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Academic literature on the topic 'Generative sequence models'
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Journal articles on the topic "Generative sequence models"
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Wang, Yongkang, Xuan Liu, Feng Huang, Zhankun Xiong, and Wen Zhang. "A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation." Proceedings of the AAAI Conference on Artificial Intelligence 38, no. 1 (2024): 3–11. http://dx.doi.org/10.1609/aaai.v38i1.27749.
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Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only utilize sequence or structure information alone, which hinders the performance in generation. In this study, we propose a Multi-Modal Contrastive Diffusion model (MMCD), fusing both sequence and structure modalities in a diffusion framework to co-generate novel peptide sequences and structures. Specifically, MMCD constructs the sequence-modal and structure-modal diffusion models, respectively, and devises a multi-modal contrastive learning strategy with inter-contrastive and intra-contrastive in each diffusion timestep, aiming to capture the consistency between two modalities and boost model performance. The inter-contrastive aligns sequences and structures of peptides by maximizing the agreement of their embeddings, while the intra-contrastive differentiates therapeutic and non-therapeutic peptides by maximizing the disagreement of their sequence/structure embeddings simultaneously. The extensive experiments demonstrate that MMCD performs better than other state-of-the-art deep generative methods in generating therapeutic peptides across various metrics, including antimicrobial/anticancer score, diversity, and peptide-docking.
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Wu, Zachary, Kadina E. Johnston, Frances H. Arnold, and Kevin K. Yang. "Protein sequence design with deep generative models." Current Opinion in Chemical Biology 65 (December 2021): 18–27. http://dx.doi.org/10.1016/j.cbpa.2021.04.004.
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Akl, Hoda, Brooke Emison, Xiaochuan Zhao, Arup Mondal, Alberto Perez, and Purushottam D. Dixit. "GENERALIST: A latent space based generative model for protein sequence families." PLOS Computational Biology 19, no. 11 (2023): e1011655. http://dx.doi.org/10.1371/journal.pcbi.1011655.
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Generative models of protein sequence families are an important tool in the repertoire of protein scientists and engineers alike. However, state-of-the-art generative approaches face inference, accuracy, and overfitting- related obstacles when modeling moderately sized to large proteins and/or protein families with low sequence coverage. Here, we present a simple to learn, tunable, and accurate generative model, GENERALIST: GENERAtive nonLInear tenSor-factorizaTion for protein sequences. GENERALIST accurately captures several high order summary statistics of amino acid covariation. GENERALIST also predicts conservative local optimal sequences which are likely to fold in stable 3D structure. Importantly, unlike current methods, the density of sequences in GENERALIST-modeled sequence ensembles closely resembles the corresponding natural ensembles. Finally, GENERALIST embeds protein sequences in an informative latent space. GENERALIST will be an important tool to study protein sequence variability.
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Feinauer, Christoph, Barthelemy Meynard-Piganeau, and Carlo Lucibello. "Interpretable pairwise distillations for generative protein sequence models." PLOS Computational Biology 18, no. 6 (2022): e1010219. http://dx.doi.org/10.1371/journal.pcbi.1010219.
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Many different types of generative models for protein sequences have been proposed in literature. Their uses include the prediction of mutational effects, protein design and the prediction of structural properties. Neural network (NN) architectures have shown great performances, commonly attributed to the capacity to extract non-trivial higher-order interactions from the data. In this work, we analyze two different NN models and assess how close they are to simple pairwise distributions, which have been used in the past for similar problems. We present an approach for extracting pairwise models from more complex ones using an energy-based modeling framework. We show that for the tested models the extracted pairwise models can replicate the energies of the original models and are also close in performance in tasks like mutational effect prediction. In addition, we show that even simpler, factorized models often come close in performance to the original models.
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Won, K. J., C. Saunders, and A. Prügel-Bennett. "Evolving Fisher Kernels for Biological Sequence Classification." Evolutionary Computation 21, no. 1 (2013): 83–105. http://dx.doi.org/10.1162/evco_a_00065.
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Fisher kernels have been successfully applied to many problems in bioinformatics. However, their success depends on the quality of the generative model upon which they are built. For Fisher kernel techniques to be used on novel problems, a mechanism for creating accurate generative models is required. A novel framework is presented for automatically creating domain-specific generative models that can be used to produce Fisher kernels for support vector machines (SVMs) and other kernel methods. The framework enables the capture of prior knowledge and addresses the issue of domain-specific kernels, both of which are current areas that are lacking in many kernel-based methods. To obtain the generative model, genetic algorithms are used to evolve the structure of hidden Markov models (HMMs). A Fisher kernel is subsequently created from the HMM, and used in conjunction with an SVM, to improve the discriminative power. This paper investigates the effectiveness of the proposed method, named GA-SVM. We show that its performance is comparable if not better than other state of the art methods in classifying secretory protein sequences of malaria. More interestingly, it showed better results than the sequence-similarity-based approach, without the need for additional homologous sequence information in protein enzyme family classification. The experiments clearly demonstrate that the GA-SVM is a novel way to find features with good performance from biological sequences, that does not require extensive tuning of a complex model.
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Liu, Yitian, and Zhouhui Lian. "DeepCalliFont: Few-Shot Chinese Calligraphy Font Synthesis by Integrating Dual-Modality Generative Models." Proceedings of the AAAI Conference on Artificial Intelligence 38, no. 4 (2024): 3774–82. http://dx.doi.org/10.1609/aaai.v38i4.28168.
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Few-shot font generation, especially for Chinese calligraphy fonts, is a challenging and ongoing problem. With the help of prior knowledge that is mainly based on glyph consistency assumptions, some recently proposed methods can synthesize high-quality Chinese glyph images. However, glyphs in calligraphy font styles often do not meet these assumptions. To address this problem, we propose a novel model, DeepCalliFont, for few-shot Chinese calligraphy font synthesis by integrating dual-modality generative models. Specifically, the proposed model consists of image synthesis and sequence generation branches, generating consistent results via a dual-modality representation learning strategy. The two modalities (i.e., glyph images and writing sequences) are properly integrated using a feature recombination module and a rasterization loss function. Furthermore, a new pre-training strategy is adopted to improve the performance by exploiting large amounts of uni-modality data. Both qualitative and quantitative experiments have been conducted to demonstrate the superiority of our method to other state-of-the-art approaches in the task of few-shot Chinese calligraphy font synthesis. The source code can be found at https://github.com/lsflyt-pku/DeepCalliFont.
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Safranchik, Esteban, Shiying Luo, and Stephen Bach. "Weakly Supervised Sequence Tagging from Noisy Rules." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 04 (2020): 5570–78. http://dx.doi.org/10.1609/aaai.v34i04.6009.
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We propose a framework for training sequence tagging models with weak supervision consisting of multiple heuristic rules of unknown accuracy. In addition to supporting rules that vote on tags in the output sequence, we introduce a new type of weak supervision, called linking rules, that vote on how sequence elements should be grouped into spans with the same tag. These rules are an alternative to candidate span generators that require significantly more human effort. To estimate the accuracies of the rules and combine their conflicting outputs into training data, we introduce a new type of generative model, linked hidden Markov models (linked HMMs), and prove they are generically identifiable (up to a tag permutation) without any observed training labels. We find that linked HMMs provide an average 7 F1 point boost on benchmark named entity recognition tasks versus generative models that assume the tags are i.i.d. Further, neural sequence taggers trained with these structure-aware generative models outperform comparable state-of-the-art approaches to weak supervision by an average of 2.6 F1 points.
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Polceanu, Mihai, Julie Porteous, Alan Lindsay, and Marc Cavazza. "Narrative Plan Generation with Self-Supervised Learning." Proceedings of the AAAI Conference on Artificial Intelligence 35, no. 7 (2021): 5984–92. http://dx.doi.org/10.1609/aaai.v35i7.16747.
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Narrative Generation has attracted significant interest as a novel application of Automated Planning techniques. However, the vast amount of narrative material available opens the way to the use of Deep Learning techniques. In this paper, we explore the feasibility of narrative generation through self-supervised learning, using sequence embedding techniques or auto-encoders to produce narrative sequences. We use datasets of well-formed plots generated by a narrative planning approach, using pre-existing, published, narrative planning domains, to train generative models. Our experiments demonstrate the ability of generative sequence models to produce narrative plots with similar structure to those obtained with planning techniques, but with significant plot novelty in comparison with the training set. Most importantly, generated plots share structural properties associated with narrative quality measures used in Planning-based methods. As plan-based structures account for a higher level of causality and narrative consistency, this suggests that our approach is able to extend a set of narratives with novel sequences that display the same high-level narrative properties. Unlike methods developed to extend sets of textual narratives, ours operates at the level of plot structure. Thus, it has the potential to be used across various media for plots of significant complexity, being initially limited to training and generation operating in the same narrative genre.
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Zhang, Zhiyuan, and Zhanshan Wang. "Multi-Objective Prediction of Integrated Energy System Using Generative Tractive Network." Mathematics 11, no. 20 (2023): 4350. http://dx.doi.org/10.3390/math11204350.
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Accurate load forecasting can bring economic benefits and scheduling optimization. The complexity and uncertainty arising from the coupling of different energy sources in integrated energy systems pose challenges for simultaneously predicting multiple target load sequences. Existing data-driven methods for load forecasting in integrated energy systems use multi-task learning to address these challenges. When determining the input data for multi-task learning, existing research primarily relies on data correlation analysis and considers the influence of external environmental factors in terms of feature engineering. However, such feature engineering methods lack the utilization of the characteristics of multi-target sequences. In leveraging the characteristics of multi-target sequences, language generation models trained on textual logic structures and other sequence features can generate synthetic data that can even be applied to self-training to improve model performance. This provides an idea for feature engineering in data-driven time-series forecasting models. However, because time-series data are different from textual data, existing transformer-based language generation models cannot be directly applied to generating time-series data. In order to consider the characteristics of multi-target load sequences in integrated energy system load forecasting, this paper proposed a generative tractive network (GTN) model. By selectively utilizing appropriate autoregressive feature data for temporal data, this model facilitates feature mining from time-series data. This model is capable of analyzing temporal data variations, generating novel synthetic time-series data that align with the intrinsic temporal patterns of the original sequences. Moreover, the model can generate synthetic samples that closely mimic the variations in the original time series. Subsequently, through the integration of the GTN and autoregressive feature data, various prediction models are employed in case studies to affirm the effectiveness of the proposed methodology.
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Hawkins-Hooker, Alex, Florence Depardieu, Sebastien Baur, Guillaume Couairon, Arthur Chen, and David Bikard. "Generating functional protein variants with variational autoencoders." PLOS Computational Biology 17, no. 2 (2021): e1008736. http://dx.doi.org/10.1371/journal.pcbi.1008736.
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The vast expansion of protein sequence databases provides an opportunity for new protein design approaches which seek to learn the sequence-function relationship directly from natural sequence variation. Deep generative models trained on protein sequence data have been shown to learn biologically meaningful representations helpful for a variety of downstream tasks, but their potential for direct use in the design of novel proteins remains largely unexplored. Here we show that variational autoencoders trained on a dataset of almost 70000 luciferase-like oxidoreductases can be used to generate novel, functional variants of the luxA bacterial luciferase. We propose separate VAE models to work with aligned sequence input (MSA VAE) and raw sequence input (AR-VAE), and offer evidence that while both are able to reproduce patterns of amino acid usage characteristic of the family, the MSA VAE is better able to capture long-distance dependencies reflecting the influence of 3D structure. To confirm the practical utility of the models, we used them to generate variants of luxA whose luminescence activity was validated experimentally. We further showed that conditional variants of both models could be used to increase the solubility of luxA without disrupting function. Altogether 6/12 of the variants generated using the unconditional AR-VAE and 9/11 generated using the unconditional MSA VAE retained measurable luminescence, together with all 23 of the less distant variants generated by conditional versions of the models; the most distant functional variant contained 35 differences relative to the nearest training set sequence. These results demonstrate the feasibility of using deep generative models to explore the space of possible protein sequences and generate useful variants, providing a method complementary to rational design and directed evolution approaches.