arXiv subjects

Yang Tan

Publications and source records attributed to Yang Tan.

At least 37 records · Page 2Linked to original sources

arXiv2025

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.

cs.CL↗

arXiv2025

Coherence Properties of Rare-Earth Spins in Micrometer-Thin Films

Rare-earth ions in bulk crystals are excellent solid-state quantum systems in quantum information science, owing to the exceptional optical and spin coherence properties. However, the weak fluorescence of single rare-earth ions present a significant challenge for scalability, necessitating the integration into micro-cavities. Thin films serve as a promising material platform for the integration, yet the fabrication without compromising the properties of the materials and rare-earth ions remains challenging. In this work, we fabricate micrometer-thin yttrium aluminum garnet (YAG) films from bulk crystals using ion implantation techniques. The resulting films preserve the single-crystalline structure of the original bulk crystal. Notably, the embedded rare-earth ions are photo-stable and exhibit bulk-like spin coherence properties. Our results demonstrate the compatibility of bulk-like spin properties with the thin-film fabrication technique, facilitating the efficient integration of rare-earth ions into on-chip photonic devices and advancing the applications of rare-earth ions systems in quantum technologies.

quant-ph↗

arXiv2025

VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data

In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (DMS) experiments that use surrogate readouts, which may not adequately capture the complex biochemical properties of interest. Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties, and this is particularly true for the real industrial application scenario. Therefore, the desired testing datasets, will be small-size (~10-100) experimental data for each protein, and involve as many proteins as possible and as many properties as possible, which is, however, lacking. Here, we present VenusMutHub, a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases, spanning 527 proteins across diverse functional properties including stability, activity, binding affinity, and selectivity. These datasets feature direct biochemical measurements rather than surrogate readouts, providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions. We evaluate 23 computational models across various methodological paradigms, such as sequence-based, structure-informed and evolutionary approaches. This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.

q-bio.QM↗

arXiv2025

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.

cs.CV↗

arXiv2025

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.

cs.IR↗

arXiv2024

Pro-PRIME: A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins

Designing protein mutants of both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants of improved stability and activity without any prior experimental mutagenesis data of the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive power compared to current state-of-the-art models on the public mutagenesis dataset over 283 protein assays. Furthermore, we validated PRIME's predictions on five proteins, examining the top 30-45 single-site mutations' impact on various protein properties, including thermal stability, antigen-antibody binding affinity, and the ability to polymerize non-natural nucleic acid or resilience to extreme alkaline conditions. Remarkably, over 30% of the AI-recommended mutants exhibited superior performance compared to their pre-mutation counterparts across all proteins and desired properties. Moreover, we have developed an efficient, and successful method based on PRIME to rapidly obtain multi-site mutants with enhanced activity and stability. Hence, PRIME demonstrates the general applicability in protein engineering.

q-bio.BM↗

arXiv2024

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.

cs.CL↗

arXiv2024

CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation

Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for distinguishing between experimentally resolved and computationally predicted structures, evaluating the reliability of prediction methods, and guiding downstream biological studies. Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of protein structures. CPE-Pro learns the structural information of proteins and captures inter-structural differences to achieve accurate traceability on four data classes, and is expected to be extended to more. Simultaneously, we utilized Foldseek to encode protein structures into "structure-sequences" and trained a protein Structural Sequence Language Model, SSLM. Preliminary experiments demonstrated that, compared to large-scale protein language models pre-trained on vast amounts of amino acid sequences, the "structure-sequence" enables the language model to learn more informative protein features, enhancing and optimizing structural representations. We have provided the code, model weights, and all related materials on https://github.com/GouWenrui/CPE-Pro-main.git.

q-bio.BM↗

arXiv2024

Hopping Transfer Optimizes Avalanche Multiplication in Molybdenum Disulfide

Recently, avalanche multiplication has been observed in TMDC-based FETs, enhancing sensor performance with high sensitivity. However, the high voltage required for operation can damage the FETs, making it crucial to reduce the breakdown voltage for effective sensing applications. Here, we demonstrate that the utilization of hopping transfer induced by high-density defects can effectively reduce the breakdown voltage in TMDCs FETs. By substituting oxygen atoms for sulfur atoms in a monolayer of MoS2, we create MoS2-xOx, with x carefully adjusted within the range of 0 to 0.51. Oxygen doping reduces the bandgap of TMDCs and enhances ion collision rates. Moreover, higher levels of oxygen doping (x > 0.41) in MoS2-xOx exhibit nearest-neighbor hopping behavior, leading to a significant enhancement in electron mobility. These improvements result in a decrease in the breakdown voltage of avalanche multiplication from 26.2 V to 12.6 V. Additionally, we propose avalanche multiplication in MoS2-xOx as an efficient sensing mechanism to overcome the limitations of gas sensing. The MoS2-xOx sensors display an ultra-high response to NO2 gas in the air, with a response of 5.8x103 % to NO2 gas of 50 ppb at room temperature, which is nearly two orders of magnitude higher than resistance-type gas detectors based on TMDCs. This work demonstrates that hopping transfer induced by high-density oxygen defects can effectively decrease the breakdown voltage of MoS2-xOx FETs, enhancing avalanche multiplication and serving as a promising mechanism for ultrasensitive gas detection.

physics.app-ph↗

arXiv2024

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

cs.AI↗

arXiv2024

ProtSolM: Protein Solubility Prediction with Multi-modal Features

Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein engineering. Existing methods either construct a supervised learning scheme on small-scale datasets with manually processed physicochemical properties, or blindly apply pre-trained protein language models to extract amino acid interaction information. The scale and quality of available training datasets leave significant room for improvement in terms of accuracy and generalization. To address these research gaps, we propose \sol, a novel deep learning method that combines pre-training and fine-tuning schemes for protein solubility prediction. ProtSolM integrates information from multiple dimensions, including physicochemical properties, amino acid sequences, and protein backbone structures. Our model is trained using \data, the largest solubility dataset that we have constructed. PDBSol includes over $60,000$ protein sequences and structures. We provide a comprehensive leaderboard of existing statistical learning and deep learning methods on independent datasets with computational and experimental labels. ProtSolM achieved state-of-the-art performance across various evaluation metrics, demonstrating its potential to significantly advance the accuracy of protein solubility prediction.

q-bio.QM↗

arXiv2024

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.

q-bio.QM↗

arXiv2024

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.

cs.CV↗

arXiv2024

Giant Acoustic Geometric Spin and Orbital Hall Effect

Acoustic waves in fluid with spin-0 nature have been long believed not to support spin Hall effect and strong orbital Hall effect that enables experimental observation. Here we report the first theoretical explication and experimental demonstration of giant acoustic geometric spin and orbital Hall effect characterized by a large transverse shift. We reveal that this effect occurs when a vortex beam is observed from a tilted reference frame free of wave-interface interactions or gradient-index media needed for observing conventional ones, and can be amplified by simply binding the beam tightly. Thanks to this mechanism, large transverse shifts proportional to angular momentum are observed in a compact system. Our work provides deeper insights into the physics of angular momentum of classic waves.

physics.class-ph↗

arXiv2024

A Comprehensive Survey on Heart Sound Analysis in the Deep Learning Era

Heart sound auscultation has been applied in clinical usage for early screening of cardiovascular diseases. Due to the high demand for auscultation expertise, automatic auscultation can help with auxiliary diagnosis and reduce the burden of training professional clinicians. Nevertheless, there is a limit to classic machine learning's performance improvement in the era of big data. Deep learning has outperformed classic machine learning in many research fields, as it employs more complex model architectures with a stronger capability of extracting effective representations. Moreover, it has been successfully applied to heart sound analysis in the past years. As most review works about heart sound analysis were carried out before 2017, the present survey is the first to work on a comprehensive overview to summarise papers on heart sound analysis with deep learning published in 2017--2022. This work introduces both classic machine learning and deep learning for comparison, and further offer insights about the advances and future research directions in deep learning for heart sound analysis. Our repository is publicly available at \url{https://github.com/zhaoren91/awesome-heart-sound-analysis}.

cs.SD↗

arXiv2024

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.

cs.CL↗

arXiv2024

Practical Transferability Estimation for Image Classification Tasks

Transferability estimation is an essential problem in transfer learning to predict how good the performance is when transferring a source model (or source task) to a target task. Recent analytical transferability metrics have been widely used for source model selection and multi-task learning. A major challenge is how to make transfereability estimation robust under the cross-domain cross-task settings. The recently proposed OTCE score solves this problem by considering both domain and task differences, with the help of transfer experiences on auxiliary tasks, which causes an efficiency overhead. In this work, we propose a practical transferability metric called JC-NCE score that dramatically improves the robustness of the task difference estimation in OTCE, thus removing the need for auxiliary tasks. Specifically, we build the joint correspondences between source and target data via solving an optimal transport problem with a ground cost considering both the sample distance and label distance, and then compute the transferability score as the negative conditional entropy of the matched labels. Extensive validations under the intra-dataset and inter-dataset transfer settings demonstrate that our JC-NCE score outperforms the auxiliary-task free version of OTCE for 7% and 12%, respectively, and is also more robust than other existing transferability metrics on average.

cs.CV↗

arXiv2024

Transferability Estimation for Semantic Segmentation Task

Transferability estimation is a fundamental problem in transfer learning to predict how good the performance is when transferring a source model (or source task) to a target task. With the guidance of transferability score, we can efficiently select the highly transferable source models without performing the real transfer in practice. Recent analytical transferability metrics are mainly designed for image classification problem, and currently there is no specific investigation for the transferability estimation of semantic segmentation task, which is an essential problem in autonomous driving, medical image analysis, etc. Consequently, we further extend the recent analytical transferability metric OTCE (Optimal Transport based Conditional Entropy) score to the semantic segmentation task. The challenge in applying the OTCE score is the high dimensional segmentation output, which is difficult to find the optimal coupling between so many pixels under an acceptable computation cost. Thus we propose to randomly sample N pixels for computing OTCE score and take the expectation over K repetitions as the final transferability score. Experimental evaluation on Cityscapes, BDD100K and GTA5 datasets demonstrates that the OTCE score highly correlates with the transfer performance.

cs.CV↗