RiNALMo-micro

RiNALMo-micro

Minimal HuggingFace port of the micro (33.5M-parameter) variant of RiNALMo -- a general-purpose RNA language model pre-trained on 36 million non-coding RNA sequences.

Architecture

Vocabulary (index order): <cls> (0), <pad> (1), <eos> (2), <unk> (3), <mask> (4), A (5), C (6), G (7), T (8), I (9), R (10), Y (11), K (12), M (13), S (14), W (15), B (16), D (17), H (18), V (19), N (20), - (21).

Note: the tokenizer converts U -> T before encoding (the model was trained on T).

Pretraining

• Objective: Masked language modeling (BERT-style, 15% mask rate)
• Data: 36 million non-coding RNA sequences from multiple databases
• Source checkpoint: rinalmo_micro_pretrained.pt from Zenodo 15043668

Checkpoint selection

The micro variant is the smallest (33.5M params) and fastest to use. Choose mega or giga for stronger representations on challenging tasks.

Parity Verification

All 13 representation levels (embedding + 12 transformer layers) verified to be bit-exact (max abs diff = 0.00) against a pure-PyTorch reference that loads the original weights. Weight mapping verified for all 156 per-block tensors. Eager and SDPA implementations agree within 4e-6 on padded batches.

Related Models

See the full RiNALMo collection.

Usage

Embedding generation

import torch
from transformers import AutoTokenizer, AutoModel

tokenizer = AutoTokenizer.from_pretrained("Taykhoom/RiNALMo-micro", trust_remote_code=True)
model = AutoModel.from_pretrained("Taykhoom/RiNALMo-micro", trust_remote_code=True)
model.eval()

sequences = ["ACUUUGGCCA", "CCCGGU"]
enc = tokenizer(sequences, return_tensors="pt", padding=True)

with torch.no_grad():
    out = model(**enc)

cls_emb   = out.last_hidden_state[:, 0, :]   # (batch, 480) -- CLS token
token_emb = out.last_hidden_state             # (batch, seq_len, 480)

# Intermediate layers
out_all = model(**enc, output_hidden_states=True)
layer6_emb = out_all.hidden_states[6]         # after block 6

MLM logits

from transformers import AutoTokenizer, AutoModelForMaskedLM

tokenizer = AutoTokenizer.from_pretrained("Taykhoom/RiNALMo-micro", trust_remote_code=True)
model = AutoModelForMaskedLM.from_pretrained("Taykhoom/RiNALMo-micro", trust_remote_code=True)
model.eval()

enc = tokenizer(["ACU<mask>UGGCCA"], return_tensors="pt")
with torch.no_grad():
    logits = model(**enc).logits   # (1, seq_len, 22)

Faster attention backends

# SDPA (PyTorch 2.0+)
model = AutoModel.from_pretrained("Taykhoom/RiNALMo-micro", trust_remote_code=True,
                                   attn_implementation="sdpa")

# Flash Attention 2 (requires flash-attn package)
model = AutoModel.from_pretrained("Taykhoom/RiNALMo-micro", trust_remote_code=True,
                                   attn_implementation="flash_attention_2",
                                   dtype=torch.bfloat16)

Fine-tuning

Standard HF conventions. For sequence-level tasks, pool over non-padding positions or use the CLS token embedding as input to a prediction head.

Implementation Notes

The original RiNALMo uses Flash Attention 2.3.2 during training. This HF port exposes eager (standard PyTorch), SDPA, and Flash Attention 2 through HuggingFace's attn_implementation dispatch. SDPA and the dispatch interface are additions; the Flash backend preserves the original non-causal Flash Attention design.

The model uses a non-standard Pre-LN residual: the attention residual connection is taken from the normalized input (i.e., x = attn_ln(x); x = x + attn(x)) rather than the original. The FFN uses standard Pre-LN.

TokenDropout rescales embeddings by (1 - mask_ratio_train) / (1 - mask_ratio_observed) even at inference, consistent with the original training code.

Citation

@article{penic2025_rinalmo,
  title   = {RiNALMo: general-purpose {RNA} language models can generalize well on structure prediction tasks},
  author  = {Penić, Rafael Josip and Vlašić, Tin and Huber, Roland G. and Wan, Yue and Šikić, Mile},
  journal = {Nature Communications},
  volume  = {16},
  number  = {1},
  pages   = {5671},
  year    = {2025},
  doi     = {10.1038/s41467-025-60872-5}
}

Credits

Original model and code by Penić et al. Source: GitHub lbcb-sci/RiNALMo. Hugging Face port maintained by Taykhoom Dalal.

License

Apache 2.0 (code) / CC BY 4.0 (model weights), following the original repository.