feat: Research-based protein generation enhancements #11

devin-ai-integration · 2024-11-14T09:18:05Z

Research-Based Protein Generation Enhancements

Overview

This PR implements advanced protein generation capabilities based on recent research findings from Bio-xLSTM, LaGDif, and HelixProtX papers.

Key Features

Graph Attention Layer
- Structure-aware attention mechanism
- Distance and angle embeddings
- Multi-head attention with structural features
Structure-Aware Generator
- Template-guided generation
- Structural validation
- Concept-guided generation
- Advanced sampling strategies
Comprehensive Testing
- Unit tests for all components
- Integration tests for full pipeline
- Performance benchmarks

Research Foundation

Bio-xLSTM: Generative modeling for biological sequences
LaGDif: Latent graph diffusion for protein folding
HelixProtX: Multi-modal protein understanding

Implementation Details

Enhanced structural awareness through graph attention
Improved concept guidance with latest research
Optimized training strategies
Comprehensive documentation

Link to Devin run: https://preview.devin.ai/devin/3be5f4c3b9ba4aa98728802f1f96368a

If you have any feedback, you can leave comments in the PR and I'll address them in the app!

- Add ConceptBottleneckLayer for interpretable protein generation - Implement LoRA optimization for parameter efficiency - Update forward pass with concept bottleneck integration - Enhance generate method with concept guidance - Add structural validation and concept alignment evaluation - Improve template similarity computation

…ration - Add unit tests for ConceptBottleneckLayer - Add unit tests for LoRA optimization - Add integration tests for protein generation - Test concept guidance functionality - Test structural validation - Test template-guided generation

- Replace direct device assignment with register_buffer - Add proper device property and to() method - Ensure consistent device handling in evaluation methods - Update test files for proper device handling

- Add residual connection to improve gradient flow - Update test assertions for better error messages - Ensure proper output magnitudes through residual path

- Update weight initialization to normal distribution - Adjust scaling factor for more noticeable transformations - Maintain stability through balanced initialization

- Add graph attention layer for structure-aware generation - Add structure-aware generator with concept guidance - Implement comprehensive test suites - Document research findings and implementation details Based on research from: - Bio-xLSTM (arXiv:2411.04165) - Compute-Optimal Training (arXiv:2411.02142) - LaGDif (arXiv:2411.01737) - HelixProtX (arXiv:2407.09274) Link to Devin run: https://preview.devin.ai/devin/3be5f4c3b9ba4aa98728802f1f96368a

coderabbitai · 2024-11-14T09:18:13Z

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…ture, and function prediction integration

… system

… fusion

…ESM2 output

…consistency

…etric constraints

…out pipeline

… ESM2

…m features

…multimodal integration

…coders

…oughout

… ESM2

…lidation

…quence analyzer

…ce dimensions

…estimation

devin-ai-integration bot added 6 commits November 14, 2024 09:01

fix: Improve device handling in ProteinGenerativeModel and tests

11d211f

- Replace direct device assignment with register_buffer - Add proper device property and to() method - Ensure consistent device handling in evaluation methods - Update test files for proper device handling

fix: Add residual connection to LoRA layer

be6060e

- Add residual connection to improve gradient flow - Update test assertions for better error messages - Ensure proper output magnitudes through residual path

fix: Adjust LoRA weight initialization and scaling

12e0ca2

- Update weight initialization to normal distribution - Adjust scaling factor for more noticeable transformations - Maintain stability through balanced initialization

devin-ai-integration bot added 23 commits November 14, 2024 09:34

Add multi-modal protein understanding enhancement todo list

482a589

Add multi-modal protein understanding components with sequence, struc…

4e3a6df

…ture, and function prediction integration

Add comprehensive documentation for multi-modal protein understanding…

bc3440c

… system

Add comprehensive test suite for multi-modal protein understanding

21f71ab

Fix Bio import in function predictor

6a3b0b2

Switch to ESM-1b model for better accessibility

60c0934

Update ESM1b model ID format to use underscores

84ae01e

Update to ESM2 t6 8M model for better accessibility

b7902d7

Simplify pattern recognition and fix dimension handling

b702d33

Update all components to use 320-dimensional features and add feature…

94491ca

… fusion

Update feature extractor and pattern recognition dimensions to match …

9a4168e

…ESM2 output

Update model dimensions to match 80-dim feature output from ESM2

d9eb824

Update dimensions to 80-dim across all components and fix key naming …

b95cfbd

…consistency

Fix contact map tensor construction in ContactMapPredictor

9e36c6c

Update multimodal integration with proper dimension handling and geom…

c74f720

…etric constraints

Update sequence analyzer to maintain 768-dimensional features through…

4e563d7

…out pipeline

Update sequence analyzer to use correct 320-dimensional features from…

b69ebab

… ESM2

Update all components to use 320-dimensional features consistently

779f654

Update all components to use 320-dimensional features consistently

24efe2b

Fix tensor handling in sequence analyzer and structure predictor

a97fc2a

Update StructureRefiner forward method to match new signature

27a507a

Add position predictor module to StructureRefiner

683baea

Add missing Any import and fix imports order

430733c

devin-ai-integration bot added 12 commits November 14, 2024 10:48

Simplify StructurePredictor architecture and ensure consistent 320-di…

df45071

…m features

Add dimension transformations for structure and function features in …

750f908

…multimodal integration

Update FunctionPredictor to handle ESM2 dimensions and add feature en…

2e8fc10

…coders

Update MultiModalProteinAnalyzer to use consistent 768 dimensions thr…

8f1749e

…oughout

Update EnhancedSequenceAnalyzer to use consistent 768 dimensions from…

9fdf490

… ESM2

Update EnhancedSequenceAnalyzer with proper dimension handling and va…

d8e9f26

…lidation

Update structure predictor to handle 768-dimensional features from se…

ad2f9b3

…quence analyzer

Update function encoder to handle 1000-dimensional GO terms input

5bfcdf8

Update UnifiedPredictor to handle feature dimensions consistently

2e7620f

Add debug prints for tensor shapes in UnifiedPredictor

ddc0850

Add structure encoder to transform structure features to match sequen…

2025439

…ce dimensions

Fix syntax error and implement global average pooling for confidence …

d97446d

…estimation

kasinadhsarma approved these changes Nov 14, 2024

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kasinadhsarma merged commit b8464f7 into main Nov 14, 2024
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feat: Research-based protein generation enhancements #11

feat: Research-based protein generation enhancements #11

devin-ai-integration bot commented Nov 14, 2024 •

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coderabbitai bot commented Nov 14, 2024

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feat: Research-based protein generation enhancements #11

feat: Research-based protein generation enhancements #11

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devin-ai-integration bot commented Nov 14, 2024 • edited Loading

Research-Based Protein Generation Enhancements

Overview

Key Features

Research Foundation

Implementation Details

coderabbitai bot commented Nov 14, 2024

Review skipped

Chat

CodeRabbit Commands (Invoked using PR comments)

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CodeRabbit Configuration File (.coderabbit.yaml)

Documentation and Community

devin-ai-integration bot commented Nov 14, 2024 •

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