Computing Robinson-Foulds supertree for two trees

Supertree problems are important in phylogeny estimation. Supertree construction takes in a set of input trees on subsets of species and aims to find a supertree containing all species subjective to some combinatorial or statistical criterion. As such, it can be used to combine trees estimated by different research projects, or to construct species trees from gene trees that may not contain all species, or to serve a part in divide-and-conquer pipelines that improve the scalability of large scale phylogeny estimation. Yet the most promising supertree methods, such as the popular Robinson-Foulds Supertree (RFS) methods, not only cannot guarantee an optimal solution but also are computationally intensive by themselves, as they are heuristics for NP-hard optimization problems. We present the first polynomial time algorithm to exactly solve the RFS problem on two binary input trees, and prove that finding the Robinson-Foulds Supertree of three input trees is NP-hard. We present GreedyRFS, a greedy heuristic for the Robinson-Foulds Supertree problem that operates by using our exact algorithm for RFS on pairs of trees, until all the trees are merged into a single supertree. Our experiments show that GreedyRFS has better accuracy than FastRFS, the leading heuristic for RFS, when the number of input trees is small, which is the natural case for use within divide-and-conquer pipelines

Algorithms for detecting dependencies and rigid subsystems for CAD

Geometric constraint systems underly popular Computer Aided Design soft- ware. Automated approaches for detecting dependencies in a design are critical for developing robust solvers and providing informative user feedback, and we provide algorithms for two types of dependencies. First, we give a pebble game algorithm for detecting generic dependencies. Then, we focus on identifying the "special positions" of a design in which generically independent constraints become dependent. We present combinatorial algorithms for identifying subgraphs associated to factors of a particular polynomial, whose vanishing indicates a special position and resulting dependency. Further factoring in the Grassmann- Cayley algebra may allow a geometric interpretation giving conditions (e.g., "these two lines being parallel cause a dependency") determining the special position.Comment: 37 pages, 14 figures (v2 is an expanded version of an AGD'14 abstract based on v1

Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees

One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life is enormously computationally challenging, as all the current most accurate methods are either heuristics for NP-hard optimization problems or Bayesian MCMC methods that sample from tree space. One of the most promising approaches for improving scalability and accuracy for phylogeny estimation uses divide-and-conquer: a set of species is divided into overlapping subsets, trees are constructed on the subsets, and then merged together using a "supertree method". Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard. We also present GreedyRFS (a greedy heuristic that operates by repeatedly using Exact-RFS-2 on pairs of trees, until all the trees are merged into a single supertree). We evaluate Exact-RFS-2 and GreedyRFS, and show that they have better accuracy than the current leading heuristic for RFS

Classifiability-based Optimal Discriminatory Projection Pursuit

Linear Discriminant Analysis (LDA) might be the most widely used linear feature extraction method in pattern recognition. Based on the analysis on the several limitations of traditional LDA, this paper makes an effort to propose a new computational paradigm named Optimal Discriminatory Projection Pursuit (ODPP), which is totally different from the traditional LDA and its variants. Only two simple steps are involved in the proposed ODPP: one is the construction of candidate projection set; the other is the optimal discriminatory projection pursuit. For the former step, candidate projections are generated as the difference vectors between nearest between-class boundary samples with redundancy well-controlled, while the latter is efficiently achieved by classifiability-based AdaBoost learning from the large candidate projection set. We show that the new 'projection pursuit' paradigm not only does not suffer from the limitations of the traditional LDA but also inherits good generalizability from the boundary attribute of candidate projections. Extensive experimental comparisons with LDA and its variants on synthetic and real data sets show that the proposed method consistently has better performances. ?2008 IEEE.EI

Expression and biological significance of c-FLIP in human hepatocellular carcinomas

<p>Abstract</p> <p>Background</p> <p>c-FLIP can be considered as a tumor-progression factor in regard to its anti-apoptotic functions. In the present study, we intended to investigate the expression of c-FLIP in human HCC tissues, and its relation with drug-induced cell apoptosis through the specific inhibition of c-FLIP expression by siRNA in 7721 cells.</p> <p>Methods</p> <p>c-FLIP expression was quantified immunohistochemically in HCC tissues(eighty-six cases), and corresponding noncancerous tissues (fifty-seven cases). Patients with HCC were followed up for cancer recurrence. Then, the c-FLIP gene was silenced with specific siRNA in 7721 HCC cells. c-FLIP expression was detected by RT-PCR, Western Blot and immunocytochemical staining. The cellular viability and cell apoptosis were assayed <it>in vitro </it>with cells treated with doxorubicin.</p> <p>Results</p> <p>Positive immunostaining was detected for c-FLIP in 83.72% (72/86) human HCC tissues, 14.81% (4/27) hepatic cirrhosis, 11.11% (2/18) hepatic hemangioma tissues, and absent in normal hepatic tissues. The overexpression(more than 50%) of c-FLIP in HCC adversely affected the recurrence-free survival. Through c-FLIP gene silencing with siRNA, the expressions of c-FLIP mRNA and protein were remarkably down-regulated in 7721 HCC cells. And doxorubicin showed apparent inhibition on cell proliferations, and induced more apoptosis.</p> <p>Conclusion</p> <p>These results indicate that c-FLIP is frequently expressed in human HCCs, and its overexpression implied a lesser probability of recurrence-free survival. The specific silencing of c-FLIP gene can apparently up-regulate drug-induced HCC cell apoptosis, and may have therapeutic potential for the treatment of human HCC.</p

Improving Face Sketch Recognition via Adversarial Sketch-Photo Transformation

International audiencefeature learning [7]-[10]. The benefit of the former category relates to the conversion of sketches into the same modality as photos, and hence lies in the ability to utilize existing photo-based face recognition methods. Thus, the applicability of the existing photo-based face recognition algorithms can be greatly expanded. Current methods for face photo-sketch transformation can be mainly grouped into example-based methods and regression-based methods. Example-based methods assume that the corresponding sketches (or patches of sketches) of two similar face photos (or patches of face photos) are also similar. Such methods rely on face photo-sketch pairs in the training set to synthesize images. In order to achieve good transformation results, these methods usually require a large number of photo-sketch pairs. However, the computational cost may also grow linearly with the increase of the training set size. Regression-based methods overcome the issues mentioned above and the most time-consuming part only exists in the training stage when learning the mapping between face photos and sketches, but the inference/testing stage can be fast. In this paper, we propose a Generative Adversarial Network (GAN) for face sketch-to-photo transformation , leveraging the advantages of CycleGAN [11] and conditional GANs [12]. We have designed a new feature-level loss, which is jointly used with the traditional image-level adversarial loss to ensure the quality of the synthesized photos. The proposed approach outperforms state-of-the-art approaches for synthesizing photos in terms of structural similarity index (SSIM). More importantly, the synthesized photos of our approach are found to be more instrumental in improving the sketch-to-photo matching accuracy. The rest of this paper is organized as follows: Section II summarizes representative methods of face photo-to-sketch transformation, and GANs. Section III provides details of the proposed method and the designed feature-level loss. Experimental results and analysis are presented in Section IV. Finally, we conclude this work in Section V. Abstract-Face sketch-photo transformation has broad applications in forensics, law enforcement, and digital entertainment, particular for face recognition systems that are designed for photo-to-photo matching. While there are a number of methods for face photo-to-sketch transformation, studies on sketch-to-photo transformation remain limited. In this paper, we propose a novel conditional CycleGAN for face sketch-to-photo transformation. Specifically, we leverage the advantages of CycleGAN and conditional GANs and design a feature-level loss to assure the high quality of the generated face photos from sketches. The generated face photos are used, as a replacement of face sketches, and particularly for face identification against a gallery set of mugshot photos. Experimental results on the public-domain database CUFSF show that the proposed approach is able to generate realistic photos from sketches, and the generated photos are instrumental in improving the sketch identification accuracy against a large gallery set