Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics

Protein-protein interaction (PPI) identification is an integral component of many biomedical research and database curation tools. Automation of this task through classification is one of the key goals of text mining (TM). However, labelled PPI corpora required to train classifiers are generally small. In order to overcome this sparsity in the training data, we propose a novel method of integrating corpora that do not contain relevance judgements. Our approach uses a semantic language model to gather word similarity from a large unlabelled corpus. This additional information is integrated into the sentence classification process using kernel transformations and has a re-weighting effect on the training features that leads to an 8% improvement in F-score over the baseline results. Furthermore, we discover that some words which are generally considered indicative of interactions are actually neutralised by this process

Borrowing Treasures from the Wealthy: Deep Transfer Learning through Selective Joint Fine-tuning

Deep neural networks require a large amount of labeled training data during supervised learning. However, collecting and labeling so much data might be infeasible in many cases. In this paper, we introduce a source-target selective joint fine-tuning scheme for improving the performance of deep learning tasks with insufficient training data. In this scheme, a target learning task with insufficient training data is carried out simultaneously with another source learning task with abundant training data. However, the source learning task does not use all existing training data. Our core idea is to identify and use a subset of training images from the original source learning task whose low-level characteristics are similar to those from the target learning task, and jointly fine-tune shared convolutional layers for both tasks. Specifically, we compute descriptors from linear or nonlinear filter bank responses on training images from both tasks, and use such descriptors to search for a desired subset of training samples for the source learning task. Experiments demonstrate that our selective joint fine-tuning scheme achieves state-of-the-art performance on multiple visual classification tasks with insufficient training data for deep learning. Such tasks include Caltech 256, MIT Indoor 67, Oxford Flowers 102 and Stanford Dogs 120. In comparison to fine-tuning without a source domain, the proposed method can improve the classification accuracy by 2% - 10% using a single model.Comment: To appear in 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2017

ForestHash: Semantic Hashing With Shallow Random Forests and Tiny Convolutional Networks

Hash codes are efficient data representations for coping with the ever growing amounts of data. In this paper, we introduce a random forest semantic hashing scheme that embeds tiny convolutional neural networks (CNN) into shallow random forests, with near-optimal information-theoretic code aggregation among trees. We start with a simple hashing scheme, where random trees in a forest act as hashing functions by setting `1' for the visited tree leaf, and `0' for the rest. We show that traditional random forests fail to generate hashes that preserve the underlying similarity between the trees, rendering the random forests approach to hashing challenging. To address this, we propose to first randomly group arriving classes at each tree split node into two groups, obtaining a significantly simplified two-class classification problem, which can be handled using a light-weight CNN weak learner. Such random class grouping scheme enables code uniqueness by enforcing each class to share its code with different classes in different trees. A non-conventional low-rank loss is further adopted for the CNN weak learners to encourage code consistency by minimizing intra-class variations and maximizing inter-class distance for the two random class groups. Finally, we introduce an information-theoretic approach for aggregating codes of individual trees into a single hash code, producing a near-optimal unique hash for each class. The proposed approach significantly outperforms state-of-the-art hashing methods for image retrieval tasks on large-scale public datasets, while performing at the level of other state-of-the-art image classification techniques while utilizing a more compact and efficient scalable representation. This work proposes a principled and robust procedure to train and deploy in parallel an ensemble of light-weight CNNs, instead of simply going deeper.Comment: Accepted to ECCV 201

Aggregated Deep Local Features for Remote Sensing Image Retrieval

Remote Sensing Image Retrieval remains a challenging topic due to the special nature of Remote Sensing Imagery. Such images contain various different semantic objects, which clearly complicates the retrieval task. In this paper, we present an image retrieval pipeline that uses attentive, local convolutional features and aggregates them using the Vector of Locally Aggregated Descriptors (VLAD) to produce a global descriptor. We study various system parameters such as the multiplicative and additive attention mechanisms and descriptor dimensionality. We propose a query expansion method that requires no external inputs. Experiments demonstrate that even without training, the local convolutional features and global representation outperform other systems. After system tuning, we can achieve state-of-the-art or competitive results. Furthermore, we observe that our query expansion method increases overall system performance by about 3%, using only the top-three retrieved images. Finally, we show how dimensionality reduction produces compact descriptors with increased retrieval performance and fast retrieval computation times, e.g. 50% faster than the current systems.Comment: Published in Remote Sensing. The first two authors have equal contributio