alphagenome-pytorch 0.0.1__tar.gz

alphagenome_pytorch-0.0.1/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

alphagenome_pytorch-0.0.1/.github/workflows/test.yml

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+name: Pytest
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e .[test]
+    - name: Test with pytest
+      run: |
+        python -m pytest tests/

alphagenome_pytorch-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the enitre vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore

alphagenome_pytorch-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Phil Wang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

alphagenome_pytorch-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: alphagenome-pytorch
+Version: 0.0.1
+Summary: AlphaGenome
+Project-URL: Homepage, https://pypi.org/project/alphagenome-pytorch/
+Project-URL: Repository, https://github.com/lucidrains/alphagenome
+Author-email: Phil Wang <lucidrains@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2025 Phil Wang
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Keywords: artificial intelligence,attention mechanism,deep learning,genomics,splicing,transformers
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.9
+Requires-Dist: einops>=0.8.0
+Requires-Dist: einx>=0.3.0
+Requires-Dist: torch>=2.4
+Provides-Extra: examples
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+<img src="./extended-figure-1.png" width="450px"></img>
+
+## AlphaGenome (wip)
+
+Implementation of [AlphaGenome](https://deepmind.google/discover/blog/alphagenome-ai-for-better-understanding-the-genome/), Deepmind's updated genomic attention model
+
+## Install
+
+```bash
+$ pip install alphagenome-pytorch
+```
+
+## Usage
+
+```python
+import torch
+from alphagenome import TransformerTower
+
+transformer = TransformerTower(dim = 768, dim_pairwise = 128)
+
+single = torch.randn(2, 512, 768)
+
+attended_single, attended_pairwise = transformer(single)
+```
+
+## Citations
+
+```bibtex
+@article{avsec2025alphagenome,
+  title   = {AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model},
+  author  = {Avsec, {\v{Z}}iga and Latysheva, Natasha and Cheng, Jun and Novati, Guido and Taylor, Kyle R and Ward, Tom and Bycroft, Clare and Nicolaisen, Lauren and Arvaniti, Eirini and Pan, Joshua and Thomas, Raina and Dutordoir, Vincent and Perino, Matteo and De, Soham and Karollus, Alexander and Gayoso, Adam and Sargeant, Toby and Mottram, Anne and Wong, Lai Hong and Drot{\'a}r, Pavol and Kosiorek, Adam and Senior, Andrew and Tanburn, Richard and Applebaum, Taylor and Basu, Souradeep and Hassabis, Demis and Kohli, Pushmeet},
+  year    = {2025}
+}
+```

alphagenome_pytorch-0.0.1/README.md

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+<img src="./extended-figure-1.png" width="450px"></img>
+
+## AlphaGenome (wip)
+
+Implementation of [AlphaGenome](https://deepmind.google/discover/blog/alphagenome-ai-for-better-understanding-the-genome/), Deepmind's updated genomic attention model
+
+## Install
+
+```bash
+$ pip install alphagenome-pytorch
+```
+
+## Usage
+
+```python
+import torch
+from alphagenome import TransformerTower
+
+transformer = TransformerTower(dim = 768, dim_pairwise = 128)
+
+single = torch.randn(2, 512, 768)
+
+attended_single, attended_pairwise = transformer(single)
+```
+
+## Citations
+
+```bibtex
+@article{avsec2025alphagenome,
+  title   = {AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model},
+  author  = {Avsec, {\v{Z}}iga and Latysheva, Natasha and Cheng, Jun and Novati, Guido and Taylor, Kyle R and Ward, Tom and Bycroft, Clare and Nicolaisen, Lauren and Arvaniti, Eirini and Pan, Joshua and Thomas, Raina and Dutordoir, Vincent and Perino, Matteo and De, Soham and Karollus, Alexander and Gayoso, Adam and Sargeant, Toby and Mottram, Anne and Wong, Lai Hong and Drot{\'a}r, Pavol and Kosiorek, Adam and Senior, Andrew and Tanburn, Richard and Applebaum, Taylor and Basu, Souradeep and Hassabis, Demis and Kohli, Pushmeet},
+  year    = {2025}
+}
+```

alphagenome_pytorch-0.0.1/alphagenome/__init__.py

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+from alphagenome.alphagenome import (
+    AlphaGenome,
+    Attention,
+    TransformerTower
+)

alphagenome_pytorch-0.0.1/alphagenome/alphagenome.py

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+from __future__ import annotations
+from functools import partial
+
+import torch
+from torch import nn, cat, stack, arange
+import torch.nn.functional as F
+from torch.nn import Linear, Sequential, Module, ModuleList
+
+import einx
+from einops.layers.torch import Rearrange, Reduce
+from einops import rearrange, repeat, einsum
+
+# ein notation
+
+# b - batch
+# h - heads
+# n - sequence
+# d - feature dimension
+
+# constants
+
+LinearNoBias = partial(Linear, bias = False)
+
+# functions
+
+def exists(v):
+    return v is not None
+
+def divisible_by(num, den):
+    return (num % den) == 0
+
+def is_odd(num):
+    return not divisible_by(num, 2)
+
+def is_even(num):
+    return divisible_by(num, 2)
+
+def default(v, d):
+    return v if exists(v) else d
+
+def softclamp(t, value = 5.):
+    return (t / value).tanh() * value
+
+# rotary, but with attenuation of short relative distance frequencies
+
+class RotaryEmbedding(Module):
+    def __init__(
+        self,
+        dim,
+        max_positions = 8192
+    ):
+        super().__init__()
+        num_freqs = dim // 2
+        inv_freq = 1. / (arange(num_freqs).float() + torch.logspace(1, max_positions - num_freqs + 1, num_freqs))
+        self.register_buffer('inv_freq', inv_freq)
+
+    def forward(
+        self,
+        seq_len
+    ):
+        device = self.inv_freq.device
+        t = arange(seq_len, device = device).type_as(self.inv_freq)
+        freqs = einsum(t, self.inv_freq, 'i , j -> i j')
+        return cat((freqs, freqs), dim = -1)
+
+def rotate_half(x):
+    x1, x2 = x.chunk(2, dim = -1)
+    return torch.cat((-x2, x1), dim = -1)
+
+def apply_rotary_pos_emb(pos, t):
+    return t * pos.cos() + rotate_half(t) * pos.sin()
+
+# prenorm and sandwich norm - they use sandwich norm for single rep, prenorm for pairwise rep
+
+class NormWrapper(Module):
+    def __init__(
+        self,
+        dim,
+        block: Module,
+        dropout = 0.,
+        sandwich = False
+    ):
+        super().__init__()
+        self.block = block
+        self.pre_rmsnorm = nn.RMSNorm(dim) # they use an interesting variant of batchnorm, batch-rmsnorm. craft later and make sure it works distributed
+
+        self.post_block_dropout = nn.Dropout(dropout)
+        self.post_rmsnorm = nn.RMSNorm(dim) if sandwich else nn.Identity()
+
+    def forward(
+        self,
+        x,
+        **kwargs
+    ):
+        x = self.pre_rmsnorm(x)
+        out = self.block(x, **kwargs)
+        out = self.post_block_dropout(out)
+        return self.post_rmsnorm(out)
+
+# attention
+
+class Attention(Module):
+    def __init__(
+        self,
+        dim,
+        dim_head = 64,
+        heads = 8,
+        dim_head_qk = 128,
+        dim_head_v = 192,
+        dim_pairwise = None,
+        softclamp_value = 5. # they employ attention softclamping
+    ):
+        super().__init__()
+        dim_pairwise = default(dim_pairwise, dim)
+
+        self.scale = dim_head ** -0.5
+
+        qkv_proj_dim_out = (dim_head_qk * heads, dim_head_qk, dim_head_v)
+
+        # splitting and merging of attention heads
+
+        self.split_q_heads = Rearrange('b n (h d) -> b h n d', h = heads)
+        self.merge_heads = Rearrange('b h n d -> b n (h d)')
+
+        # projections
+
+        self.to_qkv = LinearNoBias(dim, sum(qkv_proj_dim_out))
+        self.to_out = LinearNoBias(dim_head_v * heads, dim)
+
+        # they add layernorms to queries, keys, and interestingly enough, values as well. first time i've seen this
+
+        self.q_norm = nn.LayerNorm(dim_head_qk, bias = False)
+        self.k_norm = nn.LayerNorm(dim_head_qk, bias = False)
+        self.v_norm = nn.LayerNorm(dim_head_v, bias = False)
+
+        # to attention bias
+
+        self.to_attn_bias = Sequential(
+            nn.RMSNorm(dim_pairwise), # replace with BatchRMSNorm once crafted
+            nn.GELU(),
+            LinearNoBias(dim_pairwise, heads),
+            Rearrange('b i j h -> b h i j')
+        )
+        # variables
+
+        self.qkv_dim_splits = qkv_proj_dim_out
+        self.softclamp_value = softclamp_value
+
+    def forward(
+        self,
+        x,
+        pairwise = None, # Float['b i j dp']
+        rotary_emb = None
+    ):
+
+        q, k, v = self.to_qkv(x).split(self.qkv_dim_splits, dim = -1)
+
+        # they use multi-query attention, with only 1 key / value head - pretty unconventional, but maybe enough for genomic modeling
+
+        q = self.split_q_heads(q)
+
+        q, k, v = self.q_norm(q), self.k_norm(k), self.v_norm(v)
+
+        q = q * self.scale
+
+        # maybe rotary
+
+        if exists(rotary_emb):
+            q, k = tuple(apply_rotary_pos_emb(rotary_emb, t) for t in (q, k))
+
+        # similarities
+
+        sim = einsum(q, k, 'b h i d, b j d -> b h i j')
+
+        # add attention bias + softclamping
+
+        if exists(pairwise):
+            attn_bias = self.to_attn_bias(pairwise)
+
+            assert divisible_by(sim.shape[-1], attn_bias.shape[-1])
+            expand_factor = sim.shape[-1] // attn_bias.shape[-1]
+
+            attn_bias = repeat(attn_bias, 'b h i j -> b h (i r1) (j r2)', r1 = expand_factor, r2 = expand_factor)
+
+            sim = softclamp(sim + attn_bias, value = self.softclamp_value)
+
+        # attention
+
+        attn = sim.softmax(dim = -1)
+
+        # aggregate
+
+        out = einsum(attn, v, 'b h i j, b j d -> b h i d')
+
+        out = self.merge_heads(out)
+        return self.to_out(out)
+
+# single to pairwise
+
+class SingleToPairwise(Module):
+    def __init__(
+        self,
+        dim,
+        pool_size = 16,
+        dim_pairwise = 128,
+        heads = 32
+    ):
+        super().__init__()
+        self.avg_pool = Reduce('b (n pool) d -> b n d', 'mean', pool = pool_size)
+
+        dim_inner = heads * dim_pairwise
+
+        self.split_heads = Rearrange('b n (h d) -> b n h d', h = heads)
+
+        self.to_outer_sum = Sequential(
+            LinearNoBias(dim, dim_pairwise * 2),
+            nn.GELU()
+        )
+
+        self.to_qk = LinearNoBias(dim, dim_inner * 2)
+        self.qk_to_pairwise = Linear(heads, dim_pairwise)
+
+    def forward(self, single):
+
+        single = self.avg_pool(single)
+
+        q, k = self.to_qk(single).chunk(2, dim = -1)
+        q, k = tuple(self.split_heads(t) for t in (q, k))
+
+        sim = einsum(q, k, 'b i h d, b j h d -> b i j h')
+
+        pairwise_from_sim = self.qk_to_pairwise(sim)
+
+        outer_q, outer_k = self.to_outer_sum(single).chunk(2, dim = -1)
+
+        outer_sum = einx.add('b i d, b j d -> b i j d', outer_q, outer_k)
+
+        return outer_sum
+
+# pairwise attention is a single headed attention across rows, they said columns did not help
+
+class PairwiseRowAttention(Module):
+    def __init__(
+        self,
+        dim
+    ):
+        super().__init__()
+        self.scale = dim ** -0.5
+
+        self.to_qk = LinearNoBias(dim, dim * 2)
+        self.to_v = Linear(dim, dim)
+
+    def forward(
+        self,
+        x
+    ):
+
+        q, k = self.to_qk(x).chunk(2, dim = -1)
+        v = self.to_v(x)
+
+        # similarity
+
+        sim = einsum(q, k, 'b n i d, b n j d -> b n i j')
+
+        # attention
+
+        attn = sim.softmax(dim = -1)
+
+        # aggregate
+
+        return einsum(attn, v, 'b n i j, b n j d -> b n i d')
+
+# feedforward for both single and pairwise
+
+def FeedForward(
+    dim,
+    *,
+    dropout = 0.,
+    expansion_factor = 2.,  # they only do expansion factor of 2, no glu
+):
+    dim_inner = int(dim * expansion_factor)
+
+    return Sequential(
+        Linear(dim, dim_inner),
+        nn.ReLU(),
+        nn.Dropout(dropout),
+        Linear(dim_inner, dim)
+    )
+
+# transformer
+
+class TransformerTower(Module):
+    def __init__(
+        self,
+        dim,
+        *,
+        depth = 8,
+        heads = 8,
+        dim_head_qk = 128,
+        dim_head_v = 192,
+        dropout = 0.,
+        ff_expansion_factor = 2.,
+        max_positions = 8192,
+        dim_pairwise = None,
+        pairwise_every_num_single_blocks = 2,   # how often to do a pairwise block
+        single_to_pairwise_heads = 32,          # they did 32
+        attn_kwargs: dict = dict(),
+        ff_kwargs: dict = dict()
+    ):
+        super().__init__()
+        dim_pairwise = default(dim_pairwise, dim)
+
+        layers = []
+
+        self.pairwise_every = pairwise_every_num_single_blocks
+
+        self.rotary_emb = RotaryEmbedding(dim_head_qk, max_positions = max_positions)
+
+        for layer_index in range(depth):
+
+            attn = Attention(dim = dim, dim_head_qk = dim_head_qk, dim_head_v = dim_head_v, heads = heads, dim_pairwise = dim_pairwise)
+
+            ff = FeedForward(dim = dim, expansion_factor = ff_expansion_factor)
+
+            attn = NormWrapper(dim = dim, block = attn, dropout = dropout, sandwich = True)
+            ff = NormWrapper(dim = dim, block = ff, dropout = dropout, sandwich = True)
+
+            # maybe pairwise
+
+            single_to_pairwise, pairwise_attn, pairwise_ff = None, None, None
+
+            if divisible_by(layer_index, self.pairwise_every):
+                single_to_pairwise = SingleToPairwise(dim = dim, dim_pairwise = dim_pairwise, heads = single_to_pairwise_heads)
+                pairwise_attn = PairwiseRowAttention(dim_pairwise)
+                pairwise_ff = FeedForward(dim = dim_pairwise, expansion_factor = ff_expansion_factor)
+
+                single_to_pairwise = NormWrapper(dim = dim, block = single_to_pairwise, dropout = dropout)
+                pairwise_attn = NormWrapper(dim = dim_pairwise, block = pairwise_attn, dropout = dropout)
+                pairwise_ff = NormWrapper(dim = dim_pairwise, block = pairwise_ff, dropout = dropout)
+
+            # add to layers
+
+            layers.append(ModuleList([
+                attn,
+                ff,
+                single_to_pairwise,
+                pairwise_attn,
+                pairwise_ff
+            ]))
+
+
+        self.layers = ModuleList(layers)
+
+    def forward(
+        self,
+        single
+    ):
+
+        seq_len = single.shape[1]
+
+        pairwise = None
+
+        rotary_emb = self.rotary_emb(seq_len)
+
+        for (
+            attn,
+            ff,
+            maybe_single_to_pair,
+            maybe_pairwise_attn,
+            maybe_pairwise_ff
+        ) in self.layers:
+
+            single = attn(single, rotary_emb = rotary_emb, pairwise = None) + single
+            single = ff(single) + single
+
+            if exists(maybe_single_to_pair):
+                pairwise = maybe_single_to_pair(single) + default(pairwise, 0.)
+                pairwise = maybe_pairwise_attn(pairwise) + pairwise
+                pairwise = maybe_pairwise_ff(pairwise) + pairwise
+
+        return single, pairwise
+
+# embedding
+
+class DNAEmbed(Module):
+    def __init__(
+        self,
+        dim,
+        dim_input = 5, # 5 basepairs
+        width = 15
+    ):
+        super().__init__()
+        assert is_odd(width)
+        self.dim_input = dim_input
+        self.conv = nn.Conv1d(dim_input, dim, width, padding = width // 2)
+        self.pointwise = nn.Conv1d(dim, dim, 1)
+
+    def forward(
+        self,
+        seq # Int['b n']
+    ):
+        onehot = F.one_hot(seq, num_classes = self.dim_input).float()
+        x = rearrange(onehot, 'b n d -> b d n')
+
+        out = self.conv(x)
+        out = out + self.pointwise(out)
+        return rearrange(out, 'b d n -> b n d')
+
+# classes
+
+class AlphaGenome(Module):
+    def __init__(
+        self,
+        dim = 768,
+        basepairs = 5,
+        dna_embed_width = 15,
+        dim_pairwise = None,
+        transformer_kwargs: dict = dict()
+    ):
+        super().__init__()
+        assert is_odd(dna_embed_width)
+
+        self.to_dna_embed = DNAEmbed(dim, dim_input = basepairs, width = dna_embed_width)
+
+        self.transformer = Transformer(
+            dim = dim,
+            dim_pairwise = dim_pairwise,
+            **transformer_kwargs
+        )
+
+    def forward(
+        self,
+        seq,
+        pairwise
+    ):
+
+        dna_embed = self.to_dna_embed(seq)
+
+        attended = self.transformer(dna_embed)
+
+        return attended

alphagenome_pytorch-0.0.1/pyproject.toml

@@ -0,0 +1,61 @@
+[project]
+name = "alphagenome-pytorch"
+version = "0.0.1"
+description = "AlphaGenome"
+authors = [
+    { name = "Phil Wang", email = "lucidrains@gmail.com" }
+]
+readme = "README.md"
+requires-python = ">= 3.9"
+license = { file = "LICENSE" }
+keywords = [
+    'artificial intelligence',
+    'deep learning',
+    'transformers',
+    'attention mechanism',
+    'genomics',
+    'splicing',
+]
+
+classifiers=[
+    'Development Status :: 4 - Beta',
+    'Intended Audience :: Developers',
+    'Topic :: Scientific/Engineering :: Artificial Intelligence',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python :: 3.9',
+]
+
+dependencies = [
+    "einx>=0.3.0",
+    "einops>=0.8.0",
+    "torch>=2.4",
+]
+
+[project.urls]
+Homepage = "https://pypi.org/project/alphagenome-pytorch/"
+Repository = "https://github.com/lucidrains/alphagenome"
+
+[project.optional-dependencies]
+examples = []
+test = [
+    "pytest"
+]
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.rye]
+managed = true
+dev-dependencies = []
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["alphagenome"]

alphagenome_pytorch-0.0.1/tests/test_alphagenome.py

@@ -0,0 +1,14 @@
+import pytest
+import torch
+from alphagenome.alphagenome import TransformerTower
+
+def test_attention():
+
+    transformer = TransformerTower(dim = 768, dim_pairwise = 128)
+
+    single = torch.randn(2, 512, 768)
+
+    single_repr, pairwise_repr = transformer(single)
+
+    assert single_repr.shape == (2, 512, 768)
+    assert pairwise_repr.shape == (2, 512 // 16, 512 // 16, 128)