Sentence Transformers on GitHub
• Hugging Face: Sentence Transformers on Hugging Face

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
  (2): Normalize()
)

Usage

Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

pip install -U sentence-transformers

Then you can load this model and run inference.

from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
sentences = [
    'query: Which tool can be used to qiime2 diversity pcoa-biplot?',
    'passage: qiime2 diversity pcoa-biplot. Principal Coordinate Analysis Biplot. QIIME 2: diversity pcoa-biplot ============================== Principal Coordinate Analysis Biplot   Outputs: -------- :biplot.qza: The resulting PCoA matrix.  |    Description: ------------ Project features into a principal coordinates matrix. The features used should be the features used to compute the distance matrix. It is recommended that these variables be normalized in cases of dimensionally heterogeneous physical variables.   |',
    'passage: Manipulate loom object. Add layers, or row/column attributes to a loom file. This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]

Training Details

Training Dataset

Unnamed Dataset

• Size: 68,840 training samples
• Columns: sentence_0 and sentence_1
• Approximate statistics based on the first 1000 samples:

  	sentence_0	sentence_1
  type	string	string
  details	min: 7 tokens mean: 14.66 tokens max: 42 tokens	min: 21 tokens mean: 298.3 tokens max: 512 tokens

• Samples:

  sentence_0	sentence_1
  query: Tool for vcf/bcf conversion, view, subset and filter vcf/bcf files	passage: bcftools view. VCF/BCF conversion, view, subset and filter VCF/BCF files. ===================================== bcftools view ===================================== VCF/BCF conversion, view, subset and filter VCF/BCF files. Region Selections ----------------- Regions can be specified in a VCF, BED, or tab-delimited file (the default). The columns of the tab-delimited file are: CHROM, POS, and, optionally, POS_TO, where positions are 1-based and inclusive. Uncompressed files are stored in memory, while bgzip-compressed and tabix-indexed region files are streamed. Note that sequence names must match exactly, "chr20" is not the same as "20". Also note that chromosome ordering in FILE will be respected, the VCF will be processed in the order in which chromosomes first appear in FILE. However, within chromosomes, the VCF will always be processed in ascending genomic coordinate order no matter what order they appear in FILE. Note that overlapping regions in FILE can resul...
  query: Tool for de novo assembly of rna-seq data	passage: Trinity. de novo assembly of RNA-Seq data. Trinity_ assembles transcript sequences from Illumina RNA-Seq data. .. _Trinity: http://trinityrnaseq.github.io
  query: I want to das tool in Galaxy	passage: DAS Tool. for genome-resolved metagenomics. What it does ============ DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Inputs ====== - Bins: Tab-separated files of contig-IDs and bin-IDs. Contigs to bin file example: :: Contig_1 bin.01 Contig_8 bin.01 Contig_42 bin.02 Contig_49 bin.03 - Contigs: Assembled contigs in fasta format: :: >Contig_1 ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA... >Contig_2 GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG... - [Optional] Proteins: Predicted proteins in prodigal fasta format. The header contains contig-ID and gene number: :: >Contig_1_1 MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG... >Contig_1_2 MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN... Outputs ======= - Summary of output bins including quality and c...

• Loss: MultipleNegativesRankingLoss with these parameters:

  {
      "scale": 20.0,
      "similarity_fct": "cos_sim"
  }
  

Training Hyperparameters

Non-Default Hyperparameters

• per_device_train_batch_size: 16
• per_device_eval_batch_size: 16
• num_train_epochs: 4
• multi_dataset_batch_sampler: round_robin

All Hyperparameters

Click to expand

• overwrite_output_dir: False
• do_predict: False
• eval_strategy: no
• prediction_loss_only: True
• per_device_train_batch_size: 16
• per_device_eval_batch_size: 16
• per_gpu_train_batch_size: None
• per_gpu_eval_batch_size: None
• gradient_accumulation_steps: 1
• eval_accumulation_steps: None
• torch_empty_cache_steps: None
• learning_rate: 5e-05
• weight_decay: 0.0
• adam_beta1: 0.9
• adam_beta2: 0.999
• adam_epsilon: 1e-08
• max_grad_norm: 1
• num_train_epochs: 4
• max_steps: -1
• lr_scheduler_type: linear
• lr_scheduler_kwargs: {}
• warmup_ratio: 0.0
• warmup_steps: 0
• log_level: passive
• log_level_replica: warning
• log_on_each_node: True
• logging_nan_inf_filter: True
• save_safetensors: True
• save_on_each_node: False
• save_only_model: False
• restore_callback_states_from_checkpoint: False
• no_cuda: False
• use_cpu: False
• use_mps_device: False
• seed: 42
• data_seed: None
• jit_mode_eval: False
• use_ipex: False
• bf16: False
• fp16: False
• fp16_opt_level: O1
• half_precision_backend: auto
• bf16_full_eval: False
• fp16_full_eval: False
• tf32: None
• local_rank: 0
• ddp_backend: None
• tpu_num_cores: None
• tpu_metrics_debug: False
• debug: []
• dataloader_drop_last: False
• dataloader_num_workers: 0
• dataloader_prefetch_factor: None
• past_index: -1
• disable_tqdm: False
• remove_unused_columns: True
• label_names: None
• load_best_model_at_end: False
• ignore_data_skip: False
• fsdp: []
• fsdp_min_num_params: 0
• fsdp_config: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
• fsdp_transformer_layer_cls_to_wrap: None
• accelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
• deepspeed: None
• label_smoothing_factor: 0.0
• optim: adamw_torch
• optim_args: None
• adafactor: False
• group_by_length: False
• length_column_name: length
• ddp_find_unused_parameters: None
• ddp_bucket_cap_mb: None
• ddp_broadcast_buffers: False
• dataloader_pin_memory: True
• dataloader_persistent_workers: False
• skip_memory_metrics: True
• use_legacy_prediction_loop: False
• push_to_hub: False
• resume_from_checkpoint: None
• hub_model_id: None
• hub_strategy: every_save
• hub_private_repo: None
• hub_always_push: False
• gradient_checkpointing: False
• gradient_checkpointing_kwargs: None
• include_inputs_for_metrics: False
• include_for_metrics: []
• eval_do_concat_batches: True
• fp16_backend: auto
• push_to_hub_model_id: None
• push_to_hub_organization: None
• mp_parameters:
• auto_find_batch_size: False
• full_determinism: False
• torchdynamo: None
• ray_scope: last
• ddp_timeout: 1800
• torch_compile: False
• torch_compile_backend: None
• torch_compile_mode: None
• dispatch_batches: None
• split_batches: None
• include_tokens_per_second: False
• include_num_input_tokens_seen: False
• neftune_noise_alpha: None
• optim_target_modules: None
• batch_eval_metrics: False
• eval_on_start: False
• use_liger_kernel: False
• eval_use_gather_object: False
• average_tokens_across_devices: False
• prompts: None
• batch_sampler: batch_sampler
• multi_dataset_batch_sampler: round_robin

Training Logs

Epoch	Step	Training Loss
0.1162	500	0.0921
0.2324	1000	0.0066
0.3486	1500	0.0062
0.4648	2000	0.0081
0.5810	2500	0.0073
0.6972	3000	0.0091
0.8134	3500	0.0053
0.9296	4000	0.0083
1.0458	4500	0.0073
1.1620	5000	0.0059
1.2782	5500	0.0068
1.3944	6000	0.0047
1.5106	6500	0.0077
1.6268	7000	0.0071
1.7430	7500	0.0067
1.8592	8000	0.0069
1.9754	8500	0.0077
2.0916	9000	0.0064
2.2078	9500	0.0073
2.3240	10000	0.0075
2.4402	10500	0.0049
2.5564	11000	0.0071
2.6726	11500	0.0075
2.7888	12000	0.0078
2.9050	12500	0.0086
3.0211	13000	0.0069
3.1373	13500	0.0052
3.2535	14000	0.0065
3.3697	14500	0.0066
3.4859	15000	0.0068
3.6021	15500	0.0079
3.7183	16000	0.0077
3.8345	16500	0.0066
3.9507	17000	0.0046

Framework Versions

• Python: 3.12.8
• Sentence Transformers: 3.4.1
• Transformers: 4.49.0
• PyTorch: 2.6.0+cu124
• Accelerate: 1.4.0
• Datasets: 3.3.2
• Tokenizers: 0.21.0

Citation

BibTeX

Sentence Transformers

@inproceedings{reimers-2019-sentence-bert,
    title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
    author = "Reimers, Nils and Gurevych, Iryna",
    booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
    month = "11",
    year = "2019",
    publisher = "Association for Computational Linguistics",
    url = "https://arxiv.org/abs/1908.10084",
}

MultipleNegativesRankingLoss

@misc{henderson2017efficient,
    title={Efficient Natural Language Response Suggestion for Smart Reply},
    author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
    year={2017},
    eprint={1705.00652},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}