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| Ecosystem | 1 | 1 |
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| Pricing | Free | Free |
| Capabilities | 6 decomposed | 9 decomposed |
| Times Matched | 0 | 0 |
Predicts masked amino acid tokens in protein sequences using a 33-layer transformer encoder trained on 250M unlabeled protein sequences from UniRef50. The model uses bidirectional attention to infer missing residues by learning contextual patterns from evolutionary and structural relationships encoded in the training corpus. Outputs probability distributions over the 20 standard amino acids plus special tokens for each masked position.
Unique: Trained on 250M unlabeled UniRef50 sequences with 33 transformer layers (650M parameters) using masked language modeling, capturing evolutionary and functional relationships at scale — larger and more diverse training corpus than earlier ESM-1b (1.2B sequences, 33 layers) and competitive with AlphaFold2's sequence understanding but optimized specifically for token-level prediction rather than structure
vs alternatives: Outperforms ProtBERT and ESM-1b on masked token prediction accuracy due to larger model capacity and training data, while remaining computationally efficient enough for real-time inference on modest hardware compared to full structure prediction models like OmegaFold
Extracts dense vector representations (embeddings) from protein sequences by passing them through the 33-layer transformer encoder and extracting hidden states at specified layers. These embeddings capture semantic and functional properties of proteins and can be used as input features for downstream ML tasks like classification, clustering, or similarity search. Supports per-token embeddings (one vector per amino acid) or sequence-level pooling (single vector per protein).
Unique: Provides 1280-dimensional embeddings from a 650M-parameter transformer trained on 250M diverse protein sequences, capturing both sequence-level and structural patterns — embeddings are shown to correlate with protein function and structure better than sequence-based features alone, and the model's scale enables transfer learning to low-data protein engineering tasks
vs alternatives: Produces more functionally-informative embeddings than ProtBERT (due to larger training data and model size) and more computationally efficient than structure-based embeddings from AlphaFold2 while maintaining competitive performance on downstream tasks like remote homology detection
Processes multiple protein sequences in parallel through the transformer encoder using batching and dynamic padding to maximize GPU utilization. Automatically handles variable-length sequences by padding to the longest sequence in the batch and masking padded positions during attention computation. Supports both CPU and GPU inference with automatic device selection and memory-efficient gradient checkpointing for large batches.
Unique: Implements dynamic padding with attention masking and supports gradient checkpointing for memory-efficient batching — the model's 33-layer depth makes checkpointing particularly valuable, reducing peak memory by ~50% at the cost of ~20% inference latency, enabling batch sizes 2-3x larger than naive batching
vs alternatives: More memory-efficient than naive transformer batching due to gradient checkpointing support, and faster than sequential inference by 10-50x depending on batch size and hardware, though slower per-sequence than smaller models like ProtBERT due to the larger 650M parameter count
Converts raw protein sequences (strings of amino acid letters) into numerical token IDs compatible with the transformer model using a learned vocabulary of 33 tokens (20 standard amino acids + special tokens for padding, masking, unknown, and start/end markers). Handles edge cases like lowercase letters, non-standard amino acids (X, U, O), and sequence length constraints by truncating or padding to a configurable maximum length (default 1024 tokens).
Unique: Uses a 33-token vocabulary specifically designed for protein sequences (20 amino acids + 13 special tokens) with learned token embeddings from the 250M-sequence training corpus — the vocabulary is optimized for evolutionary and functional signal rather than generic subword tokenization, enabling more efficient representation of protein patterns
vs alternatives: More protein-specific than generic BPE tokenizers used in ProtBERT, and simpler than multi-sequence alignment tokenization used in MSA-Transformer, making it faster to tokenize while maintaining competitive downstream task performance
Predicts amino acid identities at masked positions by computing logits over the 20 standard amino acids using the transformer's contextual understanding of surrounding residues. The model learns to infer missing positions by leveraging evolutionary patterns, structural constraints, and functional requirements encoded in the 250M-sequence training corpus. Outputs ranked predictions with confidence scores (softmax probabilities) for each masked position.
Unique: Leverages 33 transformer layers trained on 250M diverse protein sequences to capture multi-scale evolutionary and functional patterns — the model learns implicit structural constraints and functional requirements without explicit 3D structure input, enabling predictions that correlate with experimentally-validated amino acid substitutions better than simple conservation-based methods
vs alternatives: More accurate than position-specific scoring matrices (PSSMs) or conservation-based methods for predicting functional amino acids, and faster than structure-based design tools like Rosetta while maintaining competitive performance on protein engineering benchmarks
Enables fine-tuning of the pre-trained ESM2 model on custom protein datasets for domain-specific tasks (e.g., predicting protein properties, classifying protein families, or optimizing sequences for specific functions). The model's 33-layer transformer encoder can be partially or fully fine-tuned using standard PyTorch/TensorFlow training loops, with support for gradient accumulation, mixed precision training, and learning rate scheduling to optimize convergence on limited labeled data.
Unique: The pre-trained 650M-parameter model provides strong initialization for protein understanding, enabling effective fine-tuning with as few as 100-500 labeled examples — the model's 33-layer depth and 250M-sequence training corpus encode rich protein knowledge that transfers well to downstream tasks, reducing data requirements compared to training from scratch
vs alternatives: Requires 10-100x fewer labeled examples than training a protein model from scratch, and outperforms shallow baselines (logistic regression on sequence features) by 20-40% on typical protein property prediction tasks, though full fine-tuning is more computationally expensive than parameter-efficient methods like LoRA
Converts English text passages into 1024-dimensional dense vector embeddings using a fine-tuned BERT architecture with contrastive learning objectives. The model applies mean pooling over token representations and normalizes outputs to unit vectors, enabling efficient similarity computations via cosine distance or dot product. Trained on diverse text pairs using in-batch negatives and hard negative mining to optimize for semantic relevance across retrieval and ranking tasks.
Unique: Achieves top-tier MTEB ranking (56.9 on NDCG@10 for retrieval) through contrastive pre-training on 430M text pairs with hard negatives, then instruction-tuning on 50+ retrieval/ranking tasks — architectural choice of mean pooling + L2 normalization enables efficient batch similarity computation without query-specific fine-tuning
vs alternatives: Outperforms OpenAI's text-embedding-3-small on MTEB retrieval benchmarks while remaining fully open-source and deployable on-premise without API costs
Computes cosine similarity between pairs of embedded texts by taking the dot product of L2-normalized vectors, producing scores in range [-1, 1] where 1.0 indicates semantic equivalence. The normalization step is built into the embedding generation pipeline, allowing single-pass similarity computation without additional normalization overhead. Supports batch processing of multiple query-document pairs simultaneously for throughput optimization.
Unique: Embeddings are pre-normalized to unit vectors during generation, eliminating the need for post-hoc normalization in similarity computation — this design choice reduces latency for high-throughput ranking scenarios by ~15% compared to models requiring explicit normalization
vs alternatives: Faster similarity computation than sparse BM25 for large-scale ranking due to vector normalization baked into the model, while maintaining competitive NDCG scores on MTEB benchmarks
bge-large-en-v1.5 scores higher at 52/100 vs esm2_t33_650M_UR50D at 45/100.
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Generates fixed-dimensional embeddings compatible with FAISS, Annoy, HNSW, and other ANN index structures for sub-linear retrieval over large document collections. The 1024-dimensional output and L2-normalization enable efficient index construction and querying; typical index sizes are 4 bytes per dimension per document. Supports both exact brute-force search and approximate methods with configurable recall-speed tradeoffs.
Unique: 1024-dimensional vectors with L2-normalization are optimized for HNSW graph construction, achieving 95%+ recall at 10ms latency on 1M-document indices — this dimensionality-normalization combination balances index size, construction time, and query latency better than higher-dimensional alternatives
vs alternatives: Smaller index footprint than OpenAI embeddings (1024 vs 1536 dims) while maintaining superior MTEB retrieval scores, reducing storage and memory costs for large-scale deployments
Provides pre-converted model weights in PyTorch, ONNX, and SafeTensors formats, enabling deployment across diverse inference runtimes without custom conversion pipelines. ONNX export includes quantization-friendly graph structures; SafeTensors format enables fast weight loading and memory-mapped access. Supports both CPU and GPU inference with automatic device selection via sentence-transformers library.
Unique: Provides SafeTensors format alongside ONNX and PyTorch, enabling secure weight loading without code execution and memory-mapped access for efficient large-model inference — architectural choice to support three formats simultaneously reduces friction for diverse deployment targets
vs alternatives: Multi-format export reduces deployment friction compared to models requiring custom conversion pipelines; SafeTensors format provides security advantages over pickle-based PyTorch checkpoints
Accepts optional instruction prefixes (e.g., 'Represent this document for retrieval:') that guide embedding generation toward specific downstream tasks without model fine-tuning. Instructions are concatenated with input text and processed through the same BERT encoder, allowing single-model deployment across retrieval, clustering, and classification tasks. Instruction tuning was performed on 50+ diverse tasks during training, enabling zero-shot adaptation to new domains.
Unique: Instruction tuning on 50+ diverse tasks enables zero-shot task adaptation without fine-tuning, allowing single-model deployment across retrieval, clustering, and classification — architectural choice to embed instructions in the input stream rather than as separate model parameters reduces deployment complexity
vs alternatives: Enables task-specific embeddings without separate models or fine-tuning, reducing deployment overhead compared to task-specific embedding models while maintaining competitive performance on MTEB benchmarks
Processes multiple text inputs simultaneously through vectorized matrix operations, achieving 10-50x throughput improvement over sequential embedding generation. Batch size is configurable (typical: 32-256) and automatically optimized based on available GPU memory. Supports dynamic batching where variable-length sequences are padded to the longest sequence in the batch, minimizing wasted computation.
Unique: Dynamic batching with automatic padding enables 10-50x throughput improvement over sequential processing while maintaining numerical consistency — architectural choice to vectorize padding and masking operations in the BERT encoder reduces per-token overhead
vs alternatives: Batch processing throughput exceeds OpenAI's embedding API (which charges per-token) by 5-10x on large corpora, enabling cost-effective offline embedding pipelines
Model includes pre-computed evaluation results on MTEB (Massive Text Embedding Benchmark) covering 56 tasks across retrieval, clustering, semantic similarity, and reranking domains. Results are published on HuggingFace model card with detailed breakdowns by task category, enabling direct comparison against 200+ alternative embedding models. Evaluation methodology is standardized and reproducible via the MTEB library.
Unique: Ranks #1 on MTEB retrieval leaderboard (56.9 NDCG@10) through instruction-tuned contrastive learning on 430M pairs — architectural choice to optimize for MTEB tasks during training enables transparent performance comparison against 200+ alternatives
vs alternatives: Achieves top MTEB ranking while remaining fully open-source, providing transparent performance comparison unavailable for proprietary APIs like OpenAI embeddings
Model is compatible with Text Embeddings Inference (TEI) server, a Rust-based inference engine optimized for embedding workloads with features like batching, quantization, and multi-GPU support. TEI automatically handles model loading, request routing, and response formatting, enabling production-grade embedding APIs without custom inference code. Supports both HTTP and gRPC interfaces.
Unique: TEI compatibility enables production-grade embedding APIs without custom inference code — architectural choice to support TEI's Rust-based engine provides 2-3x throughput improvement over Python-based servers while maintaining model compatibility
vs alternatives: TEI deployment provides higher throughput and lower latency than custom Python inference servers, enabling cost-effective embedding APIs at scale
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