scholarly journals Conditional Generative Modeling for De Novo Protein Design with Hierarchical Functions

2021 ◽  
Author(s):  
Tim Kucera ◽  
Matteo Togninalli ◽  
Laetitia Meng-Papaxanthos
Keyword(s):  
Protein Design ◽  
De Novo ◽  
General Purpose ◽  
Generative Models ◽  
Generative Adversarial Network ◽  
Sequence Generation ◽  
Adversarial Network ◽  
Evaluation Scheme ◽  
Generative Modeling ◽  
Experimental Protocols

Motivation: Protein Design has become increasingly important for medical and biotechnological applications. Because of the complex mechanisms underlying protein formation, the creation of a novel protein requires tedious and time-consuming computational or experimental protocols. At the same time, Machine Learning has enabled to solve complex problems by leveraging the large amounts of available data, more recently with great improvements on the domain of generative modeling. Yet, generative models have mainly been applied to specific sub-problems of protein design. Results: Here we approach the problem of general purpose Protein Design conditioned on functional labels of the hierarchical Gene Ontology. Since a canonical way to evaluate generative models in this domain is missing, we devise an evaluation scheme of several biologically and statistically inspired metrics. We then develop the conditional generative adversarial network ProteoGAN and show that it outperforms several classic and more recent deep learning baselines for protein sequence generation. We further give insights into the model by analysing hyperparameters and ablation baselines. Lastly, we hypothesize that a functionally conditional model could create proteins with novel functions by combining labels and provide first steps into this direction of research.

De Novo Generation of Hit-like Molecules from Gene Expression Signatures Using Artificial Intelligence

2018 ◽  
Author(s):  
Oscar Mendez-Lucio ◽  
Benoit Baillif ◽  
Djork-Arné Clevert ◽  
David Rouquié ◽  
Joerg Wichard
Keyword(s):  
Gene Expression ◽  
Artificial Intelligence ◽  
De Novo ◽  
Molecular Design ◽  
Gene Expression Signature ◽  
Cellular Level ◽  
Generative Models ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Gene Expression Signatures

Finding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular <i>de novo</i> design and compound optimization. Herein, we report the first generative model that bridges systems biology and molecular design conditioning a generative adversarial network with transcriptomic data. By doing this we could generate molecules that have high probability to produce a desired biological effect at cellular level. We show that this model is able to design active-like molecules for desired targets without any previous target annotation of the training compounds as long as the gene expression signature of the desired state is provided. The molecules generated by this model are more similar to active compounds than the ones identified by similarity of gene expression signatures, which is the state-of-the-art method for navigating compound-induced gene expression data. Overall, this method represents a novel way to bridge chemistry and biology to advance in the long and difficult road of drug discovery.

De Novo Generation of Hit-like Molecules from Gene Expression Signatures Using Artificial Intelligence

2018 ◽  
Author(s):  
Oscar Mendez-Lucio ◽  
Benoit Baillif ◽  
Djork-Arné Clevert ◽  
David Rouquié ◽  
Joerg Wichard
Keyword(s):  
Gene Expression ◽  
Artificial Intelligence ◽  
De Novo ◽  
Molecular Design ◽  
Gene Expression Signature ◽  
Cellular Level ◽  
Generative Models ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Gene Expression Signatures

Finding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular <i>de novo</i> design and compound optimization. Herein, we report the first generative model that bridges systems biology and molecular design conditioning a generative adversarial network with transcriptomic data. By doing this we could generate molecules that have high probability to produce a desired biological effect at cellular level. We show that this model is able to design active-like molecules for desired targets without any previous target annotation of the training compounds as long as the gene expression signature of the desired state is provided. The molecules generated by this model are more similar to active compounds than the ones identified by similarity of gene expression signatures, which is the state-of-the-art method for navigating compound-induced gene expression data. Overall, this method represents a novel way to bridge chemistry and biology to advance in the long and difficult road of drug discovery.

scholarly journals Improving de novo Molecule Generation by Embedding LSTM and Attention Mechanism in CycleGAN

2021 ◽  
Vol 12 ◽  
Author(s):  
Feng Wang ◽  
Xiaochen Feng ◽  
Xiao Guo ◽  
Lei Xu ◽  
Liangxu Xie ◽  
...  
Keyword(s):  
Short Term Memory ◽  
De Novo ◽  
Chemical Space ◽  
Chemical Properties ◽  
Generative Models ◽  
Attention Mechanism ◽  
Generation Model ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Starting Compound

The application of deep learning in the field of drug discovery brings the development and expansion of molecular generative models along with new challenges in this field. One of challenges in de novo molecular generation is how to produce new reasonable molecules with desired pharmacological, physical, and chemical properties. To improve the similarity between the generated molecule and the starting molecule, we propose a new molecule generation model by embedding Long Short-Term Memory (LSTM) and Attention mechanism in CycleGAN architecture, LA-CycleGAN. The network layer of the generator in CycleGAN is fused head and tail to improve the similarity of the generated structure. The embedded LSTM and Attention mechanism can overcome long-term dependency problems in treating the normally used SMILES input. From our quantitative evaluation, we present that LA-CycleGAN expands the chemical space of the molecules and improves the ability of structure conversion. The generated molecules are highly similar to the starting compound structures while obtaining expected molecular properties during cycle generative adversarial network learning, which comprehensively improves the performance of the generative model.

scholarly journals De novo generation of hit-like molecules from gene expression signatures using artificial intelligence

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Oscar Méndez-Lucio ◽  
Benoit Baillif ◽  
Djork-Arné Clevert ◽  
David Rouquié ◽  
Joerg Wichard
Keyword(s):  
Gene Expression ◽  
Artificial Intelligence ◽  
De Novo ◽  
Molecular Design ◽  
Gene Expression Signature ◽  
Generative Models ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Alternative Approach ◽  
Gene Expression Signatures

AbstractFinding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular de novo design and compound optimization. Herein, we report a generative model that bridges systems biology and molecular design, conditioning a generative adversarial network with transcriptomic data. By doing so, we can automatically design molecules that have a high probability to induce a desired transcriptomic profile. As long as the gene expression signature of the desired state is provided, this model is able to design active-like molecules for desired targets without any previous target annotation of the training compounds. Molecules designed by this model are more similar to active compounds than the ones identified by similarity of gene expression signatures. Overall, this method represents an alternative approach to bridge chemistry and biology in the long and difficult road of drug discovery.

scholarly journals WHITE-BOX CARTOONIZATION USING AN EXTENDED GAN FRAMEWORK

2021 ◽  
Vol 5 (12) ◽  
Author(s):  
Amey Thakur ◽  
Hasan Rizvi ◽  
Mega Satish
Keyword(s):  
Smooth Surface ◽  
Generative Models ◽  
Surface Representation ◽  
High Quality ◽  
Generative Adversarial Network ◽  
Structure Representation ◽  
Texture Representation ◽  
Adversarial Network ◽  
Representation Structure ◽  
New Framework

In the present study, we propose to implement a new framework for estimating generative models via an adversarial process to extend an existing GAN framework and develop a white-box controllable image cartoonization, which can generate high-quality cartooned images/videos from real-world photos and videos. The learning purposes of our system are based on three distinct representations: surface representation, structure representation, and texture representation. The surface representation refers to the smooth surface of the images. The structure representation relates to the sparse colour blocks and compresses generic content. The texture representation shows the texture, curves, and features in cartoon images. Generative Adversarial Network (GAN) framework decomposes the images into different representations and learns from them to generate cartoon images. This decomposition makes the framework more controllable and flexible which allows users to make changes based on the required output. This approach overcomes any previous system in terms of maintaining clarity, colours, textures, shapes of images yet showing the characteristics of cartoon images.

scholarly journals 3D-StyleGAN: A Style-Based Generative Adversarial Network for Generative Modeling of Three-Dimensional Medical Images

2021 ◽  
pp. 24-34
Author(s):  
Sungmin Hong ◽  
Razvan Marinescu ◽  
Adrian V. Dalca ◽  
Anna K. Bonkhoff ◽  
Martin Bretzner ◽  
...  
Keyword(s):  
Medical Images ◽  
Three Dimensional ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Generative Modeling

Sound Field Reconstruction in Rooms with Deep Generative Models

2021 ◽  
Vol 263 (5) ◽  
pp. 1527-1538
Author(s):  
Xenofon Karakonstantis ◽  
Efren Fernandez Grande
Keyword(s):  
Plane Waves ◽  
Sound Field ◽  
Real Data ◽  
Generative Models ◽  
Random Wave ◽  
Generative Adversarial Network ◽  
Underlying Distribution ◽  
Adversarial Network ◽  
Reconstruction Methods ◽  
Free Region

The characterization of Room Impulse Responses (RIR) over an extended region in a room by means of measurements requires dense spatial with many microphones. This can often become intractable and time consuming in practice. Well established reconstruction methods such as plane wave regression show that the sound field in a room can be reconstructed from sparsely distributed measurements. However, these reconstructions usually rely on assuming physical sparsity (i.e. few waves compose the sound field) or trait in the measured sound field, making the models less generalizable and problem specific. In this paper we introduce a method to reconstruct a sound field in an enclosure with the use of a Generative Adversarial Network (GAN), which s new variants of the data distributions that it is trained upon. The goal of the proposed GAN model is to estimate the underlying distribution of plane waves in any source free region, and map these distributions from a stochastic, latent representation. A GAN is trained on a large number of synthesized sound fields represented by a random wave field and then tested on both simulated and real data sets, of lightly damped and reverberant rooms.

scholarly journals Vehicle trajectory prediction and generation using LSTM models and GANs

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253868
Author(s):  
Luca Rossi ◽  
Andrea Ajmar ◽  
Marina Paolanti ◽  
Roberto Pierdicca
Keyword(s):  
Traffic Congestion ◽  
Short Term Memory ◽  
Autonomous Driving ◽  
Generative Models ◽  
Trajectory Prediction ◽  
Generative Adversarial Network ◽  
Displacement Error ◽  
Adversarial Network ◽  
Vehicle Trajectories ◽  
Vehicle Trajectory

Vehicles’ trajectory prediction is a topic with growing interest in recent years, as there are applications in several domains ranging from autonomous driving to traffic congestion prediction and urban planning. Predicting trajectories starting from Floating Car Data (FCD) is a complex task that comes with different challenges, namely Vehicle to Infrastructure (V2I) interaction, Vehicle to Vehicle (V2V) interaction, multimodality, and generalizability. These challenges, especially, have not been completely explored by state-of-the-art works. In particular, multimodality and generalizability have been neglected the most, and this work attempts to fill this gap by proposing and defining new datasets, metrics, and methods to help understand and predict vehicle trajectories. We propose and compare Deep Learning models based on Long Short-Term Memory and Generative Adversarial Network architectures; in particular, our GAN-3 model can be used to generate multiple predictions in multimodal scenarios. These approaches are evaluated with our newly proposed error metrics N-ADE and N-FDE, which normalize some biases in the standard Average Displacement Error (ADE) and Final Displacement Error (FDE) metrics. Experiments have been conducted using newly collected datasets in four large Italian cities (Rome, Milan, Naples, and Turin), considering different trajectory lengths to analyze error growth over a larger number of time-steps. The results prove that, although LSTM-based models are superior in unimodal scenarios, generative models perform best in those where the effects of multimodality are higher. Space-time and geographical analysis are performed, to prove the suitability of the proposed methodology for real cases and management services.

scholarly journals Creativity in Generative Musical Networks: Evidence From Two Case Studies

2021 ◽  
Vol 8 ◽  
Author(s):  
Rodrigo F. Cádiz ◽  
Agustín Macaya ◽  
Manuel Cartagena ◽  
Denis Parra
Keyword(s):  
Case Studies ◽  
Generative Models ◽  
Training Data ◽  
Current Understanding ◽  
Generative Adversarial Network ◽  
Training Time ◽  
Adversarial Network ◽  
The Arts ◽  
Musical Excerpts ◽  
Musical Chords

Deep learning, one of the fastest-growing branches of artificial intelligence, has become one of the most relevant research and development areas of the last years, especially since 2012, when a neural network surpassed the most advanced image classification techniques of the time. This spectacular development has not been alien to the world of the arts, as recent advances in generative networks have made possible the artificial creation of high-quality content such as images, movies or music. We believe that these novel generative models propose a great challenge to our current understanding of computational creativity. If a robot can now create music that an expert cannot distinguish from music composed by a human, or create novel musical entities that were not known at training time, or exhibit conceptual leaps, does it mean that the machine is then creative? We believe that the emergence of these generative models clearly signals that much more research needs to be done in this area. We would like to contribute to this debate with two case studies of our own: TimbreNet, a variational auto-encoder network trained to generate audio-based musical chords, and StyleGAN Pianorolls, a generative adversarial network capable of creating short musical excerpts, despite the fact that it was trained with images and not musical data. We discuss and assess these generative models in terms of their creativity and we show that they are in practice capable of learning musical concepts that are not obvious based on the training data, and we hypothesize that these deep models, based on our current understanding of creativity in robots and machines, can be considered, in fact, creative.

scholarly journals A De Novo Molecular Generation Method Using Latent Vector Based Generative Adversarial Network

2019 ◽  
Author(s):  
Oleksii Prykhodko ◽  
Simon Viet Johansson ◽  
Panagiotis-Christos Kotsias ◽  
Esben Jannik Bjerrum ◽  
Ola Engkvist ◽  
...  
Keyword(s):  
Deep Learning ◽  
De Novo ◽  
Chemical Space ◽  
Learning Method ◽  
Training Set ◽  
Generative Adversarial Network ◽  
Structure Generation ◽  
Adversarial Network ◽  
Molecule Design ◽  
Novel Structures

<p>Recently deep learning method has been used for generating novel structures. In the current study, we proposed a new deep learning method, LatentGAN, which combine an autoencoder and a generative adversarial neural network for doing de novo molecule design. We applied the method for structure generation in two scenarios, one is to generate random drug-like compounds and the other is to generate target biased compounds. Our results show that the method works well in both cases, in which sampled compounds from the trained model can largely occupy the same chemical space of the training set and still a substantial fraction of the generated compound are novel. The distribution of drug-likeness score for compounds sampled from LatentGAN is also similar to that of the training set.</p>

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