scholarly journals LMPred: Predicting Antimicrobial Peptides Using Pre-Trained Language Models and Deep Learning

2021 ◽  
Author(s):  
William Dee
Keyword(s):  
Antimicrobial Peptides ◽  
Bacterial Resistance ◽  
State Of The Art ◽  
Language Models ◽  
Peptide Sequence ◽  
Independent Dataset ◽  
Therapeutic Drugs ◽  
Novel Approach ◽  
Previous State ◽  
In Silico Models

Antimicrobial peptides (AMPs) are increasingly being used in the development of new therapeutic drugs, in areas such as cancer therapy and hypertension. Additionally, they are seen as an alternative to antibiotics due to the increasing occurrence of bacterial resistance. Wet-laboratory experimental identification, however, is both time consuming and costly, so in-silico models are now commonly used in order to screen new AMP candidates. This paper proposes a novel approach of creating model inputs; using pre-trained language models to produce contextualized embeddings representing the amino acids within each peptide sequence, before a convolutional neural network is then trained as the classifier. The optimal model was validated on two datasets, being one previously used in AMP prediction research, and an independent dataset, created by this paper. Predictive accuracies of 93.33% and 88.26% were achieved respectively, outperforming all previous state-of-the-art classification models.

scholarly journals Towards Making the Most of BERT in Neural Machine Translation

2020 ◽  
Vol 34 (05) ◽  
pp. 9378-9385
Author(s):  
Jiacheng Yang ◽  
Mingxuan Wang ◽  
Hao Zhou ◽  
Chengqi Zhao ◽  
Weinan Zhang ◽  
...  
Keyword(s):  
Machine Translation ◽  
Language Processing ◽  
State Of The Art ◽  
Fine Tuning ◽  
Language Models ◽  
German Language ◽  
Neural Machine Translation ◽  
Dynamic Switching ◽  
Previous State ◽  
Language Pair

GPT-2 and BERT demonstrate the effectiveness of using pre-trained language models (LMs) on various natural language processing tasks. However, LM fine-tuning often suffers from catastrophic forgetting when applied to resource-rich tasks. In this work, we introduce a concerted training framework (CTnmt) that is the key to integrate the pre-trained LMs to neural machine translation (NMT). Our proposed CTnmt} consists of three techniques: a) asymptotic distillation to ensure that the NMT model can retain the previous pre-trained knowledge; b) a dynamic switching gate to avoid catastrophic forgetting of pre-trained knowledge; and c) a strategy to adjust the learning paces according to a scheduled policy. Our experiments in machine translation show CTnmt gains of up to 3 BLEU score on the WMT14 English-German language pair which even surpasses the previous state-of-the-art pre-training aided NMT by 1.4 BLEU score. While for the large WMT14 English-French task with 40 millions of sentence-pairs, our base model still significantly improves upon the state-of-the-art Transformer big model by more than 1 BLEU score.

scholarly journals Boosted Prediction of Antihypertensive Peptides Using Deep Learning

2021 ◽  
Vol 11 (5) ◽  
pp. 2316
Author(s):  
Anum Rauf ◽  
Aqsa Kiran ◽  
Malik Tahir Hassan ◽  
Sajid Mahmood ◽  
Ghulam Mustafa ◽  
...  
Keyword(s):  
Deep Learning ◽  
In Silico ◽  
Bioactive Peptides ◽  
State Of The Art ◽  
Peptide Sequence ◽  
Antihypertensive Activity ◽  
Support Vector ◽  
Dipeptide Composition ◽  
Independent Dataset ◽  
Antihypertensive Peptides

Heart attack and other heart-related diseases are among the main causes of fatalities in the world. These diseases and some other severe problems like kidney failure and paralysis are mainly caused by hypertension. Since bioactive peptides extracted from naturally existing food substances possess antihypertensive activity, these antihypertensive peptides (AHTP) can function as prospective replacements for existing pharmacological drugs with no or fewer side effects. Such naturally existing peptides can be identified using in-silico approaches. The in-silico methods have been proven to save huge amounts of time and money in the identification of effective peptides. The proposed methodology is a deep learning-based in-silico approach for the identification of antihypertensive peptides (AHTPs). An ensemble method is proposed that combines convolutional neural network (CNN) and support vector machine (SVM) classifiers. Amino acid composition (AAC) and g-gap dipeptide composition (DPC) techniques are used for feature extraction. The proposed methodology has been evaluated on two standard antihypertensive peptide sequence datasets. The model yields 95% accuracy on the benchmarking dataset and 88.9% accuracy on the independent dataset. Comparative analysis is provided to demonstrate that the proposed method outperforms existing state-of-the-art methods on both of the benchmarking and independent datasets.

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.

scholarly journals Deep Learning for Transient Image Reconstruction from ToF Data

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 1962
Author(s):  
Enrico Buratto ◽  
Adriano Simonetto ◽  
Gianluca Agresti ◽  
Henrik Schäfer ◽  
Pietro Zanuttigh
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Light Response ◽  
Real Data ◽  
Depth Image ◽  
Learning Approach ◽  
Multiple Reflections ◽  
Noisy Input ◽  
Novel Approach ◽  
Incoming Light

In this work, we propose a novel approach for correcting multi-path interference (MPI) in Time-of-Flight (ToF) cameras by estimating the direct and global components of the incoming light. MPI is an error source linked to the multiple reflections of light inside a scene; each sensor pixel receives information coming from different light paths which generally leads to an overestimation of the depth. We introduce a novel deep learning approach, which estimates the structure of the time-dependent scene impulse response and from it recovers a depth image with a reduced amount of MPI. The model consists of two main blocks: a predictive model that learns a compact encoded representation of the backscattering vector from the noisy input data and a fixed backscattering model which translates the encoded representation into the high dimensional light response. Experimental results on real data show the effectiveness of the proposed approach, which reaches state-of-the-art performances.

scholarly journals A New Multi-Person Pose Estimation Method Using the Partitioned CenterPose Network

2021 ◽  
Vol 11 (9) ◽  
pp. 4241
Author(s):  
Jiahua Wu ◽  
Hyo Jong Lee
Keyword(s):  
Pose Estimation ◽  
Human Body ◽  
State Of The Art ◽  
Estimation Method ◽  
Bottom Up ◽  
Center Point ◽  
Novel Approach ◽  
Body Joints

In bottom-up multi-person pose estimation, grouping joint candidates into the appropriately structured corresponding instance of a person is challenging. In this paper, a new bottom-up method, the Partitioned CenterPose (PCP) Network, is proposed to better cluster the detected joints. To achieve this goal, we propose a novel approach called Partition Pose Representation (PPR) which integrates the instance of a person and its body joints based on joint offset. PPR leverages information about the center of the human body and the offsets between that center point and the positions of the body’s joints to encode human poses accurately. To enhance the relationships between body joints, we divide the human body into five parts, and then, we generate a sub-PPR for each part. Based on this PPR, the PCP Network can detect people and their body joints simultaneously, then group all body joints according to joint offset. Moreover, an improved l1 loss is designed to more accurately measure joint offset. Using the COCO keypoints and CrowdPose datasets for testing, it was found that the performance of the proposed method is on par with that of existing state-of-the-art bottom-up methods in terms of accuracy and speed.

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.

Towards corpus and model: Hierarchical structured-attention-based features for Indonesian named entity recognition

2021 ◽  
pp. 1-12
Author(s):  
Yingwen Fu ◽  
Nankai Lin ◽  
Xiaotian Lin ◽  
Shengyi Jiang
Keyword(s):  
Language Processing ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Language Models ◽  
Neural Models ◽  
Performance Models ◽  
Named Entity ◽  
High Resource ◽  
Benchmark Datasets

Named entity recognition (NER) is fundamental to natural language processing (NLP). Most state-of-the-art researches on NER are based on pre-trained language models (PLMs) or classic neural models. However, these researches are mainly oriented to high-resource languages such as English. While for Indonesian, related resources (both in dataset and technology) are not yet well-developed. Besides, affix is an important word composition for Indonesian language, indicating the essentiality of character and token features for token-wise Indonesian NLP tasks. However, features extracted by currently top-performance models are insufficient. Aiming at Indonesian NER task, in this paper, we build an Indonesian NER dataset (IDNER) comprising over 50 thousand sentences (over 670 thousand tokens) to alleviate the shortage of labeled resources in Indonesian. Furthermore, we construct a hierarchical structured-attention-based model (HSA) for Indonesian NER to extract sequence features from different perspectives. Specifically, we use an enhanced convolutional structure as well as an enhanced attention structure to extract deeper features from characters and tokens. Experimental results show that HSA establishes competitive performance on IDNER and three benchmark datasets.

scholarly journals Density Guarantee on Finding Multiple Subgraphs and Subtensors

2021 ◽  
Vol 15 (5) ◽  
pp. 1-32
Author(s):  
Quang-huy Duong ◽  
Heri Ramampiaro ◽  
Kjetil Nørvåg ◽  
Thu-lan Dam
Keyword(s):  
Lower Bound ◽  
State Of The Art ◽  
The State ◽  
The Other ◽  
Exact Methods ◽  
Practical Solution ◽  
Novel Approach ◽  
Wide Range ◽  
Real World Datasets ◽  
Tensor Data

Dense subregion (subgraph & subtensor) detection is a well-studied area, with a wide range of applications, and numerous efficient approaches and algorithms have been proposed. Approximation approaches are commonly used for detecting dense subregions due to the complexity of the exact methods. Existing algorithms are generally efficient for dense subtensor and subgraph detection, and can perform well in many applications. However, most of the existing works utilize the state-or-the-art greedy 2-approximation algorithm to capably provide solutions with a loose theoretical density guarantee. The main drawback of most of these algorithms is that they can estimate only one subtensor, or subgraph, at a time, with a low guarantee on its density. While some methods can, on the other hand, estimate multiple subtensors, they can give a guarantee on the density with respect to the input tensor for the first estimated subsensor only. We address these drawbacks by providing both theoretical and practical solution for estimating multiple dense subtensors in tensor data and giving a higher lower bound of the density. In particular, we guarantee and prove a higher bound of the lower-bound density of the estimated subgraph and subtensors. We also propose a novel approach to show that there are multiple dense subtensors with a guarantee on its density that is greater than the lower bound used in the state-of-the-art algorithms. We evaluate our approach with extensive experiments on several real-world datasets, which demonstrates its efficiency and feasibility.

New Multi-View Classification Method with Uncertain Data

2021 ◽  
Vol 16 (1) ◽  
pp. 1-23
Author(s):  
Bo Liu ◽  
Haowen Zhong ◽  
Yanshan Xiao
Keyword(s):  
Learning Strategy ◽  
State Of The Art ◽  
Uncertain Data ◽  
Real Life ◽  
Support Vector ◽  
Classification Methods ◽  
Complementary Information ◽  
Novel Approach ◽  
Svm Model ◽  
Iterative Framework

Multi-view classification aims at designing a multi-view learning strategy to train a classifier from multi-view data, which are easily collected in practice. Most of the existing works focus on multi-view classification by assuming the multi-view data are collected with precise information. However, we always collect the uncertain multi-view data due to the collection process is corrupted with noise in real-life application. In this case, this article proposes a novel approach, called uncertain multi-view learning with support vector machine (UMV-SVM) to cope with the problem of multi-view learning with uncertain data. The method first enforces the agreement among all the views to seek complementary information of multi-view data and takes the uncertainty of the multi-view data into consideration by modeling reachability area of the noise. Then it proposes an iterative framework to solve the proposed UMV-SVM model such that we can obtain the multi-view classifier for prediction. Extensive experiments on real-life datasets have shown that the proposed UMV-SVM can achieve a better performance for uncertain multi-view classification in comparison to the state-of-the-art multi-view classification methods.

scholarly journals Accurate Instance-Based Segmentation for Boundary Detection in Robot Grasping Application

2021 ◽  
Vol 11 (9) ◽  
pp. 4248
Author(s):  
Hong Hai Hoang ◽  
Bao Long Tran
Keyword(s):  
Object Segmentation ◽  
State Of The Art ◽  
Rapid Development ◽  
Spatial Relationship ◽  
Learning Technologies ◽  
Average Precision ◽  
Novel Approach ◽  
3D Camera ◽  
Robot Grasping ◽  
Instance Segmentation

With the rapid development of cameras and deep learning technologies, computer vision tasks such as object detection, object segmentation and object tracking are being widely applied in many fields of life. For robot grasping tasks, object segmentation aims to classify and localize objects, which helps robots to be able to pick objects accurately. The state-of-the-art instance segmentation network framework, Mask Region-Convolution Neural Network (Mask R-CNN), does not always perform an excellent accurate segmentation at the edge or border of objects. The approach using 3D camera, however, is able to extract the entire (foreground) objects easily but can be difficult or require a large amount of computation effort to classify it. We propose a novel approach, in which we combine Mask R-CNN with 3D algorithms by adding a 3D process branch for instance segmentation. Both outcomes of two branches are contemporaneously used to classify the pixels at the edge objects by dealing with the spatial relationship between edge region and mask region. We analyze the effectiveness of the method by testing with harsh cases of object positions, for example, objects are closed, overlapped or obscured by each other to focus on edge and border segmentation. Our proposed method is about 4 to 7% higher and more stable in IoU (intersection of union). This leads to a reach of 46% of mAP (mean Average Precision), which is a higher accuracy than its counterpart. The feasibility experiment shows that our method could be a remarkable promoting for the research of the grasping robot.

Sign in / Sign up

Export Citation Format

Share Document