Unsupervised non-rigid point cloud shape correspondence underpins a multitude of 3D vision tasks, yet itself is non-trivial given the exponential complexity stemming from inter-point degree-of-freedom, i.e., pose transformations. Based on the assumption of local rigidity, one solution for reducing complexity is to decompose the overall shape into independent local regions using Local Reference Frames (LRFs) that are equivariant to SE(3) transformations. However, the focus solely on local structure neglects global geometric contexts, resulting in less distinctive LRFs that lack crucial semantic information necessary for effective matching. Furthermore, such complexity introduces out-of-distribution geometric contexts during inference, thus complicating generalization. To this end, we introduce 1) EquiShape, a novel structure tailored to learn pair-wise LRFs with global structural cues for both spatial and semantic consistency, and 2) LRF-Refine, an optimization strategy generally applicable to LRF-based methods, aimed at addressing the generalization challenges. Specifically, for EquiShape, we employ cross-talk within separate equivariant graph neural networks (Cross-GVP) to build long-range dependencies to compensate for the lack of semantic information in local structure modeling, deducing pair-wise independent SE(3)-equivariant LRF vectors for each point. For LRF-Refine, the optimization adjusts LRFs within specific contexts and knowledge, enhancing the geometric and semantic generalizability of point features. Our overall framework surpasses the state-of-the-art methods by a large margin on three benchmarks. Codes are available at https://github.com/2019EPWL/EquiShape.

Person re-identification is a hot topic in computer vision, and the loss function plays a vital role in improving the discrimination of the learned features. However, most existing models utilize the hand-crafted loss functions, which are usually sub-optimal and challenging to be designed. In this paper, we propose a novel method, AutoLoss-GMS, to search the better loss function in the space of generalized margin-based softmax loss function for person reidentification automatically. Specifically, the generalized margin-based softmax loss function is first decomposed into two computational graphs and a constant. Then a general searching framework built upon the evolutionary algorithm is proposed to search for the loss function efficiently. The computational graph is constructed with a forward method, which can construct much richer loss function forms than the backward method used in existing works. In addition to the basic in-graph mutation operations, the cross-graph mutation operation is designed to further improve the offspring's diversity. The loss-rejection protocol, equivalence-check strategy and the predictor-based promising-loss chooser are developed to improve the search efficiency. Finally, experimental results demonstrate that the searched loss functions can achieve state-of-the-art performance and be transferable across different models and datasets in person re-identification.

On-demand meal delivery (ODMD) platforms such as DoorDash and Ele.me have experienced explosive growth in recent years. Effective logistics optimization strategies that could guarantee high service standards with controlled costs are crucial for the long-term sustainability of these platforms, and yet are also non-trivial due to the nature of ODMD operations. In particular, most of the orders are not known until they are placed by the customers, and any dispatching policy that only considers known requests would risk making myopic decisions in such a setting.

Abstract Single hyperspectral image (HSI) super‐resolution (SR) has attracted researcher's attention; however, most existing methods directly model the mapping between low‐ and high‐resolution images from an external training dataset, which requires large memory and computing resources. Moreover, there are few such available training datasets in real cases, which prevent deep‐learning‐based methods from further improving performance. Here, a novel single HSI SR method based on transfer learning is proposed. The proposed method is composed of two stages: spectral down‐sampled image SR reconstruction based on transfer learning and HSI reconstruction via spectral recovery module. Instead of directly applying the learned knowledge from the colour image domain to HSI SR, the spectral down‐sampled image is fed into a spatial SR model to obtain a high‐resolution image, which acts as a bridge between the colour image and HSI. The spectral recovery network is used to restore the HSI from the bridge image. In addition, pre‐training and collaborative fine‐tuning are proposed to promote the performance of SR and spectral recovery. Experiments on two public HSI datasets show that the proposed method achieves promising SR performance with a small paired HSI dataset.

Gene Ontology (GO) is a controlled vocabulary of terms that describe molecule function, biological roles, and cellular locations of gene products (i.e., proteins and RNAs), it hierarchically organizes more than 43,000 GO terms via the direct acyclic graph. A gene is generally annotated with several of these GO terms. Therefore, accurately predicting the association between genes and massive terms is a difficult challenge. To combat with this challenge, we propose an matrix factorization based approach called NMFGO. NMFGO stores the available GO annotations of genes in a gene-term association matrix and adopts an ontological structure based taxonomic similarity measure to capture the GO hierarchy. Next, it factorizes the association matrix into two low-rank matrices via nonnegative matrix factorization regularized with the GO hierarchy. After that, it employs a semantic similarity based k nearest neighbor classifier in the low-rank matrices approximated subspace to predict gene functions. Empirical study on three model species (S. cerevisiae, H. sapiens, and A. thaliana) shows that NMFGO is robust to the input parameters and achieves significantly better prediction performance than GIC, TO, dRW- kNN, and NtN, which were re-implemented based on the instructions of the original papers. The supplementary file and demo codes of NMFGO are available at http://mlda.swu.edu.cn/codes.php?name=NMFGO.

The traditional reversible data hiding technique is based on cover image modification which inevitably leaves some traces of rewriting that can be more easily analyzed and attacked by the warder. Inspired by the cover synthesis steganography-based generative adversarial networks, in this paper, a novel generative reversible data hiding (GRDH) scheme by image translation is proposed. First, an image generator is used to obtain a realistic image, which is used as an input to the image-to-image translation model with CycleGAN. After image translation, a stego image with different semantic information will be obtained. The secret message and the original input image can be recovered separately by a well-trained message extractor and the inverse transform of the image translation. The experimental results have verified the effectiveness of the scheme.

Motivation: Long non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention and treatment, but only a small portion of lncRNA-disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA-disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be. Results: To accurately identify lncRNA-disease associations, we propose a Matrix Factorization based LncRNA-Disease Association prediction model (MFLDA in short). MFLDA decomposes data matrices of heterogeneous data sources into low-rank matrices via matrix tri-factorization to explore and exploit their intrinsic and shared structure. MFLDA can select and integrate the data sources by assigning different weights to them. An iterative solution is further introduced to simultaneously optimize the weights and low-rank matrices. Next, MFLDA uses the optimized low-rank matrices to reconstruct the lncRNA-disease association matrix and thus to identify potential associations. In 5-fold cross validation experiments to identify verified lncRNA-disease associations, MFLDA achieves an area under the receiver operating characteristic curve (AUC) of 0.7408, at least 3% higher than those given by state-of-the-art data fusion based computational models. An empirical study on identifying masked lncRNA-disease associations again shows that MFLDA can identify potential associations more accurately than competing models. A case study on identifying lncRNAs associated with breast, lung and stomach cancers show that 38 out of 45 (84%) associations predicted by MFLDA are supported by recent biomedical literature and further proves the capability of MFLDA in identifying novel lncRNA-disease associations. MFLDA is a general data fusion framework, and as such it can be adopted to predict associations between other biological entities. Availability and implementation: The source code for MFLDA is available at: http://mlda.swu.edu.cn/codes.php? name = MFLDA. Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many of them are incomplete. We proposed a method called NewGOA to predict new Gene Ontology (GO) annotations for incompletely annotated proteins and for completely un-annotated ones. NewGOA employs a hybrid graph, composed of two types of nodes (proteins and GO terms), to encode interactions between proteins, hierarchical relationships between terms and available annotations of proteins. To account for structural difference between GO terms subgraph and proteins subgraph, NewGOA applies a bi-random walks algorithm, which executes asynchronous random walks on the hybrid graph, to predict new GO annotations of proteins. Experimental study on archived GO annotations of two model species (H. Sapiens and S. cerevisiae) shows that NewGOA can more accurately and efficiently predict new annotations of proteins than other related methods. Experimental results also indicate the bi-random walks can explore and further exploit the structural difference between GO terms subgraph and proteins subgraph. The supplementary files and codes of NewGOA are available at: http://mlda.swu.edu.cn/codes.php?name=NewGOA.

MOTIVATION: Predicting the biological functions of proteins is one of the key challenges in the post-genomic era. Computational models have demonstrated the utility of applying machine learning methods to predict protein function. Most prediction methods explicitly require a set of negative examples-proteins that are known not carrying out a particular function. However, Gene Ontology (GO) almost always only provides the knowledge that proteins carry out a particular function, and functional annotations of proteins are incomplete. GO structurally organizes more than tens of thousands GO terms and a protein is annotated with several (or dozens) of these terms. For these reasons, the negative examples of a protein can greatly help distinguishing true positive examples of the protein from such a large candidate GO space. RESULTS: In this paper, we present a novel approach (called NegGOA) to select negative examples. Specifically, NegGOA takes advantage of the ontology structure, available annotations and potentiality of additional annotations of a protein to choose negative examples of the protein. We compare NegGOA with other negative examples selection algorithms and find that NegGOA produces much fewer false negatives than them. We incorporate the selected negative examples into an efficient function prediction model to predict the functions of proteins in Yeast, Human, Mouse and Fly. NegGOA also demonstrates improved accuracy than these comparing algorithms across various evaluation metrics. In addition, NegGOA is less suffered from incomplete annotations of proteins than these comparing methods. AVAILABILITY AND IMPLEMENTATION: The Matlab and R codes are available at https://sites.google.com/site/guoxian85/neggoa CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Determining the biological functions of proteins is one of the key challenges in the post-genomic era. The rapidly accumulated large volumes of proteomic and genomic data drives to develop computational models for automatically predicting protein function in large scale. Recent approaches focus on integrating multiple heterogeneous data sources and they often get better results than methods that use single data source alone. In this paper, we investigate how to integrate multiple biological data sources with the biological knowledge, i.e., Gene Ontology (GO), for protein function prediction. We propose a method, called SimNet, to Semantically integrate multiple functional association Networks derived from heterogenous data sources. SimNet firstly utilizes GO annotations of proteins to capture the semantic similarity between proteins and introduces a semantic kernel based on the similarity. Next, SimNet constructs a composite network, obtained as a weighted summation of individual networks, and aligns the network with the kernel to get the weights assigned to individual networks. Then, it applies a network-based classifier on the composite network to predict protein function. Experiment results on heterogenous proteomic data sources of Yeast, Human, Mouse, and Fly show that, SimNet not only achieves better (or comparable) results than other related competitive approaches, but also takes much less time. The Matlab codes of SimNet are available at https://sites.google.com/site/guoxian85/simnet.