diff --git a/esm_scripts/__init__.py b/esm_scripts/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc
--- /dev/null
+++ b/esm_scripts/__init__.py
@@ -0,0 +1 @@
+
diff --git a/esm_scripts/atlas/README.md b/esm_scripts/atlas/README.md
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+# ESM Metagenomic Atlas
+
+The [ESM Metagenomic Atlas](https://esmatlas.com) is a resource of more than 700 million metagenomic protein structures predicted by ESMFold.
+See our [blog post](https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/) to learn more.
+
+The first `v0` version of the Atlas was released on November 1st 2022,
+corresponding to the sequences in the `2022_05` release of the MGnify protein database described [here](https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2022_05/README.txt).
+An update `v2023_02` was released on March 17th 2023, corresponding to the sequences in the `2023_02` release of the MGnify protein database described [here](https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2023_02/).
+
+Here we provide bulk download instructions for the tarballs of predicted structures, as well as foldseek databases, and LM embeddings for every sequence in the Atlas.
+
+The structures in the ESM Metagenomic Atlas were predicted with `esm.pretrained.esmfold_v0()` for Atlas `v0`, while Atlas `v2023_02` used `esm.pretrained.esmfold_v1()`.
+We find that protein structures with predicted LDDT > 0.7 and predict TM > 0.7 to be both reasonably well structured and interesting.
+Therefore, we provide both the small set of "high confidence" metagenomic structures from Atlas `v0`, as well as the full set.
+The small set of structures is built from taking a 30% sequence identity clustering of MGnify90 `2022_05`, and using the best structure from each cluster.
+The best structure is selected using the score pTM * pLDDT.
+
+The high confidence structures are around 1TB in size.
+
+The full database is available as PDB structures and is 15TB in size for `v0`.
+
+As an entrypoint into the database, the metadata is available as a small (~25 GB) file [metadata.sqlite](https://dl.fbaipublicfiles.com/esmatlas/v2023_02/metadata-rc2.sqlite.gz) / [metadata.parquet](https://dl.fbaipublicfiles.com/esmatlas/v2023_02/metadata-rc2.parquet).
+You can load the file with pandas: `df = pd.read_parquet('metadata.parquet')`.
+The dataframe has 773,846,840 records, and the file size is around 16GB.
+This dataframe has 10 columns:
+- `id` is the MGnify ID
+- `ptm` is the predicted TM score
+- `plddt` is the predicted average lddt
+- `num_conf` is the number of residues with plddt > 0.7
+- `len` is the total residues in the protein
+- `is_fragment` indicates whether the protein sequence is identified as a fragment in the MGnify90 sequence database.
+- `sequenceChecksum` is the CRC64 hash of the sequence. Can be used for cheaper lookups.
+- `esmfold_version` is the version of ESMFold, matching the model accessible as `esm.pretrained.esmfold_v{0,1}`
+- `atlas_version` is the Atlas version where this structure first appeared. Note: some of the predictions appearing for the first time in `v0` are also part of Atlas `v2023_02`.
+- `sequence_dbs` is the metagenomic source databases where this structure is part of, as `MGnify90_2022_05`, comma-separated if it exists in more than one release, as `MGnify90_2022_05,MGnify90_2023_02`.
+
+Proteins longer than 1280 residues were not folded. To select only the records without missing structures use  `df[~df.plddt.isna()]`.
+
+We recommend using `s5cmd` or `aria2c` to download files (can be installed via conda package manager).
+To download any of the structures provided, you can use this `aria2c` command:
+```
+aria2c --dir=/path/to/download/to --input-file=url-file-provided.txt
+```
+
+
+# Full database
+
+We separate the database by pTM and pLDDT.
+This will allow you to download structures based on your needs - for example you can choose to download only the most high confidence structures.
+Structures are provided by the bins given in this repo under [v0/full/bins.txt](v0/full/bins.txt) and [v2023_02/full/bins.txt](v2023_02/full/bins.txt).
+For example, the foldseek database containing ptm from 0.60 to 0.70 and plddt from 0.80 to 0.90 is named `tm_.60_.70_plddt_.80_.90.DB`.
+The data are given as bundles of 500k or 1M structures each.
+
+* **Bulk Predicted structures**: see `{v0,v2023_02}/full/tarballs/`. The URLs for all shards of a single bundle will be in e.g. [v0/full/tarballs/tm_.60_.70_plddt_.80_.90.txt](v0/full/tarballs/tm_.60_.70_plddt_.80_.90.txt). The URLs for all tarballs across bins and their shards is available under `{v0,v2023_02}/full/tarballs.txt`.
+* **Foldseek DBs** `{v0,v2023_02}/full/foldseekdb/` and `{v0,v2023_02}/full/foldseekdb.txt`
+* **Bulk Embeddings (NEW)** under `{v0,v2023_02}/full/esm2_embeddings/` and `{v0,v2023_02}/full/esm2_embeddings.txt`.
+  * Note: Individual LM embeddings can be fetched via the API endpoint `/fetchEmbedding/ESM2/:id` as described on <https://esmatlas.com/about#api>
+
+
+# High confidence MGnify30 structures
+
+The high confidence MGnify30 structures are built using this procedure:
+1. MGnify90 is clustered down to 30% sequence similarity with `mmseqs easy-linclust --kmer-per-seq 100 -cluster-mode 2 --cov-mode 1 -c 0.8`.
+1. Structures are filtered to >0.7 pTM and pLDDT
+1. Structures are sorted by `pTM * pLDDT` and the best from each cluster is chosen as the representative.
+
+
+We provide the urls to v0 in [v0/highquality_clust30/tarballs.txt](v0/highquality_clust30/tarballs.txt) and [v0/highquality_clust30/foldseekdb.txt](v0/highquality_clust30/foldseekdb.txt).
+
+As a reminder, please use `aria2c --dir=/path/to/download/to --input-file=v0/highquality_clust30/foldseekdb.txt` to download the foldseek database
+
+The sequences corresponding to the high confidence structures can be downloaded from <https://dl.fbaipublicfiles.com/esmatlas/v0/highquality_clust30/highquality_clust30.fasta>.
+
+# Citation
+If you use any of the ESM Metagenomic Atlas data in your work, please cite
+
+
+```bibtex
+@article{lin2022evolutionary,
+  title={Evolutionary-scale prediction of atomic level protein structure with a language model},
+  author={Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and Smetanin, Nikita and Verkuil, Robert and Kabeli, Ori and Shmueli, Yaniv and dos Santos Costa, Allan and Fazel-Zarandi, Maryam and Sercu, Tom and Candido, Salvatore and Rives, Alexander},
+  year={2022},
+  journal={bioRxiv},
+  note={bioRxiv 2022.07.20.500902},
+  url={https://doi.org/10.1101/2022.07.20.500902},
+}
+```
+
+## License <a name="license"></a>
+
+ESM Metagenomic Atlas (also referred to as “ESM Metagenomic Structure Atlas” or “ESM Atlas”) data is available under a CC BY 4.0 license for academic and commercial use. Copyright (c) Meta Platforms, Inc. All Rights Reserved. Use of the ESM Metagenomic Atlas data is subject to the Meta Open Source [Terms of Use](https://opensource.fb.com/legal/terms/) and [Privacy Policy](https://opensource.fb.com/legal/privacy/).
+
+If you make use of a structure predicted by ESMFold, please cite the following paper:
+
+```
+Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Robert Verkuil, Ori Kabeli, Yaniv Shmueli, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives.
+Evolutionary-scale prediction of atomic level protein structure with a language model.
+Science 379, 6637 (2023).
+https://www.science.org/doi/abs/10.1126/science.ade2574
+```
diff --git a/esm_scripts/atlas/v0/full/bins.txt b/esm_scripts/atlas/v0/full/bins.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54ab0908a6ae6a5f031c4594d3aaffdd15e40e4f
--- /dev/null
+++ b/esm_scripts/atlas/v0/full/bins.txt
@@ -0,0 +1,72 @@
+tm_.40_.50_plddt_.40_.50
+tm_.40_.50_plddt_.50_.60
+tm_.40_.50_plddt_.60_.70
+tm_.40_.50_plddt_.70_.80
+tm_.40_.50_plddt_.80_.90
+tm_.40_.50_plddt_.90_1
+tm_.40_.50_plddt_0_.40
+tm_.50_.60_plddt_.40_.50
+tm_.50_.60_plddt_.50_.60
+tm_.50_.60_plddt_.60_.70
+tm_.50_.60_plddt_.70_.80
+tm_.50_.60_plddt_.80_.90
+tm_.50_.60_plddt_.90_1
+tm_.50_.60_plddt_0_.40
+tm_.60_.70_plddt_.40_.50
+tm_.60_.70_plddt_.50_.60
+tm_.60_.70_plddt_.60_.70
+tm_.60_.70_plddt_.70_.80
+tm_.60_.70_plddt_.80_.90
+tm_.60_.70_plddt_.90_1
+tm_.60_.70_plddt_0_.40
+tm_.70_.80_plddt_.40_.50
+tm_.70_.80_plddt_.50_.60
+tm_.70_.80_plddt_.60_.70
+tm_.70_.80_plddt_.70_.80
+tm_.70_.80_plddt_.80_.90
+tm_.70_.80_plddt_.90_1
+tm_.70_.80_plddt_0_.40
+tm_.80_.90_plddt_.50_.60
+tm_.80_.90_plddt_.60_.70
+tm_.80_.90_plddt_.70_.80
+tm_.80_.90_plddt_.80_.90
+tm_.80_.90_plddt_.90_1
+tm_.90_1_plddt_.70_.80
+tm_.90_1_plddt_.80_.90
+tm_.90_1_plddt_.90_1
+tm_0_.40_plddt_.40_.50
+tm_0_.40_plddt_.50_.60
+tm_0_.40_plddt_.60_.70
+tm_0_.40_plddt_.70_.80
+tm_0_.40_plddt_.80_.90
+tm_0_.40_plddt_.90_1
+tm_0_.40_plddt_0_.40
+backfill_v0_tm_.40_.50_plddt_.40_.50
+backfill_v0_tm_.50_.60_plddt_0_.40    
+backfill_v0_tm_.70_.80_plddt_.70_.80  
+backfill_v0_tm_.90_1_plddt_.80_.90
+backfill_v0_tm_.40_.50_plddt_.50_.60  
+backfill_v0_tm_.60_.70_plddt_.40_.50  
+backfill_v0_tm_.70_.80_plddt_.80_.90  
+backfill_v0_tm_.90_1_plddt_.90_1
+backfill_v0_tm_.40_.50_plddt_.60_.70  
+backfill_v0_tm_.60_.70_plddt_.50_.60  
+backfill_v0_tm_.70_.80_plddt_.90_1    
+backfill_v0_tm_0_.40_plddt_.40_.50
+backfill_v0_tm_.40_.50_plddt_0_.40    
+backfill_v0_tm_.60_.70_plddt_.60_.70  
+backfill_v0_tm_.80_.90_plddt_.60_.70  
+backfill_v0_tm_0_.40_plddt_.50_.60
+backfill_v0_tm_.50_.60_plddt_.40_.50  
+backfill_v0_tm_.60_.70_plddt_.70_.80  
+backfill_v0_tm_.80_.90_plddt_.70_.80  
+backfill_v0_tm_0_.40_plddt_0_.40
+backfill_v0_tm_.50_.60_plddt_.50_.60  
+backfill_v0_tm_.60_.70_plddt_.80_.90  
+backfill_v0_tm_.80_.90_plddt_.80_.90
+backfill_v0_tm_.50_.60_plddt_.60_.70  
+backfill_v0_tm_.70_.80_plddt_.50_.60  
+backfill_v0_tm_.80_.90_plddt_.90_1
+backfill_v0_tm_.50_.60_plddt_.70_.80  
+backfill_v0_tm_.70_.80_plddt_.60_.70  
+backfill_v0_tm_.90_1_plddt_.70_.80
diff --git a/esm_scripts/atlas/v0/full/esm2_embeddings.txt b/esm_scripts/atlas/v0/full/esm2_embeddings.txt
new file mode 100644
index 0000000000000000000000000000000000000000..628a950e06ac1dd1baf121d958975b9f885b810f
--- /dev/null
+++ b/esm_scripts/atlas/v0/full/esm2_embeddings.txt
@@ -0,0 +1,673 @@
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diff --git a/esm_scripts/download_weights.sh b/esm_scripts/download_weights.sh
new file mode 100644
index 0000000000000000000000000000000000000000..c95247ceaca7db52af476625d58b4e74d558b8de
--- /dev/null
+++ b/esm_scripts/download_weights.sh
@@ -0,0 +1,65 @@
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+#! /bin/sh
+# Usage: bash <repo>/esm/scripts/download_weights.sh /path/to/weights/
+# re run the command to continue downloading incomplete files.
+echo $0
+run_dir=$(readlink -f $(dirname $0)) ;
+
+if [[ "$(which aria2c)" == "" ]];then
+  echo aria2c is required for downloading!
+  exit 1
+fi
+
+for _sh_exec in /bin/sh bash zsh;do
+  # only bash and zsh are tested.
+  _sh_exec=$(which ${_sh_exec})
+  if [[ "$(${_sh_exec} --version)" =~ "bash" || "$(${_sh_exec} --version)" =~ "zsh" ]];then
+    echo $(which ${_sh_exec});
+    break
+  fi
+done
+
+model_pth=$1
+if [[ "$model_pth" == "" ]];then
+  model_pth=$PWD
+fi
+
+mkdir -p $model_pth/checkpoints
+
+pushd $model_pth/checkpoints
+cat $run_dir/../README.md |grep -e '^|' |grep -e 'fair-esm/models' |tr -d '|' | \
+  awk 'BEGIN{print "set -e"};
+  {
+      # read urls starts with https
+      split($0,arr,"https");
+      url="https"arr[2];
+
+      # remove blank spaces after url string
+      split(url,url_arr," ")
+      url=url_arr[1]
+
+      # guessing regression pt url
+      url_regression=url;
+      sub("models","regression",url_regression);
+      sub(".pt","-contact-regression.pt",url_regression);
+
+      # downloading weight
+      url_basename_idx=split(url,url_arr,"/")
+      url_basename=url_arr[url_basename_idx]
+      print "if [[ ! -f "url_basename" || -f "url_basename".aria2 ]];then echo Download not complete: "url_basename";aria2c -x 10 "url";else echo Download complete: "url_basename";fi"
+
+      # downloading regression, if not existing and through an error, we just ignore it.
+      url_regression_basename_idx=split(url_regression,url_arr,"/")
+      url_regression_basename=url_arr[url_regression_basename_idx]
+      print "if [[ ! -f "url_regression_basename" || -f "url_regression_basename".aria2 ]];then echo Download not complete: "url_regression_basename";aria2c -x 10 "url_regression" 2>/dev/null || echo Never mind. "url_regression_basename" may not exist. ;else echo Download complete: "url_regression_basename";fi"
+
+      }' |$_sh_exec
+
+
+echo "Your model directory is located at \`$(readlink -f ${model_pth})\`."
+
+popd
\ No newline at end of file
diff --git a/esm_scripts/extract.py b/esm_scripts/extract.py
new file mode 100644
index 0000000000000000000000000000000000000000..9e5bcb35a9d91e792b01a0c8f80e4f81885e1f20
--- /dev/null
+++ b/esm_scripts/extract.py
@@ -0,0 +1,140 @@
+#!/usr/bin/env python3 -u
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+#
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+import argparse
+import pathlib
+
+import torch
+
+from esm import Alphabet, FastaBatchedDataset, ProteinBertModel, pretrained, MSATransformer
+
+
+def create_parser():
+    parser = argparse.ArgumentParser(
+        description="Extract per-token representations and model outputs for sequences in a FASTA file"  # noqa
+    )
+
+    parser.add_argument(
+        "model_location",
+        type=str,
+        help="PyTorch model file OR name of pretrained model to download (see README for models)",
+    )
+    parser.add_argument(
+        "fasta_file",
+        type=pathlib.Path,
+        help="FASTA file on which to extract representations",
+    )
+    parser.add_argument(
+        "output_dir",
+        type=pathlib.Path,
+        help="output directory for extracted representations",
+    )
+
+    parser.add_argument("--toks_per_batch", type=int, default=4096, help="maximum batch size")
+    parser.add_argument(
+        "--repr_layers",
+        type=int,
+        default=[-1],
+        nargs="+",
+        help="layers indices from which to extract representations (0 to num_layers, inclusive)",
+    )
+    parser.add_argument(
+        "--include",
+        type=str,
+        nargs="+",
+        choices=["mean", "per_tok", "bos", "contacts"],
+        help="specify which representations to return",
+        required=True,
+    )
+    parser.add_argument(
+        "--truncation_seq_length",
+        type=int,
+        default=1022,
+        help="truncate sequences longer than the given value",
+    )
+
+    parser.add_argument("--nogpu", action="store_true", help="Do not use GPU even if available")
+    return parser
+
+
+def run(args):
+    model, alphabet = pretrained.load_model_and_alphabet(args.model_location)
+    model.eval()
+    if isinstance(model, MSATransformer):
+        raise ValueError(
+            "This script currently does not handle models with MSA input (MSA Transformer)."
+        )
+    if torch.cuda.is_available() and not args.nogpu:
+        model = model.cuda()
+        print("Transferred model to GPU")
+
+    dataset = FastaBatchedDataset.from_file(args.fasta_file)
+    batches = dataset.get_batch_indices(args.toks_per_batch, extra_toks_per_seq=1)
+    data_loader = torch.utils.data.DataLoader(
+        dataset, collate_fn=alphabet.get_batch_converter(args.truncation_seq_length), batch_sampler=batches
+    )
+    print(f"Read {args.fasta_file} with {len(dataset)} sequences")
+
+    args.output_dir.mkdir(parents=True, exist_ok=True)
+    return_contacts = "contacts" in args.include
+
+    assert all(-(model.num_layers + 1) <= i <= model.num_layers for i in args.repr_layers)
+    repr_layers = [(i + model.num_layers + 1) % (model.num_layers + 1) for i in args.repr_layers]
+
+    with torch.no_grad():
+        for batch_idx, (labels, strs, toks) in enumerate(data_loader):
+            print(
+                f"Processing {batch_idx + 1} of {len(batches)} batches ({toks.size(0)} sequences)"
+            )
+            if torch.cuda.is_available() and not args.nogpu:
+                toks = toks.to(device="cuda", non_blocking=True)
+
+            out = model(toks, repr_layers=repr_layers, return_contacts=return_contacts)
+
+            logits = out["logits"].to(device="cpu")
+            representations = {
+                layer: t.to(device="cpu") for layer, t in out["representations"].items()
+            }
+            if return_contacts:
+                contacts = out["contacts"].to(device="cpu")
+
+            for i, label in enumerate(labels):
+                args.output_file = args.output_dir / f"{label}.pt"
+                args.output_file.parent.mkdir(parents=True, exist_ok=True)
+                result = {"label": label}
+                truncate_len = min(args.truncation_seq_length, len(strs[i]))
+                # Call clone on tensors to ensure tensors are not views into a larger representation
+                # See https://github.com/pytorch/pytorch/issues/1995
+                if "per_tok" in args.include:
+                    result["representations"] = {
+                        layer: t[i, 1 : truncate_len + 1].clone()
+                        for layer, t in representations.items()
+                    }
+                if "mean" in args.include:
+                    result["mean_representations"] = {
+                        layer: t[i, 1 : truncate_len + 1].mean(0).clone()
+                        for layer, t in representations.items()
+                    }
+                if "bos" in args.include:
+                    result["bos_representations"] = {
+                        layer: t[i, 0].clone() for layer, t in representations.items()
+                    }
+                if return_contacts:
+                    result["contacts"] = contacts[i, : truncate_len, : truncate_len].clone()
+
+                torch.save(
+                    result,
+                    args.output_file,
+                )
+
+
+def main():
+    parser = create_parser()
+    args = parser.parse_args()
+    run(args)
+
+if __name__ == "__main__":
+    main()
diff --git a/esm_scripts/fold.py b/esm_scripts/fold.py
new file mode 100644
index 0000000000000000000000000000000000000000..482cdc911b2b68c6fc773b7935611764ecd1aa63
--- /dev/null
+++ b/esm_scripts/fold.py
@@ -0,0 +1,205 @@
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+
+from pathlib import Path
+import sys,os
+import argparse
+import logging
+import sys
+import typing as T
+from pathlib import Path
+from timeit import default_timer as timer
+
+import torch
+
+import esm
+from esm.data import read_fasta
+
+logger = logging.getLogger()
+logger.setLevel(logging.INFO)
+
+formatter = logging.Formatter(
+    "%(asctime)s | %(levelname)s | %(name)s | %(message)s",
+    datefmt="%y/%m/%d %H:%M:%S",
+)
+
+console_handler = logging.StreamHandler(sys.stdout)
+console_handler.setLevel(logging.INFO)
+console_handler.setFormatter(formatter)
+logger.addHandler(console_handler)
+
+
+PathLike = T.Union[str, Path]
+
+
+def enable_cpu_offloading(model):
+    from torch.distributed.fsdp import CPUOffload, FullyShardedDataParallel
+    from torch.distributed.fsdp.wrap import enable_wrap, wrap
+
+    torch.distributed.init_process_group(
+        backend="nccl", init_method="tcp://localhost:9999", world_size=1, rank=0
+    )
+
+    wrapper_kwargs = dict(cpu_offload=CPUOffload(offload_params=True))
+
+    with enable_wrap(wrapper_cls=FullyShardedDataParallel, **wrapper_kwargs):
+        for layer_name, layer in model.layers.named_children():
+            wrapped_layer = wrap(layer)
+            setattr(model.layers, layer_name, wrapped_layer)
+        model = wrap(model)
+
+    return model
+
+
+def init_model_on_gpu_with_cpu_offloading(model):
+    model = model.eval()
+    model_esm = enable_cpu_offloading(model.esm)
+    del model.esm
+    model.cuda()
+    model.esm = model_esm
+    return model
+
+
+def create_batched_sequence_datasest(
+    sequences: T.List[T.Tuple[str, str]], max_tokens_per_batch: int = 1024
+) -> T.Generator[T.Tuple[T.List[str], T.List[str]], None, None]:
+
+    batch_headers, batch_sequences, num_tokens = [], [], 0
+    for header, seq in sequences:
+        if (len(seq) + num_tokens > max_tokens_per_batch) and num_tokens > 0:
+            yield batch_headers, batch_sequences
+            batch_headers, batch_sequences, num_tokens = [], [], 0
+        batch_headers.append(header)
+        batch_sequences.append(seq)
+        num_tokens += len(seq)
+
+    yield batch_headers, batch_sequences
+
+
+def create_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-i",
+        "--fasta",
+        help="Path to input FASTA file",
+        type=Path,
+        required=True,
+    )
+    parser.add_argument(
+        "-o", "--pdb", help="Path to output PDB directory", type=Path, required=True
+    )
+    parser.add_argument(
+        "-m", "--model-dir", help="Parent path to Pretrained ESM data directory. ", type=Path, default=None
+    )
+    parser.add_argument(
+        "--num-recycles",
+        type=int,
+        default=None,
+        help="Number of recycles to run. Defaults to number used in training (4).",
+    )
+    parser.add_argument(
+        "--max-tokens-per-batch",
+        type=int,
+        default=1024,
+        help="Maximum number of tokens per gpu forward-pass. This will group shorter sequences together "
+        "for batched prediction. Lowering this can help with out of memory issues, if these occur on "
+        "short sequences.",
+    )
+    parser.add_argument(
+        "--chunk-size",
+        type=int,
+        default=None,
+        help="Chunks axial attention computation to reduce memory usage from O(L^2) to O(L). "
+        "Equivalent to running a for loop over chunks of of each dimension. Lower values will "
+        "result in lower memory usage at the cost of speed. Recommended values: 128, 64, 32. "
+        "Default: None.",
+    )
+    parser.add_argument("--cpu-only", help="CPU only", action="store_true")
+    parser.add_argument("--cpu-offload", help="Enable CPU offloading", action="store_true")
+    return parser
+
+
+def run(args):
+    if not args.fasta.exists():
+        raise FileNotFoundError(args.fasta)
+
+    args.pdb.mkdir(exist_ok=True)
+
+    # Read fasta and sort sequences by length
+    logger.info(f"Reading sequences from {args.fasta}")
+    all_sequences = sorted(read_fasta(args.fasta), key=lambda header_seq: len(header_seq[1]))
+    logger.info(f"Loaded {len(all_sequences)} sequences from {args.fasta}")
+
+    logger.info("Loading model")
+
+    # Use pre-downloaded ESM weights from model_pth.
+    if args.model_dir is not None:
+        # if pretrained model path is available
+        torch.hub.set_dir(args.model_dir)
+
+    model = esm.pretrained.esmfold_v1()
+
+
+    model = model.eval()
+    model.set_chunk_size(args.chunk_size)
+
+    if args.cpu_only:
+        model.esm.float()  # convert to fp32 as ESM-2 in fp16 is not supported on CPU
+        model.cpu()
+    elif args.cpu_offload:
+        model = init_model_on_gpu_with_cpu_offloading(model)
+    else:
+        model.cuda()
+    logger.info("Starting Predictions")
+    batched_sequences = create_batched_sequence_datasest(all_sequences, args.max_tokens_per_batch)
+
+    num_completed = 0
+    num_sequences = len(all_sequences)
+    for headers, sequences in batched_sequences:
+        start = timer()
+        try:
+            output = model.infer(sequences, num_recycles=args.num_recycles)
+        except RuntimeError as e:
+            if e.args[0].startswith("CUDA out of memory"):
+                if len(sequences) > 1:
+                    logger.info(
+                        f"Failed (CUDA out of memory) to predict batch of size {len(sequences)}. "
+                        "Try lowering `--max-tokens-per-batch`."
+                    )
+                else:
+                    logger.info(
+                        f"Failed (CUDA out of memory) on sequence {headers[0]} of length {len(sequences[0])}."
+                    )
+
+                continue
+            raise
+
+        output = {key: value.cpu() for key, value in output.items()}
+        pdbs = model.output_to_pdb(output)
+        tottime = timer() - start
+        time_string = f"{tottime / len(headers):0.1f}s"
+        if len(sequences) > 1:
+            time_string = time_string + f" (amortized, batch size {len(sequences)})"
+        for header, seq, pdb_string, mean_plddt, ptm in zip(
+            headers, sequences, pdbs, output["mean_plddt"], output["ptm"]
+        ):
+            output_file = args.pdb / f"{header}.pdb"
+            output_file.write_text(pdb_string)
+            num_completed += 1
+            logger.info(
+                f"Predicted structure for {header} with length {len(seq)}, pLDDT {mean_plddt:0.1f}, "
+                f"pTM {ptm:0.3f} in {time_string}. "
+                f"{num_completed} / {num_sequences} completed."
+            )
+
+
+def main():
+    parser = create_parser()
+    args = parser.parse_args()
+    run(args)
+
+if __name__ == "__main__":
+    main()
diff --git a/examples/blip2_itm.py b/examples/blip2_itm.py
new file mode 100644
index 0000000000000000000000000000000000000000..3e5e8f293cb272701609d20ba7c235a2f47e4858
--- /dev/null
+++ b/examples/blip2_itm.py
@@ -0,0 +1,520 @@
+import re
+
+import torch
+from PIL import Image
+
+from lavis.models import load_model_and_preprocess
+from lavis.processors import load_processor
+from lavis.common.registry import registry
+from torch.nn import functional as F
+from lavis.models.base_model import all_gather_with_grad, concat_all_gather
+import numpy as np
+import pandas as pd
+import time
+from fuzzywuzzy import process
+from multiprocessing import Pool, Queue, Process
+import difflib
+import Levenshtein
+import os
+# import obonet
+
+
+def fuzzy_match(texts):
+    text_dict = {}
+    for context in texts:
+        if context not in choices:
+            # txt_dict[txt] = process.extractOne(txt, choices)[0]
+            text_dict[context] = difflib.get_close_matches(context, choices, n=1, cutoff=0.)[0]
+    return text_dict
+
+
+def txt_map(x, txt_dict):
+    if type(x) == str:
+        x = eval(x)
+    x_ = []
+    for i in x:
+        if i in txt_dict:
+            x_.append(txt_dict[i])
+        else:
+            x_.append(i)
+    return x_
+
+
+def levenshtein_sim(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+def func(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def stage2_output(df_test):
+    config = {'arch': 'blip2_protein_opt', 'load_finetuned': False,
+              'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage2/20230924220/checkpoint_5.pth',
+              'finetuned': '', 'num_query_token': 32, 'opt_model': 'facebook/opt-2.7b', 'prompt': '',
+              'model_type': 'pretrain_protein_opt2.7b', 'load_pretrained': True, 'freeze_vit': True,
+              'max_protein_len': 600,
+              'max_txt_len': 25}
+
+    model_cls = registry.get_model_class(config['arch'])
+    model = model_cls.from_config(config)
+    model.to(device)
+    model.eval()
+
+    images = df_test['protein'].tolist()
+    n = len(images)
+    bsz = 12
+    iter = n // bsz + 1
+
+    for i in range(iter):
+        image = images[i*bsz: min(n, (i+1)*bsz)]
+        image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+
+        with model.maybe_autocast():
+            _, _, batch_tokens = model.visual_encoder(image)
+            image_embeds = model.ln_vision(batch_tokens.to(device), repr_layers=[model.vis_layers], return_contacts=True)["representations"][model.vis_layers].contiguous()
+
+        image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+        query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+        query_output = model.Qformer.bert(
+            query_embeds=query_tokens,
+            encoder_hidden_states=image_embeds,
+            encoder_attention_mask=image_atts,
+            return_dict=True,
+        )
+
+        inputs_opt = model.opt_proj(query_output.last_hidden_state)
+        atts_opt = torch.ones(inputs_opt.size()[:-1], dtype=torch.long).to(device)
+
+        model.opt_tokenizer.padding_side = "right"
+
+        text = ['' for i in range(len(image))]
+        opt_tokens = model.opt_tokenizer(
+            text,
+            return_tensors="pt",
+            padding="longest",
+            truncation=True,
+            max_length=model.max_txt_len,
+        ).to(device)
+        inputs_embeds = model.opt_model.model.decoder.embed_tokens(opt_tokens.input_ids)
+        inputs_embeds = torch.cat([inputs_opt, inputs_embeds], dim=1)
+        attention_mask = torch.cat([atts_opt, opt_tokens.attention_mask], dim=1)
+        num_txt = 10
+        return_num_txt = 5
+        with model.maybe_autocast():
+            outputs = model.opt_model.generate(inputs_embeds=inputs_embeds, attention_mask=attention_mask, min_length=3,
+                                               max_length=30,
+                                               repetition_penalty=5., num_beams=num_txt, eos_token_id=50118,
+                                               length_penalty=1., num_return_sequences=return_num_txt, temperature=1.)
+        output_text = model.opt_tokenizer.batch_decode(outputs, skip_special_tokens=True)
+        output_text = [text.strip() for text in output_text]
+        output_text_ = []
+        for i in range(len(image)):
+            output_text_.append(';'.join(output_text[i * return_num_txt:(i + 1) * return_num_txt]))
+        with open('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix), 'a+') as f:
+            for i in range(len(image)):
+                f.write(image[i][1] + "|" + output_text_[i] + '\n')
+
+
+cat = 'mf'
+fix = '_mf'
+if cat == 'bp':
+    fix = '_bp'
+if cat == 'cc':
+    fix = '_cc'
+
+# model_pth = {'mf': 'uniprot_swissprot_mf_stage1_epo19.pth', 'bp': 'checkpoint17_GO_swissprot_reviewed_bp_stage1.pth', 'cc': ''}
+
+# graph = obonet.read_obo("http://purl.obolibrary.org/obo/go.obo")
+
+# setup device to use
+device = torch.device("cuda") if torch.cuda.is_available() else "cpu"
+# device = 'cpu'
+
+### Levenshtein similarity
+test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/sim_split/test{}.csv'.format(fix), sep='|')[:10000]
+test['function'] = test['function'].apply(lambda x: x.lower())
+
+
+if os.path.exists('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix)):
+    os.remove('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix))
+print("stage 2 predict starting")
+stage2_output(test)
+print("stage 2 predict completed")
+
+
+
+df_pred = pd.read_csv('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix), sep='|', header=None, on_bad_lines='warn')
+df_pred.columns = ['protein', 'function']
+df_pred = df_pred.drop_duplicates()
+df_pred['function'] = df_pred['function'].apply(lambda x: str(x).split(';'))
+df_pred['function'] = df_pred['function'].apply(lambda x: [i.strip() for i in list(set(x))])
+
+test.columns
+test_g = test.groupby(['protein']).agg({'function': lambda x: list(x)}).reset_index()
+test_g.columns = ['protein', 'label']
+
+data = pd.merge(df_pred, test_g, on='protein', how='left')
+data = data[data['label'].notnull()]
+
+sim = []
+for text, label in zip(data['function'].tolist(), data['label'].tolist()):
+    sim.append(func(text, label))
+
+data['sim'] = sim
+data['avg_score'] = data['sim'].apply(lambda x: round(np.mean(x), 3))
+print("average similarity score: {}".format(round(data['avg_score'].mean(), 3)))
+# data.to_csv('/home/nilin/LAVIS/predict_{}.csv'.format(cat), index=False, sep='|')
+
+
+test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/sim_split/test{}.csv'.format(fix), sep='|', usecols=['function', 'GO_label'])
+test['function'] = test['function'].apply(lambda x: x.lower())
+test = test.drop_duplicates()
+test_dict = dict(zip(test['function'], test['GO_label']))
+val = pd.read_csv('/cluster/home/wenkai/LAVIS/data/sim_split/val{}.csv'.format(fix), sep='|', usecols=['function', 'GO_label'])
+val['function'] = val['function'].apply(lambda x: x.lower())
+val = val.drop_duplicates()
+val_dict = dict(zip(val['function'], val['GO_label']))
+train = pd.read_csv('/cluster/home/wenkai/LAVIS/data/sim_split/train{}.csv'.format(fix), sep='|', usecols=['function', 'GO_label'])
+train['function'] = train['function'].apply(lambda x: x.lower())
+train = train.drop_duplicates()
+train_dict = dict(zip(train['function'], train['GO_label']))
+
+
+# go_des = pd.read_csv('/home/nilin/LAVIS/data/go_descriptions_new.txt', sep='|', header=None)
+# # go_des = pd.read_csv('/home/nilin/LAVIS/data/go_descriptions.txt', sep='|', header=None)
+# go_des.columns = ['GO', 'function']
+# go_des = go_des[go_des['function'].notnull()]
+# go_des['function'] = go_des['function'].apply(lambda x: x.lower())
+# GO_dict = dict(zip(go_des['function'], go_des['GO']))
+GO_dict = {}
+GO_dict.update(train_dict)
+GO_dict.update(val_dict)
+GO_dict.update(test_dict)
+choices = list(GO_dict.keys())
+
+
+
+# data = pd.read_csv('/home/nilin/LAVIS/predict_{}.csv'.format(cat), sep='|')
+data = data.sort_values(by='protein')
+data = data.drop_duplicates('protein')
+# data = data.sample(1000)
+
+### 预测的文本如果不在GO标签词中，则算作最相似的GO标签
+t0 = time.time()
+txt_dict = {}
+
+all_txt = []
+for txt in data['function']:
+    if type(txt) == str:
+        all_txt.extend(eval(txt))
+    else:
+        all_txt.extend(txt)
+all_txt = list(set(all_txt))
+
+n = len(all_txt)
+thread = 20
+size = int(n/thread)
+inds = list(range(0, n, size))
+inds.append(n)
+all_txt_sep = [all_txt[i: min(i+size, n)] for i in inds[:-1]]
+
+with Pool(processes=thread) as pool:
+    result = pool.map(fuzzy_match, all_txt_sep)
+pool.close()
+pool.join()
+for d in result:
+    txt_dict.update(d)
+
+# for txt in all_txt[:10]:
+#     fuzzy_match(txt)
+
+data['function'] = data['function'].apply(lambda x: txt_map(x, txt_dict))
+data['function'] = data['function'].apply(lambda x: list(set(x)))
+print("fuzzy matching time: {}".format(time.time() - t0))
+
+
+
+
+### Find the generated GO text that not included in the ground truth. Then generate pairs between them.
+# pair_a, pair_b = [], []
+# for preds, labels in zip(data['function'], data['label']):
+#     if type(preds) == str:
+#         preds = eval(preds)
+#     if type(labels) == str:
+#         labels = eval(labels)
+#     l = len(labels)
+#     for pred in preds:
+#         if pred not in labels:
+#             pair_a.extend([pred]*l)
+#             pair_b.extend(labels[:])
+# pair_a = [re.sub('_', ':', GO_dict[i]) for i in pair_a]
+# pair_b = [re.sub('_', ':', GO_dict[i]) for i in pair_b]
+# with open('/home/nilin/LAVIS/examples/GO_pair{}.txt'.format(fix), 'w+') as f:
+#     for i, j in zip(pair_a, pair_b):
+#         f.write(i+' '+j+'\n')
+
+
+# load model
+model_config = {'arch': 'blip2_protein', 'load_finetuned': False,
+                'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage1/20230922185/checkpoint_15.pth',
+                'finetuned': '', 'num_query_token': 32, 'prompt': '',
+                'model_type': 'pretrain', 'load_pretrained': True, 'freeze_vit': False,
+                'max_protein_len': 512, 'max_txt_len': 25}
+
+model_cls = registry.get_model_class(model_config['arch'])
+model = model_cls.from_config(model_config)
+model = model.to(device)
+model.eval()
+
+# evaluate
+t0 = time.time()
+proteins = list(data['protein'])
+txts = list(data['function'])
+scores = []
+for seq, txt in zip(proteins, txts):
+    image = [('protein1', seq)]
+    _, _, batch_tokens = model.visual_encoder(image)
+    image_embeds = model.ln_vision(batch_tokens.to(device), repr_layers=[30], return_contacts=True)["representations"][
+        30].contiguous()
+
+    image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+    query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+
+    query_output = model.Qformer.bert(
+        query_embeds=query_tokens,
+        encoder_hidden_states=image_embeds,
+        encoder_attention_mask=image_atts,
+        use_cache=True,
+        return_dict=True,
+    )
+
+    image_feats = F.normalize(model.vision_proj(query_output.last_hidden_state), dim=-1)
+
+    image_feats_all = concat_all_gather(image_feats)
+
+    if type(txt) == str:
+        txt = eval(txt)
+    length = len(txt)
+    with torch.no_grad():
+        text_tokens = model.tokenizer(
+            txt,
+            padding="max_length",
+            truncation=True,
+            max_length=model.max_txt_len,
+            return_tensors="pt",
+        ).to(device)
+        text_output = model.Qformer.bert(
+            text_tokens.input_ids,
+            attention_mask=text_tokens.attention_mask,
+            return_dict=True,
+        )
+
+        text_feat = F.normalize(
+            model.text_proj(text_output.last_hidden_state[:, 0, :]), dim=-1
+        )
+
+        text_feat_all = concat_all_gather(text_feat)
+        sim_q2t = torch.matmul(image_feats.unsqueeze(1), text_feat_all.unsqueeze(-1)).squeeze()
+        sim_i2t, _ = sim_q2t.max(-1)
+        # print('sim_i2t: {}'.format(sim_i2t))
+    if length > 1:
+        scores.append(list(sim_i2t.detach().cpu().numpy()))
+    else:
+        scores.append([sim_i2t.item()])
+print("model evaluate time: {}".format(time.time() - t0))
+data['score'] = scores
+
+# precision and recall top-k
+topk = 2
+threshould = 0.1
+labels = []
+pred_labels = []
+for l in data['label']:
+    if type(l) == str:
+        l = eval(l)
+    labels.extend(l)
+
+labels = list(set(labels))
+total = len(labels)
+for topk in range(1,7):
+    for threshould in range(1, 25, 1):
+        threshould /= 100
+        filter_txts = []
+        recalls = []
+        precisions = []
+        f1 = []
+        tp_dict, fp_dict, fn_dict = dict(zip(labels, [0]*len(labels))), dict(zip(labels, [0]*len(labels))), dict(zip(labels, [0]*len(labels)))
+        for txts, scores, label in zip(data['function'], data['score'], data['label']):
+            if type(label) == str:
+                label = eval(label)
+            txts_ = np.array(txts)
+            scores = np.array(scores)
+            txts = txts_[scores > threshould]
+            if len(txts) < 1:
+                txts = txts_[np.argmax(scores)]
+            scores = scores[scores > threshould]
+            
+            l = len(scores)
+            ll = len(label)
+            if l <= topk:
+                filter_txts.append(list(txts))
+            else:
+                ind = np.argpartition(scores, -topk)[-topk:]
+                txts = txts[ind]
+                filter_txts.append(list(txts))
+                l = topk
+            for t in label:
+                if t in txts:
+                    tp_dict[t] += 1
+                else:
+                    fn_dict[t] += 1
+            for p in txts:
+                if p not in label:
+                    if p in fp_dict:
+                        fp_dict[p] += 1
+                    else:
+                        fp_dict[p] = 1
+            pred_labels.extend(txts)
+        p_total = len(set(pred_labels))
+        re, pr = 0., 0.
+        for x in labels:
+            re += tp_dict[x] / (1.0 * (tp_dict[x] + fn_dict[x] + 1e-8))
+            pr += tp_dict[x] / (1.0 * (tp_dict[x] + fp_dict[x]+1e-8))
+        r = re / total
+        p = pr / total
+        f1 = 2 * p * r / (p + r)
+        print("Topk: {}, threshould: {}, macro_recall: {}, macro_precision: {}, micro_f1: {}".format(topk, threshould, r, p, f1))
+        #     num_r = 0
+        #     num_p = 0
+        #     for x in label:
+        #         if x in txts:
+        #             num_r += 1
+        #     for x in txts:
+        #         if x in label:
+        #             num_p += 1
+        #     recall = num_r/ll
+        #     precision = num_p/(l+0.0001)
+        #     recalls.append(recall)
+        #     precisions.append(precision)
+        #     f1.append((2*recall*precision)/(recall+precision+0.0001))
+        #
+        # data['predict'] = filter_txts
+        # data['precision'] = precisions
+        # data['recall'] = recalls
+        # data['f1'] = f1
+        # print("Topk: {}, threshould: {}, macro_recall: {}, macro_precision: {}, micro_f1: {}".format(topk, threshould, round(data['recall'].mean(), 4), round(data['precision'].mean(), 4), round(data['f1'].mean(), 4)))
+    
+
+
+
+
+
+# sim = []
+# for text, label in zip(data['predict'].tolist(), data['label'].tolist()):
+#     sim.append(levenshtein_sim(text, label))
+#
+# data['sim_filter'] = sim
+# data['avg_score'] = data['sim_filter'].apply(lambda x: round(np.mean(x), 3))
+
+
+# data['function'] = data['function'].apply(lambda x: eval(re.sub(';', ',', str(x))))
+# data['label'] = data['label'].apply(lambda x: eval(re.sub(';', ',', str(x))))
+# data['sim'] = data['sim'].apply(lambda x: eval(re.sub(';', ',', str(x))))
+#
+# data['function'] = data['function'].apply(lambda x: re.sub(',', ';', str(x)))
+# data['label'] = data['label'].apply(lambda x: re.sub(',', ';', str(x)))
+# data['sim'] = data['sim'].apply(lambda x: re.sub(',', ';', str(x)))
+# data['predict'] = data['predict'].apply(lambda x: re.sub(',', ';', str(x)))
+# data['sim_filter'] = data['sim_filter'].apply(lambda x: re.sub(',', ';', str(x)))
+
+data.to_csv('/cluster/home/wenkai/LAVIS/output/predict_sim{}.csv'.format(fix), sep='|', index=False)
+# data = pd.read_csv('/cluster/home/wenkai/LAVIS/output/predict_sim{}.csv'.format(fix), sep='|')
+
+
+
+
+
+
+
+
+#
+# # example
+# image = ['MIELKHVTFGYNKKQMVLQDINITIPDGENVGILGESGCGKSTLASLVLGLFKPVKGEIYLSDNAVLTIFQHPLTSFNPDWTIETSLKEALYYYRGLTDNTAQDQLLLQHLSTFELNAQLLTKLPSEVSGGQLQRFNVMRSLLAQPRVLICDEITSNLDVIAEQNVINILKAQTITNLNHFIVISHDLSVLQRLVNRIIVLKDGMIVDDFAIEELFNVDRHPYTKELVQTFSY']
+# image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+#
+# _, _, batch_tokens = model.visual_encoder(image)
+# image_embeds = model.ln_vision(batch_tokens.to(device), repr_layers=[30], return_contacts=True)["representations"][30].contiguous()
+#
+# image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+#
+# query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+#
+# query_output = model.Qformer.bert(
+#     query_embeds=query_tokens,
+#     encoder_hidden_states=image_embeds,
+#     encoder_attention_mask=image_atts,
+#     use_cache=True,
+#     return_dict=True,
+# )
+#
+# image_feats = F.normalize(model.vision_proj(query_output.last_hidden_state), dim=-1)
+#
+# image_feats_all = concat_all_gather(image_feats)
+#
+# functions = ['transmembrane transporter activity', 'nickel cation transmembrane transporter activity', 'nickel cation binding', 'atp hydrolysis activity', 'atp hydrolysis', 'cadmium binding', 'abc-type nickel transmembrane transporter activity', 'abc-type nickel transporter activity', 'nickel transmembrane transporter activity', 'atp binding']
+# for text in functions:
+#     with torch.no_grad():
+#         # text = 'flavin adenine dinucleotide binding'
+#         text_tokens = model.tokenizer(
+#             text,
+#             padding="max_length",
+#             truncation=True,
+#             max_length=model.max_txt_len,
+#             return_tensors="pt",
+#         ).to(device)
+#         text_output = model.Qformer.bert(
+#             text_tokens.input_ids,
+#             attention_mask=text_tokens.attention_mask,
+#             return_dict=True,
+#         )
+#
+#         text_feat = F.normalize(
+#             model.text_proj(text_output.last_hidden_state[:, 0, :]), dim=-1
+#         )
+#
+#         text_feat_all = concat_all_gather(text_feat)
+#         sim_q2t = torch.matmul(image_feats.unsqueeze(1), text_feat_all.unsqueeze(-1)).squeeze()
+#         sim_i2t, _ = sim_q2t.max(-1)
+#         print('sim_i2t: {}'.format(sim_i2t))
+#
+#         # # text-query similarity: [batch_size, batch_size*num_gpu, num_query_tokens]
+#         # sim_t2q = torch.matmul(
+#         #     text_feat.unsqueeze(1).unsqueeze(1), image_feats_all.permute(0, 2, 1)
+#         # ).squeeze()
+#         #
+#         # # text-image similarity: aggregate across all query tokens
+#         # sim_t2i, _ = sim_t2q.max(-1)
+#         # print('sim_t2i: {}'.format(sim_t2i))
+
+
+
diff --git a/examples/blip2_predict_func.py b/examples/blip2_predict_func.py
new file mode 100644
index 0000000000000000000000000000000000000000..d06919a61514c1dd6d16647cf5ee105a82347373
--- /dev/null
+++ b/examples/blip2_predict_func.py
@@ -0,0 +1,178 @@
+import os
+import re
+
+import torch
+from PIL import Image
+
+from lavis.models import load_model_and_preprocess
+from lavis.processors import load_processor
+from lavis.common.registry import registry
+from torch.nn import functional as F
+from lavis.models.base_model import all_gather_with_grad, concat_all_gather
+import numpy as np
+import pandas as pd
+import time
+from fuzzywuzzy import process
+from multiprocessing import Pool, Queue, Process
+import difflib
+import Levenshtein
+# import obonet
+
+
+# setup device to use
+device = torch.device("cuda") if torch.cuda.is_available() else "cpu"
+# device = 'cpu'
+
+
+def txt_map(x, txt_dict):
+    if type(x) == str:
+        x = eval(x)
+    x_ = []
+    for i in x:
+        if i in txt_dict:
+            x_.append(txt_dict[i])
+        else:
+            x_.append(i)
+    return x_
+
+
+def levenshtein_sim(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+def func(text, label):
+    all_s = []
+    for x in text:
+        s = 0
+        for y in label:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def stage2_output(df_test, return_num_txt=1):
+    config = {'arch': 'blip2_protein_opt', 'load_finetuned': False,
+              'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage2/20230924220/checkpoint_5.pth',
+              'finetuned': '', 'num_query_token': 32, 'opt_model': 'facebook/opt-2.7b', 'prompt': '',
+              'model_type': 'pretrain_protein_opt2.7b', 'load_pretrained': True, 'freeze_vit': True,
+              'max_protein_len': 600,
+              'max_txt_len': 25}
+
+    model_cls = registry.get_model_class(config['arch'])
+    model = model_cls.from_config(config)
+    model.to(device)
+    model.eval()
+
+    images = df_test['protein'].tolist()
+    n = len(images)
+    bsz = 12
+    iter = n // bsz + 1
+
+    for i in range(iter):
+        image = images[i*bsz: min(n, (i+1)*bsz)]
+        image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+
+        with model.maybe_autocast():
+            _, _, batch_tokens = model.visual_encoder(image)
+            image_embeds = model.ln_vision(batch_tokens.to(device), repr_layers=[model.vis_layers], return_contacts=True)["representations"][model.vis_layers].contiguous()
+
+        image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+        query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+        query_output = model.Qformer.bert(
+            query_embeds=query_tokens,
+            encoder_hidden_states=image_embeds,
+            encoder_attention_mask=image_atts,
+            return_dict=True,
+        )
+
+        inputs_opt = model.opt_proj(query_output.last_hidden_state)
+        atts_opt = torch.ones(inputs_opt.size()[:-1], dtype=torch.long).to(device)
+
+        model.opt_tokenizer.padding_side = "right"
+
+        text = ['' for i in range(len(image))]
+        opt_tokens = model.opt_tokenizer(
+            text,
+            return_tensors="pt",
+            padding="longest",
+            truncation=True,
+            max_length=model.max_txt_len,
+        ).to(device)
+        inputs_embeds = model.opt_model.model.decoder.embed_tokens(opt_tokens.input_ids)
+        inputs_embeds = torch.cat([inputs_opt, inputs_embeds], dim=1)
+        attention_mask = torch.cat([atts_opt, opt_tokens.attention_mask], dim=1)
+        num_txt = 6
+        with model.maybe_autocast():
+            outputs = model.opt_model.generate(inputs_embeds=inputs_embeds, attention_mask=attention_mask, min_length=3,
+                                               max_length=30,
+                                               repetition_penalty=1., num_beams=num_txt, eos_token_id=50118,
+                                               length_penalty=1., num_return_sequences=return_num_txt, temperature=1.)
+        output_text = model.opt_tokenizer.batch_decode(outputs, skip_special_tokens=True)
+        output_text = [text.strip() for text in output_text]
+        output_text_ = []
+        for i in range(len(image)):
+            output_text_.append(';'.join(output_text[i * return_num_txt:(i + 1) * return_num_txt]))
+        with open('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix), 'a+') as f:
+            for i in range(len(image)):
+                f.write(image[i][1] + "|" + output_text_[i] + '\n')
+
+
+cat = 'mf'
+fix = '_mf'
+if cat == 'bp':
+    fix = '_bp'
+if cat == 'cc':
+    fix = '_cc'
+
+return_num_txt = 1
+# graph = obonet.read_obo("http://purl.obolibrary.org/obo/go.obo")
+
+### Levenshtein similarity
+test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/sim_split/test{}.csv'.format(fix), sep='|')
+test['function'] = test['function'].apply(lambda x: x.lower())
+
+
+if os.path.exists('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix)):
+    os.remove('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix))
+print("stage 2 predict starting")
+stage2_output(test)
+print("stage 2 predict completed")
+
+df_pred = pd.read_csv('/cluster/home/wenkai/LAVIS/output/output{}.txt'.format(fix), sep='|', header=None, on_bad_lines='warn')
+df_pred.columns = ['protein', 'function']
+df_pred = df_pred.drop_duplicates()
+df_pred['function'] = df_pred['function'].apply(lambda x: str(x).split(';'))
+df_pred['function'] = df_pred['function'].apply(lambda x: [i.strip() for i in list(set(x))])
+
+test_g = test.groupby(['protein']).agg({'function': lambda x: list(x)}).reset_index()
+test_g.columns = ['protein', 'label']
+
+data = pd.merge(df_pred, test_g, on='protein', how='left')
+data = data[data['label'].notnull()]
+
+sim = []
+for text, label in zip(data['function'].tolist(), data['label'].tolist()):
+    sim.append(func(text, label))
+
+data['sim'] = sim
+data['avg_score'] = data['sim'].apply(lambda x: round(np.mean(x), 3))
+data['count'] = data['sim'].apply(lambda x: x.count(1.))
+print("average similarity score: {}".format(round(data['avg_score'].mean(), 3)))
+print("Return texts: {}; Accuracy: {}".format(return_num_txt, data['count'].sum()/(return_num_txt*data.shape[0])))
+data.to_csv('/cluster/home/wenkai/LAVIS/output/predict_{}.csv'.format(cat), index=False, sep='|')
+
+
+
+
diff --git a/examples/blip2_predict_func_concat.py b/examples/blip2_predict_func_concat.py
new file mode 100644
index 0000000000000000000000000000000000000000..a8c880a28bf56dca246cb8eabc56f056885306db
--- /dev/null
+++ b/examples/blip2_predict_func_concat.py
@@ -0,0 +1,193 @@
+import os
+import re
+
+import torch
+from PIL import Image
+
+from lavis.models import load_model_and_preprocess
+from lavis.processors import load_processor
+from lavis.common.registry import registry
+from torch.nn import functional as F
+from lavis.models.base_model import all_gather_with_grad, concat_all_gather
+import numpy as np
+import pandas as pd
+import time
+from fuzzywuzzy import process
+from multiprocessing import Pool, Queue, Process
+import difflib
+import Levenshtein
+
+# import obonet
+
+
+# setup device to use
+device = torch.device("cuda") if torch.cuda.is_available() else "cpu"
+
+
+# device = torch.device("cuda")
+
+
+def txt_map(x, txt_dict):
+    if type(x) == str:
+        x = eval(x)
+    x_ = []
+    for i in x:
+        if i in txt_dict:
+            x_.append(txt_dict[i])
+        else:
+            x_.append(i)
+    return x_
+
+
+def levenshtein_sim(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def func(text, label):
+    all_s = []
+    for x in text:
+        s = 0
+        for y in label:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def stage2_output(df_test, return_num_txt=1):
+    config = {'arch': 'blip2_protein_opt', 'load_finetuned': False,
+              'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage2/20231029182/checkpoint_0.pth',
+              'finetuned': '', 'num_query_token': 32, 'opt_model': 'facebook/opt-2.7b', 'prompt': '',
+              'model_type': 'pretrain_protein_opt2.7b', 'load_pretrained': True, 'freeze_vit': True,
+              'max_protein_len': 600,
+              'max_txt_len': 256}
+
+    model_cls = registry.get_model_class(config['arch'])
+    model = model_cls.from_config(config)
+    model.to(device)
+    model.eval()
+
+    images = df_test['protein'].tolist()
+    n = len(images)
+    bsz = 8
+    iter = n // bsz + 1
+    with open('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix), 'a+') as f:
+        for i in range(iter):
+            image = images[i * bsz: min(n, (i + 1) * bsz)]
+            image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+
+            with model.maybe_autocast():
+                _, _, batch_tokens = model.visual_encoder(image)
+                image_embeds = \
+                model.ln_vision(batch_tokens.to(device), repr_layers=[model.vis_layers], return_contacts=True)[
+                    "representations"][model.vis_layers].contiguous()
+
+            image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+            query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+            query_output = model.Qformer.bert(
+                query_embeds=query_tokens,
+                encoder_hidden_states=image_embeds,
+                encoder_attention_mask=image_atts,
+                return_dict=True,
+            )
+
+            inputs_opt = model.opt_proj(query_output.last_hidden_state)
+            atts_opt = torch.ones(inputs_opt.size()[:-1], dtype=torch.long).to(device)
+
+            model.opt_tokenizer.padding_side = "right"
+
+            text = ['' for i in range(len(image))]
+            opt_tokens = model.opt_tokenizer(
+                text,
+                return_tensors="pt",
+                padding="longest",
+                truncation=True,
+                max_length=model.max_txt_len,
+            ).to(device)
+            inputs_embeds = model.opt_model.model.decoder.embed_tokens(opt_tokens.input_ids)
+            inputs_embeds = torch.cat([inputs_opt, inputs_embeds], dim=1)
+            attention_mask = torch.cat([atts_opt, opt_tokens.attention_mask], dim=1)
+            num_txt = 5
+            with model.maybe_autocast():
+                outputs = model.opt_model.generate(inputs_embeds=inputs_embeds, attention_mask=attention_mask, min_length=1,
+                                                   max_length=256,
+                                                   repetition_penalty=1., num_beams=num_txt, eos_token_id=50118,
+                                                   length_penalty=1., num_return_sequences=return_num_txt, temperature=1.)
+            output_text = model.opt_tokenizer.batch_decode(outputs)
+
+            output_text = [re.sub('\t', '', str(x)) for x in output_text]
+            output_text = [text.strip() for text in output_text]
+            output_text_ = []
+            for i in range(len(image)):
+                output_text_.append(';'.join(output_text[i * return_num_txt:(i + 1) * return_num_txt]))
+
+            for i in range(len(image)):
+                f.write(image[i][1] + "|" + output_text_[i] + '\n')
+
+
+if __name__=="__main__":
+    split = 'test'
+    cat = 'bp'
+    fix = '_mf'
+    type_fix = ''
+    if cat == 'bp':
+        fix = '_bp'
+    if cat == 'cc':
+        fix = '_cc'
+
+    print(device)
+    return_num_txt = 1
+    # graph = obonet.read_obo("http://purl.obolibrary.org/obo/go.obo")
+
+    ### Levenshtein similarity
+    print("reading file ...")
+    test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/sim_split_concat/{}{}.csv'.format(split, fix),
+                       usecols=['name', 'protein', 'function'], sep='|')
+    # test['function'] = test['function'].apply(lambda x: x.lower().split('; '))
+    test.columns = ['name', 'protein', 'label']
+
+    if os.path.exists('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix)):
+        os.remove('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix))
+    print("stage 2 predict starting")
+    stage2_output(test)
+    print("stage 2 predict completed")
+
+    df_pred = pd.read_csv('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix), sep='|',
+                          header=None, on_bad_lines='warn')
+    df_pred.columns = ['protein', 'pred']
+    df_pred = df_pred.drop_duplicates()
+    # df_pred['function'] = df_pred['function'].apply(lambda x: str(x).split(';'))
+    # df_pred['function'] = df_pred['function'].apply(lambda x: [i.strip() for i in list(set(x))])
+
+
+    data = pd.merge(df_pred, test, on='protein', how='left')
+    data = data[data['label'].notnull()]
+
+    # sim = []
+    # for text, label in zip(data['function'].tolist(), data['label'].tolist()):
+    #    sim.append(func(text, label))
+
+    # data['sim'] = sim
+    # data['avg_score'] = data['sim'].apply(lambda x: round(np.mean(x), 3))
+    # data['count'] = data['sim'].apply(lambda x: x.count(1.))
+    # print("average similarity score: {}".format(round(data['avg_score'].mean(), 3)))
+    # print("Return texts: {}; Accuracy: {}".format(return_num_txt, data['count'].sum()/(return_num_txt*data.shape[0])))
+    data[['name', 'label', 'pred']].to_csv(
+        '/cluster/home/wenkai/LAVIS/output/predict_concat_{}{}{}.csv'.format(split, cat, type_fix), index=False, sep='|')
+
+
+
+
+
diff --git a/examples/blip2_predict_func_concat_pretrain.py b/examples/blip2_predict_func_concat_pretrain.py
new file mode 100644
index 0000000000000000000000000000000000000000..6692d62f83bb788d8c9910a3da050a4e788fe368
--- /dev/null
+++ b/examples/blip2_predict_func_concat_pretrain.py
@@ -0,0 +1,197 @@
+import os
+import re
+
+import torch
+from PIL import Image
+
+from lavis.models import load_model_and_preprocess
+from lavis.processors import load_processor
+from lavis.common.registry import registry
+from torch.nn import functional as F
+from lavis.models.base_model import all_gather_with_grad, concat_all_gather
+import numpy as np
+import pandas as pd
+import time
+from fuzzywuzzy import process
+from multiprocessing import Pool, Queue, Process
+import difflib
+import Levenshtein
+
+# import obonet
+
+
+# setup device to use
+device = torch.device("cuda") if torch.cuda.is_available() else "cpu"
+
+
+# device = torch.device("cuda")
+
+
+def txt_map(x, txt_dict):
+    if type(x) == str:
+        x = eval(x)
+    x_ = []
+    for i in x:
+        if i in txt_dict:
+            x_.append(txt_dict[i])
+        else:
+            x_.append(i)
+    return x_
+
+
+def levenshtein_sim(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def func(text, label):
+    all_s = []
+    for x in text:
+        s = 0
+        for y in label:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def stage2_output(df_test, return_num_txt=1):
+    config = {'arch': 'blip2_protein_opt', 'load_finetuned': False,
+              'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage2/20231029182/checkpoint_0.pth',
+              'finetuned': '', 'num_query_token': 32, 'opt_model': 'facebook/opt-2.7b', 'prompt': '',
+              'model_type': 'pretrain_protein_opt2.7b', 'load_pretrained': True, 'freeze_vit': True,
+              'max_protein_len': 600,
+              'max_txt_len': 256}
+
+    model_cls = registry.get_model_class(config['arch'])
+    model = model_cls.from_config(config)
+    model.to(device)
+    model.eval()
+
+    images = df_test['protein'].tolist()
+    n = len(images)
+    bsz = 8
+    iter = n // bsz + 1
+    if n > 0:
+        for i in range(iter):
+            image = images[i * bsz: min(n, (i + 1) * bsz)]
+            image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+
+            with model.maybe_autocast():
+                _, _, batch_tokens = model.visual_encoder(image)
+                image_embeds = \
+                model.ln_vision(batch_tokens.to(device), repr_layers=[model.vis_layers], return_contacts=True)[
+                    "representations"][model.vis_layers].contiguous()
+
+            image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+            query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+            query_output = model.Qformer.bert(
+                query_embeds=query_tokens,
+                encoder_hidden_states=image_embeds,
+                encoder_attention_mask=image_atts,
+                return_dict=True,
+            )
+
+            inputs_opt = model.opt_proj(query_output.last_hidden_state)
+            atts_opt = torch.ones(inputs_opt.size()[:-1], dtype=torch.long).to(device)
+
+            model.opt_tokenizer.padding_side = "right"
+
+            text = ['' for i in range(len(image))]
+            opt_tokens = model.opt_tokenizer(
+                text,
+                return_tensors="pt",
+                padding="longest",
+                truncation=True,
+                max_length=model.max_txt_len,
+            ).to(device)
+            inputs_embeds = model.opt_model.model.decoder.embed_tokens(opt_tokens.input_ids)
+            inputs_embeds = torch.cat([inputs_opt, inputs_embeds], dim=1)
+            attention_mask = torch.cat([atts_opt, opt_tokens.attention_mask], dim=1)
+            num_txt = 5
+            with model.maybe_autocast():
+                outputs = model.opt_model.generate(inputs_embeds=inputs_embeds, attention_mask=attention_mask, min_length=1,
+                                                   max_length=256,
+                                                   repetition_penalty=1., num_beams=num_txt, eos_token_id=50118,
+                                                   length_penalty=1., num_return_sequences=return_num_txt, temperature=1.)
+            output_text = model.opt_tokenizer.batch_decode(outputs)
+
+            output_text = [re.sub('\t', '', str(x)) for x in output_text]
+            output_text = [text.strip() for text in output_text]
+            output_text_ = []
+            for i in range(len(image)):
+                output_text_.append(';'.join(output_text[i * return_num_txt:(i + 1) * return_num_txt]))
+
+            f = open('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix), 'a+')
+            for i in range(len(image)):
+                f.write(image[i][1] + "|" + output_text_[i] + '\n')
+            f.close()
+
+                
+
+
+if __name__=="__main__":
+    split = 'test'
+    cat = ''
+    fix = ''
+    type_fix = '_pretrain'
+    if cat == 'bp':
+        fix = '_bp'
+    if cat == 'cc':
+        fix = '_cc'
+
+    print(device)
+    return_num_txt = 1
+    # graph = obonet.read_obo("http://purl.obolibrary.org/obo/go.obo")
+
+    ### Levenshtein similarity
+    print("reading file ...")
+    test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/pretrain/{}_sample10000.csv'.format(split),
+                       usecols=['name', 'protein', 'function'], sep='|')
+    # test['function'] = test['function'].apply(lambda x: x.lower().split('; '))
+    test.columns = ['name', 'protein', 'label']
+
+    if os.path.exists('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix)):
+        os.remove('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix))
+    print("stage 2 predict starting")
+    stage2_output(test)
+    print("stage 2 predict completed")
+
+    df_pred = pd.read_csv('/cluster/home/wenkai/LAVIS/output/output_concat_{}{}{}.txt'.format(split, fix, type_fix), sep='|',
+                          header=None, on_bad_lines='warn')
+    df_pred.columns = ['protein', 'pred']
+    df_pred = df_pred.drop_duplicates()
+    # df_pred['function'] = df_pred['function'].apply(lambda x: str(x).split(';'))
+    # df_pred['function'] = df_pred['function'].apply(lambda x: [i.strip() for i in list(set(x))])
+
+
+    data = pd.merge(df_pred, test, on='protein', how='left')
+    data = data[data['label'].notnull()]
+
+    # sim = []
+    # for text, label in zip(data['function'].tolist(), data['label'].tolist()):
+    #    sim.append(func(text, label))
+
+    # data['sim'] = sim
+    # data['avg_score'] = data['sim'].apply(lambda x: round(np.mean(x), 3))
+    # data['count'] = data['sim'].apply(lambda x: x.count(1.))
+    # print("average similarity score: {}".format(round(data['avg_score'].mean(), 3)))
+    # print("Return texts: {}; Accuracy: {}".format(return_num_txt, data['count'].sum()/(return_num_txt*data.shape[0])))
+    data[['name', 'label', 'pred']].to_csv(
+        '/cluster/home/wenkai/LAVIS/output/predict_concat_{}{}{}.csv'.format(split, cat, type_fix), index=False, sep='|')
+
+
+
+
+
diff --git a/examples/blip2_predict_func_concat_timesplit.py b/examples/blip2_predict_func_concat_timesplit.py
new file mode 100644
index 0000000000000000000000000000000000000000..28657878ef25b0463431f645bc9097aeb756e469
--- /dev/null
+++ b/examples/blip2_predict_func_concat_timesplit.py
@@ -0,0 +1,166 @@
+import os
+import re
+
+import torch
+from PIL import Image
+
+from lavis.models import load_model_and_preprocess
+from lavis.processors import load_processor
+from lavis.common.registry import registry
+from torch.nn import functional as F
+from lavis.models.base_model import all_gather_with_grad, concat_all_gather
+import numpy as np
+import pandas as pd
+import time
+from fuzzywuzzy import process
+from multiprocessing import Pool, Queue, Process
+import difflib
+import Levenshtein
+# import obonet
+
+
+# setup device to use
+device = torch.device("cuda") if torch.cuda.is_available() else "cpu"
+# device = 'cpu'
+
+
+def txt_map(x, txt_dict):
+    if type(x) == str:
+        x = eval(x)
+    x_ = []
+    for i in x:
+        if i in txt_dict:
+            x_.append(txt_dict[i])
+        else:
+            x_.append(i)
+    return x_
+
+
+def levenshtein_sim(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+def func(text, label):
+    all_s = []
+    for x in text:
+        s = 0
+        for y in label:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def stage2_output(df_test, return_num_txt=1):
+    config = {'arch': 'blip2_protein_opt', 'load_finetuned': False,
+              'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage2/20231007085/checkpoint_19.pth',
+              'finetuned': '', 'num_query_token': 32, 'opt_model': 'facebook/opt-2.7b', 'prompt': '',
+              'model_type': 'pretrain_protein_opt2.7b', 'load_pretrained': True, 'freeze_vit': True,
+              'max_protein_len': 600,
+              'max_txt_len': 256}
+
+    model_cls = registry.get_model_class(config['arch'])
+    model = model_cls.from_config(config)
+    model.to(device)
+    model.eval()
+
+    images = df_test['protein'].tolist()
+    n = len(images)
+    bsz = 12
+    iter = n // bsz + 1
+
+    for i in range(iter):
+        image = images[i*bsz: min(n, (i+1)*bsz)]
+        image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+
+        with model.maybe_autocast():
+            _, _, batch_tokens = model.visual_encoder(image)
+            image_embeds = model.ln_vision(batch_tokens.to(device), repr_layers=[model.vis_layers], return_contacts=True)["representations"][model.vis_layers].contiguous()
+
+        image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+        query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+        query_output = model.Qformer.bert(
+            query_embeds=query_tokens,
+            encoder_hidden_states=image_embeds,
+            encoder_attention_mask=image_atts,
+            return_dict=True,
+        )
+
+        inputs_opt = model.opt_proj(query_output.last_hidden_state)
+        atts_opt = torch.ones(inputs_opt.size()[:-1], dtype=torch.long).to(device)
+
+        model.opt_tokenizer.padding_side = "right"
+
+        text = ['' for i in range(len(image))]
+        opt_tokens = model.opt_tokenizer(
+            text,
+            return_tensors="pt",
+            padding="longest",
+            truncation=True,
+            max_length=model.max_txt_len,
+        ).to(device)
+        inputs_embeds = model.opt_model.model.decoder.embed_tokens(opt_tokens.input_ids)
+        inputs_embeds = torch.cat([inputs_opt, inputs_embeds], dim=1)
+        attention_mask = torch.cat([atts_opt, opt_tokens.attention_mask], dim=1)
+        num_txt = 5
+        with model.maybe_autocast():
+            outputs = model.opt_model.generate(inputs_embeds=inputs_embeds, attention_mask=attention_mask, min_length=3,
+                                               max_length=256,
+                                               repetition_penalty=1., num_beams=num_txt, eos_token_id=50118,
+                                               length_penalty=1., num_return_sequences=return_num_txt, temperature=1.)
+        output_text = model.opt_tokenizer.batch_decode(outputs)
+        output_text = [re.sub('\t', '', x) for x in output_text]
+
+        output_text = [text.strip() for text in output_text]
+        output_text_ = []
+        for i in range(len(image)):
+            output_text_.append(';'.join(output_text[i * return_num_txt:(i + 1) * return_num_txt]))
+        with open('/cluster/home/wenkai/LAVIS/output/output_timeconcat{}.txt'.format(fix), 'a+') as f:
+            for i in range(len(image)):
+                f.write(image[i][1] + "|" + output_text_[i] + '\n')
+
+
+cat = 'mf'
+fix = '_mf'
+if cat == 'bp':
+    fix = '_bp'
+if cat == 'cc':
+    fix = '_cc'
+
+return_num_txt = 1
+# graph = obonet.read_obo("http://purl.obolibrary.org/obo/go.obo")
+
+### Levenshtein similarity
+test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/review_time_concat/test{}.csv'.format(fix), usecols=['name', 'protein', 'function'], sep='|')
+#test['function'] = test['function'].apply(lambda x: x.lower().split('; '))
+test.columns = ['name', 'protein', 'label']
+
+if os.path.exists('/cluster/home/wenkai/LAVIS/output/output_timeconcat{}.txt'.format(fix)):
+    os.remove('/cluster/home/wenkai/LAVIS/output/output_timeconcat{}.txt'.format(fix))
+print("stage 2 predict starting")
+stage2_output(test)
+print("stage 2 predict completed")
+
+df_pred = pd.read_csv('/cluster/home/wenkai/LAVIS/output/output_timeconcat{}.txt'.format(fix), sep='|', header=None, on_bad_lines='warn')
+df_pred.columns = ['protein', 'pred']
+df_pred = df_pred.drop_duplicates()
+
+data = pd.merge(df_pred, test, on='protein', how='left')
+data = data[data['label'].notnull()]
+
+data[['name', 'label', 'pred']].to_csv('/cluster/home/wenkai/LAVIS/output/predict_timeconcat_{}.csv'.format(cat), index=False, sep='|')
+
+
+
+
diff --git a/examples/blip2_predict_names.py b/examples/blip2_predict_names.py
new file mode 100644
index 0000000000000000000000000000000000000000..635f5923d04016c514359a5f2f3fa33c90f735ea
--- /dev/null
+++ b/examples/blip2_predict_names.py
@@ -0,0 +1,247 @@
+import os
+import re
+
+import torch
+from PIL import Image
+
+from lavis.models import load_model_and_preprocess
+from lavis.processors import load_processor
+from lavis.common.registry import registry
+from torch.nn import functional as F
+from lavis.models.base_model import all_gather_with_grad, concat_all_gather
+import numpy as np
+import pandas as pd
+import time
+from fuzzywuzzy import process
+from multiprocessing import Pool, Queue, Process
+import difflib
+import Levenshtein
+# import obonet
+
+
+# setup device to use
+device = torch.device("cuda") if torch.cuda.is_available() else "cpu"
+# device = 'cpu'
+
+
+def txt_map(x, txt_dict):
+    if type(x) == str:
+        x = eval(x)
+    x_ = []
+    for i in x:
+        if i in txt_dict:
+            x_.append(txt_dict[i])
+        else:
+            x_.append(i)
+    return x_
+
+
+def levenshtein_sim(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+def func(text, label):
+    all_s = []
+    for x in label:
+        s = 0
+        for y in text:
+            temp = Levenshtein.ratio(x, y)
+            if temp > s:
+                s = temp
+        all_s.append(s)
+    all_s = [round(i, 3) for i in all_s]
+    return all_s
+
+
+def stage2_output(df_test):
+    config = {'arch': 'blip2_protein_opt', 'load_finetuned': False,
+              'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage2/20230926091/checkpoint_3.pth',
+              'finetuned': '', 'num_query_token': 32, 'opt_model': 'facebook/opt-2.7b', 'prompt': '',
+              'model_type': 'pretrain_protein_opt2.7b', 'load_pretrained': True, 'freeze_vit': True,
+              'max_protein_len': 600,
+              'max_txt_len': 25}
+
+    model_cls = registry.get_model_class(config['arch'])
+    model = model_cls.from_config(config)
+    model.to(device)
+    model.eval()
+
+    images = df_test['protein'].tolist()
+    n = len(images)
+    bsz = 12
+    iter = n // bsz + 1
+
+    for i in range(iter):
+        image = images[i*bsz: min(n, (i+1)*bsz)]
+        image = [('protein{}'.format(i), x) for i, x in enumerate(image)]
+
+        with model.maybe_autocast():
+            _, _, batch_tokens = model.visual_encoder(image)
+            image_embeds = model.ln_vision(batch_tokens.to(device), repr_layers=[model.vis_layers], return_contacts=True)["representations"][model.vis_layers].contiguous()
+
+        image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+        query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+        query_output = model.Qformer.bert(
+            query_embeds=query_tokens,
+            encoder_hidden_states=image_embeds,
+            encoder_attention_mask=image_atts,
+            return_dict=True,
+        )
+
+        inputs_opt = model.opt_proj(query_output.last_hidden_state)
+        atts_opt = torch.ones(inputs_opt.size()[:-1], dtype=torch.long).to(device)
+
+        model.opt_tokenizer.padding_side = "right"
+
+        text = ['' for i in range(len(image))]
+        opt_tokens = model.opt_tokenizer(
+            text,
+            return_tensors="pt",
+            padding="longest",
+            truncation=True,
+            max_length=model.max_txt_len,
+        ).to(device)
+        inputs_embeds = model.opt_model.model.decoder.embed_tokens(opt_tokens.input_ids)
+        inputs_embeds = torch.cat([inputs_opt, inputs_embeds], dim=1)
+        attention_mask = torch.cat([atts_opt, opt_tokens.attention_mask], dim=1)
+        num_txt = 5
+        return_num_txt = 2
+        with model.maybe_autocast():
+            outputs = model.opt_model.generate(inputs_embeds=inputs_embeds, attention_mask=attention_mask, min_length=3,
+                                               max_length=30,
+                                               repetition_penalty=5., num_beams=num_txt, eos_token_id=50118,
+                                               length_penalty=1., num_return_sequences=return_num_txt, temperature=1.)
+        output_text = model.opt_tokenizer.batch_decode(outputs, skip_special_tokens=True)
+        output_text = [text.strip() for text in output_text]
+        output_text_ = []
+        for i in range(len(image)):
+            output_text_.append(';'.join(output_text[i * return_num_txt:(i + 1) * return_num_txt]))
+        with open('/cluster/home/wenkai/LAVIS/output/output_names.txt', 'a+') as f:
+            for i in range(len(image)):
+                f.write(image[i][1] + "|" + output_text_[i] + '\n')
+
+
+def evaluate_score(data):
+    model_config = {'arch': 'blip2_protein', 'load_finetuned': False,
+                    'pretrained': '/cluster/home/wenkai/LAVIS/lavis/output/BLIP2/Pretrain_stage1/20230925102/checkpoint_6.pth',
+                    'finetuned': '', 'num_query_token': 32, 'prompt': '',
+                    'model_type': 'pretrain', 'load_pretrained': True, 'freeze_vit': False,
+                    'max_protein_len': 512, 'max_txt_len': 30}
+
+    model_cls = registry.get_model_class(model_config['arch'])
+    model = model_cls.from_config(model_config)
+    model = model.to(device)
+    model.eval()
+
+    # evaluate
+    t0 = time.time()
+    proteins = list(data['protein'])
+    txts = list(data['function'])
+    scores = []
+    for seq, txt in zip(proteins, txts):
+        image = [('protein1', seq)]
+        _, _, batch_tokens = model.visual_encoder(image)
+        image_embeds = \
+        model.ln_vision(batch_tokens.to(device), repr_layers=[30], return_contacts=True)["representations"][
+            30].contiguous()
+
+        image_atts = torch.ones(image_embeds.size()[:-1], dtype=torch.long).to(device)
+
+        query_tokens = model.query_tokens.expand(image_embeds.shape[0], -1, -1)
+
+        query_output = model.Qformer.bert(
+            query_embeds=query_tokens,
+            encoder_hidden_states=image_embeds,
+            encoder_attention_mask=image_atts,
+            use_cache=True,
+            return_dict=True,
+        )
+
+        image_feats = F.normalize(model.vision_proj(query_output.last_hidden_state), dim=-1)
+
+        image_feats_all = concat_all_gather(image_feats)
+
+        if type(txt) == str:
+            txt = eval(txt)
+        length = len(txt)
+        with torch.no_grad():
+            text_tokens = model.tokenizer(
+                txt,
+                padding="max_length",
+                truncation=True,
+                max_length=model.max_txt_len,
+                return_tensors="pt",
+            ).to(device)
+            text_output = model.Qformer.bert(
+                text_tokens.input_ids,
+                attention_mask=text_tokens.attention_mask,
+                return_dict=True,
+            )
+
+            text_feat = F.normalize(
+                model.text_proj(text_output.last_hidden_state[:, 0, :]), dim=-1
+            )
+
+            text_feat_all = concat_all_gather(text_feat)
+            sim_q2t = torch.matmul(image_feats.unsqueeze(1), text_feat_all.unsqueeze(-1)).squeeze()
+            sim_i2t, _ = sim_q2t.max(-1)
+            # print('sim_i2t: {}'.format(sim_i2t))
+        if length > 1:
+            scores.append(list(sim_i2t.detach().cpu().numpy()))
+        else:
+            scores.append([sim_i2t.item()])
+    print("model evaluate time: {}".format(time.time() - t0))
+    data['sim'] = scores
+    return data
+
+
+
+# graph = obonet.read_obo("http://purl.obolibrary.org/obo/go.obo")
+
+### Levenshtein similarity
+test = pd.read_csv('/cluster/home/wenkai/LAVIS/data/raw_time_split/reviewed//test.csv', sep='|')
+test['function'] = test['function'].apply(lambda x: x.lower())
+
+
+if os.path.exists('/cluster/home/wenkai/LAVIS/output/output_names.txt'):
+    os.remove('/cluster/home/wenkai/LAVIS/output/output_names.txt')
+print("stage 2 predict starting")
+stage2_output(test)
+print("stage 2 predict completed")
+
+df_pred = pd.read_csv('/cluster/home/wenkai/LAVIS/output/output_names.txt', sep='|', header=None, on_bad_lines='warn')
+df_pred.columns = ['protein', 'function']
+df_pred = df_pred.drop_duplicates()
+df_pred['function'] = df_pred['function'].apply(lambda x: str(x).split(';'))
+df_pred['function'] = df_pred['function'].apply(lambda x: [i.strip() for i in list(set(x))])
+
+test.columns
+test_g = test.groupby(['protein']).agg({'function': lambda x: list(x)}).reset_index()
+test_g.columns = ['protein', 'label']
+
+data = pd.merge(df_pred, test_g, on='protein', how='left')
+data = data[data['label'].notnull()]
+
+sim = []
+for text, label in zip(data['function'].tolist(), data['label'].tolist()):
+    sim.append(func(text, label))
+
+data['sim'] = sim
+data['avg_score'] = data['sim'].apply(lambda x: round(np.mean(x), 3))
+print("average similarity score: {}".format(round(data['avg_score'].mean(), 3)))
+data.to_csv('/cluster/home/wenkai/LAVIS/output/output_names.csv', index=False, sep='|')
+
+
+
+
+
+
diff --git a/examples/predict_test.sh b/examples/predict_test.sh
new file mode 100644
index 0000000000000000000000000000000000000000..eb061e735930bcadcaa553709d3cb547bd013d15
--- /dev/null
+++ b/examples/predict_test.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+#SBATCH -J infer_test
+#SBATCH -p gpu1
+#SBATCH -N 1
+#SBATCH -w node[84]
+#SBATCH --mem 80G
+#SBATCH --gres=gpu:1
+#SBATCH --output=log_predict_test.out
+#SBATCH --error=log_predict_test.err
+#SBATCH --cpus-per-task=8
+module load anaconda3/2021.05
+source activate LAVIS
+
+python blip2_predict_func_concat_pretrain.py
diff --git a/examples/predict_train.sh b/examples/predict_train.sh
new file mode 100644
index 0000000000000000000000000000000000000000..98777ce13a3e8ab717818128d97e292341738993
--- /dev/null
+++ b/examples/predict_train.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+#SBATCH -J infer_cc
+#SBATCH -p gpu1
+#SBATCH -N 1
+#SBATCH -w node[84]
+#SBATCH --mem 80G
+#SBATCH --gres=gpu:1
+#SBATCH --output=log_predict.out
+#SBATCH --error=log_predict.err
+#SBATCH --cpus-per-task=8
+module load anaconda3/2021.05
+source activate LAVIS
+
+python blip2_predict_func_concat.py