Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations requires sophisticated, expensive, and time-consuming wet-lab experiments that can be aided with computational methods. Most of the computational prediction techniques require protein structures that limit their applicability to protein complexes with known structures. In this work, we explore the sequence-based prediction of change in protein binding affinity upon mutation. We have used protein sequence information instead of protein structures along with machine learning techniques to accurately predict the change in protein binding affinity upon mutation. Our proposed sequence-based novel change in protein binding affinity predictor called PANDA gives better accuracy than existing methods over the same validation set as well as on an external independent test dataset. On an external test dataset, our proposed method gives a maximum Pearson correlation coefficient of 0.52 in comparison to the state-of-the-art existing protein structure-based method called MutaBind which gives a maximum Pearson correlation coefficient of 0.59. Our proposed protein sequence-based method, to predict a change in binding affinity upon mutations, has wide applicability and comparable performance in comparison to existing protein structure-based methods. A cloud-based webserver implementation of PANDA and its python code is available at //sites.google.com/view/wajidarshad/software and //github.com/wajidarshad/panda.
相關內容
There are thousands of actively spoken languages on Earth, but a single visual world. Grounding in this visual world has the potential to bridge the gap between all these languages. Our goal is to use visual grounding to improve unsupervised word mapping between languages. The key idea is to establish a common visual representation between two languages by learning embeddings from unpaired instructional videos narrated in the native language. Given this shared embedding we demonstrate that (i) we can map words between the languages, particularly the 'visual' words; (ii) that the shared embedding provides a good initialization for existing unsupervised text-based word translation techniques, forming the basis for our proposed hybrid visual-text mapping algorithm, MUVE; and (iii) our approach achieves superior performance by addressing the shortcomings of text-based methods -- it is more robust, handles datasets with less commonality, and is applicable to low-resource languages. We apply these methods to translate words from English to French, Korean, and Japanese -- all without any parallel corpora and simply by watching many videos of people speaking while doing things.
Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.
In relation extraction for knowledge-based question answering, searching from one entity to another entity via a single relation is called "one hop". In related work, an exhaustive search from all one-hop relations, two-hop relations, and so on to the max-hop relations in the knowledge graph is necessary but expensive. Therefore, the number of hops is generally restricted to two or three. In this paper, we propose UHop, an unrestricted-hop framework which relaxes this restriction by use of a transition-based search framework to replace the relation-chain-based search one. We conduct experiments on conventional 1- and 2-hop questions as well as lengthy questions, including datasets such as WebQSP, PathQuestion, and Grid World. Results show that the proposed framework enables the ability to halt, works well with state-of-the-art models, achieves competitive performance without exhaustive searches, and opens the performance gap for long relation paths.
Deep structured models are widely used for tasks like semantic segmentation, where explicit correlations between variables provide important prior information which generally helps to reduce the data needs of deep nets. However, current deep structured models are restricted by oftentimes very local neighborhood structure, which cannot be increased for computational complexity reasons, and by the fact that the output configuration, or a representation thereof, cannot be transformed further. Very recent approaches which address those issues include graphical model inference inside deep nets so as to permit subsequent non-linear output space transformations. However, optimization of those formulations is challenging and not well understood. Here, we develop a novel model which generalizes existing approaches, such as structured prediction energy networks, and discuss a formulation which maintains applicability of existing inference techniques.
There has been much recent work on training neural attention models at the sequence-level using either reinforcement learning-style methods or by optimizing the beam. In this paper, we survey a range of classical objective functions that have been widely used to train linear models for structured prediction and apply them to neural sequence to sequence models. Our experiments show that these losses can perform surprisingly well by slightly outperforming beam search optimization in a like for like setup. We also report new state of the art results on both IWSLT'14 German-English translation as well as Gigaword abstractive summarization. On the larger WMT'14 English-French translation task, sequence-level training achieves 41.5 BLEU which is on par with the state of the art.
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
We study the problem of textual relation embedding with distant supervision. To combat the wrong labeling problem of distant supervision, we propose to embed textual relations with global statistics of relations, i.e., the co-occurrence statistics of textual and knowledge base relations collected from the entire corpus. This approach turns out to be more robust to the training noise introduced by distant supervision. On a popular relation extraction dataset, we show that the learned textual relation embedding can be used to augment existing relation extraction models and significantly improve their performance. Most remarkably, for the top 1,000 relational facts discovered by the best existing model, the precision can be improved from 83.9% to 89.3%.
Typical person re-identification (ReID) methods usually describe each pedestrian with a single feature vector and match them in a task-specific metric space. However, the methods based on a single feature vector are not sufficient enough to overcome visual ambiguity, which frequently occurs in real scenario. In this paper, we propose a novel end-to-end trainable framework, called Dual ATtention Matching network (DuATM), to learn context-aware feature sequences and perform attentive sequence comparison simultaneously. The core component of our DuATM framework is a dual attention mechanism, in which both intra-sequence and inter-sequence attention strategies are used for feature refinement and feature-pair alignment, respectively. Thus, detailed visual cues contained in the intermediate feature sequences can be automatically exploited and properly compared. We train the proposed DuATM network as a siamese network via a triplet loss assisted with a de-correlation loss and a cross-entropy loss. We conduct extensive experiments on both image and video based ReID benchmark datasets. Experimental results demonstrate the significant advantages of our approach compared to the state-of-the-art methods.
The aim of knowledge graphs is to gather knowledge about the world and provide a structured representation of this knowledge. Current knowledge graphs are far from complete. To address the incompleteness of the knowledge graphs, link prediction approaches have been developed which make probabilistic predictions about new links in a knowledge graph given the existing links. Tensor factorization approaches have proven promising for such link prediction problems. In this paper, we develop a simple tensor factorization model called SimplE, through a slight modification of the Polyadic Decomposition model from 1927. The complexity of SimplE grows linearly with the size of embeddings. The embeddings learned through SimplE are interpretable, and certain types of expert knowledge in terms of logical rules can be incorporated into these embeddings through weight tying. We prove SimplE is fully-expressive and derive a bound on the size of its embeddings for full expressivity. We show empirically that, despite its simplicity, SimplE outperforms several state-of-the-art tensor factorization techniques.
We report an evaluation of the effectiveness of the existing knowledge base embedding models for relation prediction and for relation extraction on a wide range of benchmarks. We also describe a new benchmark, which is much larger and complex than previous ones, which we introduce to help validate the effectiveness of both tasks. The results demonstrate that knowledge base embedding models are generally effective for relation prediction but unable to give improvements for the state-of-art neural relation extraction model with the existing strategies, while pointing limitations of existing methods.
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191