Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition

The primate visual system achieves remarkable visual object recognition performance even in brief presentations and under changes to object exemplar, geometric transformations, and background variation (a.k.a. core visual object recognition). This remarkable performance is mediated by the representation formed in inferior temporal (IT) cortex. In parallel, recent advances in machine learning have led to ever higher performing models of object recognition using artificial deep neural networks (DNNs). It remains unclear, however, whether the representational performance of DNNs rivals that of the brain. To accurately produce such a comparison, a major difficulty has been a unifying metric that accounts for experimental limitations such as the amount of noise, the number of neural recording sites, and the number trials, and computational limitations such as the complexity of the decoding classifier and the number of classifier training examples. In this work we perform a direct comparison that corrects for these experimental limitations and computational considerations. As part of our methodology, we propose an extension of "kernel analysis" that measures the generalization accuracy as a function of representational complexity. Our evaluations show that, unlike previous bio-inspired models, the latest DNNs rival the representational performance of IT cortex on this visual object recognition task. Furthermore, we show that models that perform well on measures of representational performance also perform well on measures of representational similarity to IT and on measures of predicting individual IT multi-unit responses. Whether these DNNs rely on computational mechanisms similar to the primate visual system is yet to be determined, but, unlike all previous bio-inspired models, that possibility cannot be ruled out merely on representational performance grounds.Comment: 35 pages, 12 figures, extends and expands upon arXiv:1301.353

Deep Lesion Graphs in the Wild: Relationship Learning and Organization of Significant Radiology Image Findings in a Diverse Large-scale Lesion Database

Radiologists in their daily work routinely find and annotate significant abnormalities on a large number of radiology images. Such abnormalities, or lesions, have collected over years and stored in hospitals' picture archiving and communication systems. However, they are basically unsorted and lack semantic annotations like type and location. In this paper, we aim to organize and explore them by learning a deep feature representation for each lesion. A large-scale and comprehensive dataset, DeepLesion, is introduced for this task. DeepLesion contains bounding boxes and size measurements of over 32K lesions. To model their similarity relationship, we leverage multiple supervision information including types, self-supervised location coordinates and sizes. They require little manual annotation effort but describe useful attributes of the lesions. Then, a triplet network is utilized to learn lesion embeddings with a sequential sampling strategy to depict their hierarchical similarity structure. Experiments show promising qualitative and quantitative results on lesion retrieval, clustering, and classification. The learned embeddings can be further employed to build a lesion graph for various clinically useful applications. We propose algorithms for intra-patient lesion matching and missing annotation mining. Experimental results validate their effectiveness.Comment: Accepted by CVPR2018. DeepLesion url adde

On morphological hierarchical representations for image processing and spatial data clustering

Hierarchical data representations in the context of classi cation and data clustering were put forward during the fties. Recently, hierarchical image representations have gained renewed interest for segmentation purposes. In this paper, we briefly survey fundamental results on hierarchical clustering and then detail recent paradigms developed for the hierarchical representation of images in the framework of mathematical morphology: constrained connectivity and ultrametric watersheds. Constrained connectivity can be viewed as a way to constrain an initial hierarchy in such a way that a set of desired constraints are satis ed. The framework of ultrametric watersheds provides a generic scheme for computing any hierarchical connected clustering, in particular when such a hierarchy is constrained. The suitability of this framework for solving practical problems is illustrated with applications in remote sensing

3-D Face Analysis and Identification Based on Statistical Shape Modelling

This paper presents an effective method of statistical shape representation for automatic face analysis and identification in 3-D. The method combines statistical shape modelling techniques and the non-rigid deformation matching scheme. This work is distinguished by three key contributions. The first is the introduction of a new 3-D shape registration method using hierarchical landmark detection and multilevel B-spline warping technique, which allows accurate dense correspondence search for statistical model construction. The second is the shape representation approach, based on Laplacian Eigenmap, which provides a nonlinear submanifold that links underlying structure of facial data. The third contribution is a hybrid method for matching the statistical model and test dataset which controls the levels of the model’s deformation at different matching stages and so increases chance of the successful matching. The proposed method is tested on the public database, BU-3DFE. Results indicate that it can achieve extremely high verification rates in a series of tests, thus providing real-world practicality

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster

Toward a generic representation of random variables for machine learning

This paper presents a pre-processing and a distance which improve the performance of machine learning algorithms working on independent and identically distributed stochastic processes. We introduce a novel non-parametric approach to represent random variables which splits apart dependency and distribution without losing any information. We also propound an associated metric leveraging this representation and its statistical estimate. Besides experiments on synthetic datasets, the benefits of our contribution is illustrated through the example of clustering financial time series, for instance prices from the credit default swaps market. Results are available on the website www.datagrapple.com and an IPython Notebook tutorial is available at www.datagrapple.com/Tech for reproducible research.Comment: submitted to Pattern Recognition Letter

Matching Natural Language Sentences with Hierarchical Sentence Factorization

Semantic matching of natural language sentences or identifying the relationship between two sentences is a core research problem underlying many natural language tasks. Depending on whether training data is available, prior research has proposed both unsupervised distance-based schemes and supervised deep learning schemes for sentence matching. However, previous approaches either omit or fail to fully utilize the ordered, hierarchical, and flexible structures of language objects, as well as the interactions between them. In this paper, we propose Hierarchical Sentence Factorization---a technique to factorize a sentence into a hierarchical representation, with the components at each different scale reordered into a "predicate-argument" form. The proposed sentence factorization technique leads to the invention of: 1) a new unsupervised distance metric which calculates the semantic distance between a pair of text snippets by solving a penalized optimal transport problem while preserving the logical relationship of words in the reordered sentences, and 2) new multi-scale deep learning models for supervised semantic training, based on factorized sentence hierarchies. We apply our techniques to text-pair similarity estimation and text-pair relationship classification tasks, based on multiple datasets such as STSbenchmark, the Microsoft Research paraphrase identification (MSRP) dataset, the SICK dataset, etc. Extensive experiments show that the proposed hierarchical sentence factorization can be used to significantly improve the performance of existing unsupervised distance-based metrics as well as multiple supervised deep learning models based on the convolutional neural network (CNN) and long short-term memory (LSTM).Comment: Accepted by WWW 2018, 10 page