Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules

2019 ◽  
Author(s):  
Wengong Jin ◽  
Regina Barzilay ◽  
Tommi S Jaakkola
Keyword(s):  
Drug Discovery ◽  
State Of The Art ◽  
Molecular Graph ◽  
Biochemical Properties ◽  
Large Margin ◽  
Previous State ◽  
Translation Methods ◽  
Atom Level ◽  
Precursor Molecules ◽  
Prior State

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving trees over substructures with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its connectivity to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines by a large margin.

Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules

2019 ◽  
Author(s):  
Wengong Jin ◽  
Regina Barzilay ◽  
Tommi S Jaakkola
Keyword(s):  
Drug Discovery ◽  
State Of The Art ◽  
Molecular Graph ◽  
Biochemical Properties ◽  
Large Margin ◽  
Previous State ◽  
Translation Methods ◽  
Atom Level ◽  
Precursor Molecules ◽  
Prior State

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving trees over substructures with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its connectivity to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines by a large margin.

Identifying drug–target interactions based on graph convolutional network and deep neural network

2020 ◽  
Author(s):  
Tianyi Zhao ◽  
Yang Hu ◽  
Linda R Valsdottir ◽  
Tianyi Zang ◽  
Jiajie Peng
Keyword(s):  
Neural Network ◽  
Drug Discovery ◽  
Drug Target ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Feature Representation ◽  
Convolutional Network ◽  
Computational Approaches ◽  
Large Margin ◽  
Multiple Drugs

Abstract Identification of new drug–target interactions (DTIs) is an important but a time-consuming and costly step in drug discovery. In recent years, to mitigate these drawbacks, researchers have sought to identify DTIs using computational approaches. However, most existing methods construct drug networks and target networks separately, and then predict novel DTIs based on known associations between the drugs and targets without accounting for associations between drug–protein pairs (DPPs). To incorporate the associations between DPPs into DTI modeling, we built a DPP network based on multiple drugs and proteins in which DPPs are the nodes and the associations between DPPs are the edges of the network. We then propose a novel learning-based framework, ‘graph convolutional network (GCN)-DTI’, for DTI identification. The model first uses a graph convolutional network to learn the features for each DPP. Second, using the feature representation as an input, it uses a deep neural network to predict the final label. The results of our analysis show that the proposed framework outperforms some state-of-the-art approaches by a large margin.

scholarly journals Zero-Shot Adaptive Transfer for Conversational Language Understanding

2019 ◽  
Vol 33 ◽  
pp. 6642-6649 ◽  
Author(s):  
Sungjin Lee ◽  
Rahul Jha
Keyword(s):  
Domain Adaptation ◽  
State Of The Art ◽  
Personal Digital Assistant ◽  
Conversational Agents ◽  
Language Understanding ◽  
Training Time ◽  
Large Margin ◽  
Previous State ◽  
Conversational Language ◽  
Transfer Method

Conversational agents such as Alexa and Google Assistant constantly need to increase their language understanding capabilities by adding new domains. A massive amount of labeled data is required for training each new domain. While domain adaptation approaches alleviate the annotation cost, prior approaches suffer from increased training time and suboptimal concept alignments. To tackle this, we introduce a novel Zero-Shot Adaptive Transfer method for slot tagging that utilizes the slot description for transferring reusable concepts across domains, and enjoys efficient training without any explicit concept alignments. Extensive experimentation over a dataset of 10 domains relevant to our commercial personal digital assistant shows that our model outperforms previous state-of-the-art systems by a large margin, and achieves an even higher improvement in the low data regime.

AutoLinker: Automatic Fragment Linking with Deep Conditional Transformer Neural Networks

2020 ◽  
Author(s):  
Yuyao Yang ◽  
Shuangjia Zheng ◽  
Shimin Su ◽  
Jun Xu ◽  
Hongming Chen
Keyword(s):  
Neural Networks ◽  
Drug Discovery ◽  
Drug Design ◽  
State Of The Art ◽  
The State ◽  
Generative Model ◽  
Lead Optimization ◽  
Scaffold Hopping ◽  
Reference Models ◽  
Lead Generation

Fragment based drug design represents a promising drug discovery paradigm complimentary to the traditional HTS based lead generation strategy. How to link fragment structures to increase compound affinity is remaining a challenge task in this paradigm. Hereby a novel deep generative model (AutoLinker) for linking fragments is developed with the potential for applying in the fragment-based lead generation scenario. The state-of-the-art transformer architecture was employed to learn the linker grammar and generate novel linker. Our results show that, given starting fragments and user customized linker constraints, our AutoLinker model can design abundant drug-like molecules fulfilling these constraints and its performance was superior to other reference models. Moreover, several examples were showcased that AutoLinker can be useful tools for carrying out drug design tasks such as fragment linking, lead optimization and scaffold hopping.

The State of the Art in Anti-Malarial Drug Discovery and Development

2011 ◽  
Vol 999 (999) ◽  
pp. 1-29
Author(s):  
Jeremy N. Burrows ◽  
Kelly Chibale ◽  
Timothy N.C. Wells
Keyword(s):  
Drug Discovery ◽  
State Of The Art ◽  
The State ◽  
Drug Discovery And Development

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

scholarly journals Using spatial-temporal ensembles of convolutional neural networks for lumen segmentation in ureteroscopy

2021 ◽  
Author(s):  
Jorge F. Lazo ◽  
Aldo Marzullo ◽  
Sara Moccia ◽  
Michele Catellani ◽  
Benoit Rosa ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Automatic Segmentation ◽  
Temporal Information ◽  
Invasive Technique ◽  
Dice Similarity Coefficient ◽  
Specular Reflections ◽  
Lumen Segmentation ◽  
Previous State

Abstract Purpose Ureteroscopy is an efficient endoscopic minimally invasive technique for the diagnosis and treatment of upper tract urothelial carcinoma. During ureteroscopy, the automatic segmentation of the hollow lumen is of primary importance, since it indicates the path that the endoscope should follow. In order to obtain an accurate segmentation of the hollow lumen, this paper presents an automatic method based on convolutional neural networks (CNNs). Methods The proposed method is based on an ensemble of 4 parallel CNNs to simultaneously process single and multi-frame information. Of these, two architectures are taken as core-models, namely U-Net based in residual blocks ($$m_1$$ m 1 ) and Mask-RCNN ($$m_2$$ m 2 ), which are fed with single still-frames I(t). The other two models ($$M_1$$ M 1 , $$M_2$$ M 2 ) are modifications of the former ones consisting on the addition of a stage which makes use of 3D convolutions to process temporal information. $$M_1$$ M 1 , $$M_2$$ M 2 are fed with triplets of frames ($$I(t-1)$$ I ( t - 1 ) , I(t), $$I(t+1)$$ I ( t + 1 ) ) to produce the segmentation for I(t). Results The proposed method was evaluated using a custom dataset of 11 videos (2673 frames) which were collected and manually annotated from 6 patients. We obtain a Dice similarity coefficient of 0.80, outperforming previous state-of-the-art methods. Conclusion The obtained results show that spatial-temporal information can be effectively exploited by the ensemble model to improve hollow lumen segmentation in ureteroscopic images. The method is effective also in the presence of poor visibility, occasional bleeding, or specular reflections.

scholarly journals High-Fidelity Simulated Players for Interactive Narrative Planning

2018 ◽  
Author(s):  
Pengcheng Wang ◽  
Jonathan Rowe ◽  
Wookhee Min ◽  
Bradford Mott ◽  
James Lester
Keyword(s):  
State Of The Art ◽  
Data Driven ◽  
High Fidelity ◽  
Interactive Narrative ◽  
Interaction Data ◽  
Convolutional Networks ◽  
Novel Approach ◽  
Adaptation Policies ◽  
Narrative Planning ◽  
Prior State

Interactive narrative planning offers significant potential for creating adaptive gameplay experiences. While data-driven techniques have been devised that utilize player interaction data to induce policies for interactive narrative planners, they require enormously large gameplay datasets. A promising approach to addressing this challenge is creating simulated players whose behaviors closely approximate those of human players. In this paper, we propose a novel approach to generating high-fidelity simulated players based on deep recurrent highway networks and deep convolutional networks. Empirical results demonstrate that the proposed models significantly outperform the prior state-of-the-art in generating high-fidelity simulated player models that accurately imitate human players’ narrative interactions. Using the high-fidelity simulated player models, we show the advantage of more exploratory reinforcement learning methods for deriving generalizable narrative adaptation policies.

scholarly journals Generalized and Sub-Optimal Bipartite Constraints for Conflict-Based Search

2020 ◽  
Vol 34 (05) ◽  
pp. 7277-7284
Author(s):  
Thayne T. Walker ◽  
Nathan R. Sturtevant ◽  
Ariel Felner
Keyword(s):  
Bipartite Graph ◽  
Continuous Time ◽  
State Of The Art ◽  
Main Idea ◽  
Constraint Generation ◽  
Empirical Results ◽  
Generation Technique ◽  
Unit Costs ◽  
Previous State ◽  
Multi Agent

The main idea of conflict-based search (CBS), a popular, state-of-the-art algorithm for multi-agent pathfinding is to resolve conflicts between agents by systematically adding constraints to agents. Recently, CBS has been adapted for new domains and variants, including non-unit costs and continuous time settings. These adaptations require new types of constraints. This paper introduces a new automatic constraint generation technique called bipartite reduction (BR). BR converts the constraint generation step of CBS to a surrogate bipartite graph problem. The properties of BR guarantee completeness and optimality for CBS. Also, BR's properties may be relaxed to obtain suboptimal solutions. Empirical results show that BR yields significant speedups in 2k connected grids over the previous state-of-the-art for both optimal and suboptimal search.

scholarly journals Redundancy Removal Adversarial Active Learning Based on Norm Online Uncertainty Indicator

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Jifeng Guo ◽  
Zhiqi Pang ◽  
Wenbo Sun ◽  
Shi Li ◽  
Yu Chen
Keyword(s):  
Active Learning ◽  
Feature Vector ◽  
State Of The Art ◽  
Representation Learning ◽  
The State ◽  
Feature Representation ◽  
Learning Ability ◽  
Redundancy Removal ◽  
Previous State ◽  
Uncertainty Score

Active learning aims to select the most valuable unlabelled samples for annotation. In this paper, we propose a redundancy removal adversarial active learning (RRAAL) method based on norm online uncertainty indicator, which selects samples based on their distribution, uncertainty, and redundancy. RRAAL includes a representation generator, state discriminator, and redundancy removal module (RRM). The purpose of the representation generator is to learn the feature representation of a sample, and the state discriminator predicts the state of the feature vector after concatenation. We added a sample discriminator to the representation generator to improve the representation learning ability of the generator and designed a norm online uncertainty indicator (Norm-OUI) to provide a more accurate uncertainty score for the state discriminator. In addition, we designed an RRM based on a greedy algorithm to reduce the number of redundant samples in the labelled pool. The experimental results on four datasets show that the state discriminator, Norm-OUI, and RRM can improve the performance of RRAAL, and RRAAL outperforms the previous state-of-the-art active learning methods.

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