VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

Transfer Risk Map: Mitigating Pixel-level Negative Transfer in Medical Segmentation

How to mitigate negative transfer in transfer learning is a long-standing and challenging issue, especially in the application of medical image segmentation. Existing methods for reducing negative transfer focus on classification or regression tasks, ignoring the non-uniform negative transfer risk in different image regions. In this work, we propose a simple yet effective weighted fine-tuning method that directs the model's attention towards regions with significant transfer risk for medical semantic segmentation. Specifically, we compute a transferability-guided transfer risk map to quantify the transfer hardness for each pixel and the potential risks of negative transfer. During the fine-tuning phase, we introduce a map-weighted loss function, normalized with image foreground size to counter class imbalance. Extensive experiments on brain segmentation datasets show our method significantly improves the target task performance, with gains of 4.37% on FeTS2021 and 1.81% on iSeg2019, avoiding negative transfer across modalities and tasks. Meanwhile, a 2.9% gain under a few-shot scenario validates the robustness of our approach.

Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model

Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties. The emergence of deep learning methods for protein modeling has demonstrated superior results at lower costs compared to traditional approaches such as directed evolution and rational design. In mutation effect prediction, the key to pre-training deep learning models lies in accurately interpreting the complex relationships among protein sequence, structure, and function. This study introduces a retrieval-enhanced protein language model for comprehensive analysis of native properties from sequence and local structural interactions, as well as evolutionary properties from retrieved homologous sequences. The state-of-the-art performance of the proposed ProtREM is validated on over 2 million mutants across 217 assays from an open benchmark (ProteinGym). We also conducted post-hoc analyses of the model's ability to improve the stability and binding affinity of a VHH antibody. Additionally, we designed 10 new mutants on a DNA polymerase and conducted wet-lab experiments to evaluate their enhanced activity at higher temperatures. Both in silico and experimental evaluations confirmed that our method provides reliable predictions of mutation effects, offering an auxiliary tool for biologists aiming to evolve existing enzymes. The implementation is publicly available at https://github.com/tyang816/ProtREM.

Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection

Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce ProVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 9,500 antigen sequences, structures, and immunogenicity labels from bacteria, viruses, and tumors. Extensive experiments demonstrate that ProVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research.

A PLMs based protein retrieval framework

Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has proved the efficiency of this field. Despite the existing tools for protein retrieval, they prioritize sequence similarity and probably overlook proteins that are dissimilar but share homology or functionality. In order to tackle this problem, we propose a novel protein retrieval framework that mitigates the bias towards sequence similarity. Our framework initiatively harnesses protein language models (PLMs) to embed protein sequences within a high-dimensional feature space, thereby enhancing the representation capacity for subsequent analysis. Subsequently, an accelerated indexed vector database is constructed to facilitate expedited access and retrieval of dense vectors. Extensive experiments demonstrate that our framework can equally retrieve both similar and dissimilar proteins. Moreover, this approach enables the identification of proteins that conventional methods fail to uncover. This framework will effectively assist in protein mining and empower the development of biology.

Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion

The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared to computational or experimental methods. However, existing methods face challenges in generating proteins with diverse lengths and shapes while maintaining key structural features. To address these challenges, we introduce CPDiffusion-SS, a latent graph diffusion model that generates protein sequences based on coarse-grained secondary structural information. CPDiffusion-SS offers greater flexibility in producing a variety of novel amino acid sequences while preserving overall structural constraints, thus enhancing the reliability and diversity of generated proteins. Experimental analyses demonstrate the significant superiority of the proposed method in producing diverse and novel sequences, with CPDiffusion-SS surpassing popular baseline methods on open benchmarks across various quantitative measurements. Furthermore, we provide a series of case studies to highlight the biological significance of the generation performance by the proposed method. The source code is publicly available at https://github.com/riacd/CPDiffusion-SS

Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?

Deep learning has become a crucial tool in studying proteins. While the significance of modeling protein structure has been discussed extensively in the literature, amino acid types are typically included in the input as a default operation for many inference tasks. This study demonstrates with structure alignment task that embedding amino acid types in some cases may not help a deep learning model learn better representation. To this end, we propose ProtLOCA, a local geometry alignment method based solely on amino acid structure representation. The effectiveness of ProtLOCA is examined by a global structure-matching task on protein pairs with an independent test dataset based on CATH labels. Our method outperforms existing sequence- and structure-based representation learning methods by more quickly and accurately matching structurally consistent protein domains. Furthermore, in local structure pairing tasks, ProtLOCA for the first time provides a valid solution to highlight common local structures among proteins with different overall structures but the same function. This suggests a new possibility for using deep learning methods to analyze protein structure to infer function.

MALT: Multi-scale Action Learning Transformer for Online Action Detection

Online action detection (OAD) aims to identify ongoing actions from streaming video in real-time, without access to future frames. Since these actions manifest at varying scales of granularity, ranging from coarse to fine, projecting an entire set of action frames to a single latent encoding may result in a lack of local information, necessitating the acquisition of action features across multiple scales. In this paper, we propose a multi-scale action learning transformer (MALT), which includes a novel recurrent decoder (used for feature fusion) that includes fewer parameters and can be trained more efficiently. A hierarchical encoder with multiple encoding branches is further proposed to capture multi-scale action features. The output from the preceding branch is then incrementally input to the subsequent branch as part of a cross-attention calculation. In this way, output features transition from coarse to fine as the branches deepen. We also introduce an explicit frame scoring mechanism employing sparse attention, which filters irrelevant frames more efficiently, without requiring an additional network. The proposed method achieved state-of-the-art performance on two benchmark datasets (THUMOS'14 and TVSeries), outperforming all existing models used for comparison, with an mAP of 0.2% for THUMOS'14 and an mcAP of 0.1% for TVseries.

Simple, Efficient and Scalable Structure-aware Adapter Boosts Protein Language Models

Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in natural language processing, employing Parameter-Efficient Fine-Tuning techniques could potentially enhance the performance of PLMs. However, the direct transfer to life science tasks is non-trivial due to the different training strategies and data forms. To address this gap, we introduce SES-Adapter, a simple, efficient, and scalable adapter method for enhancing the representation learning of PLMs. SES-Adapter incorporates PLM embeddings with structural sequence embeddings to create structure-aware representations. We show that the proposed method is compatible with different PLM architectures and across diverse tasks. Extensive evaluations are conducted on 2 types of folding structures with notable quality differences, 9 state-of-the-art baselines, and 9 benchmark datasets across distinct downstream tasks. Results show that compared to vanilla PLMs, SES-Adapter improves downstream task performance by a maximum of 11% and an average of 3%, with significantly accelerated training speed by a maximum of 1034% and an average of 362%, the convergence rate is also improved by approximately 2 times. Moreover, positive optimization is observed even with low-quality predicted structures. The source code for SES-Adapter is available at https://github.com/tyang816/SES-Adapter.

PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid sequences have a smaller data volume and a limited combinatorial space. Choosing an appropriate vocabulary size to optimize the pre-trained model is a pivotal issue. Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality. Given these challenges, PETA trained language models with 14 different vocabulary sizes under three tokenization methods. It conducted thousands of tests on 33 diverse downstream datasets to assess the models' transfer learning capabilities, incorporating two classification heads and three random seeds to mitigate potential biases. Extensive experiments indicate that vocabulary sizes between 50 and 200 optimize the model, whereas sizes exceeding 800 detrimentally affect the model's representational performance. Our code, model weights and datasets are available at https://github.com/ginnm/ProteinPretraining.