Tree-like Pattern Research Articles

Boosted Convolutional Decision Trees for Translationally Invariant Pattern Recognition and Transfer Learning

Decision Tree (DT) models provide a well-known class of interpretable machine learning tools for diverse pattern recognition problems. However, applying DTs to learn floating features in images and categorical data based on their raw representation has been challenging. Convolutional Neural Networks (CNNs) are the current state-of-the-art method for classifying raw images, but have their own disadvantages, including that they are often difficult to interpret, have a large number of parameters and hyperparameters, require a fixed image size, and have only partial translational invariance directly built into its architecture. We propose a novel application of Convolutional Decision Trees (CDTs) and show that our approach is more interpretable and can learn higher quality convolutional filters compared to CNNs. CDTs have full translational invariance built into the architecture and can be trained and make predictions on variable-sized images. Using two independent test cases—protein-DNA binding prediction, and hand-written digit classification—we demonstrate that our GPU-enabled implementation of the Cross Entropy (CE) optimization method for training CDTs learns informative convolutional filters that can both facilitate accurate data classifications in a tree-like pattern and be used for transfer learning to improve CNNs themselves. These results motivate further studies on developing accurate and efficient tree-based models for pattern recognition and computer vision.

Tree-like crack patterns in clay dried in a uniform DC electric field

We report desiccation crack formation on a layer of aqueous Laponite® RD gel, exposed to a uniform static electric field varying from 357 to 928 V m−1. The cracks formed exhibit an interesting tree-like pattern. A large number of cracks (∼70) appear initially at the positive end of the sample. Several neighbouring cracks merge with each other, while proceeding towards the negative end leading to a smaller number of cracks. This process is repeated a few times before the hierarchical pattern thus formed reaches the negative end of the sample. The number of cracks is finally reduced to ∼10. The initial number of cracks increases with increasing field strength. The disc-like Laponite® RD clay particles behave as negatively charged in an aqueous medium, because of the diffusion of positive counterions into the solvent, which form a double layer. The external field causes gradual build up of density of positive counterions towards the negative electrode. The bare Laponite® discs which are negatively charged repel each other to create the cracks at the positive end. We develop a simple model to calculate the charge distribution of counterions along the sample. We offer an explanation for the structure of the anisotropic tree-like crack patterns observed on the basis of this model.

Preliminary study of single-operator cholangioscopy for diagnosing pancreatic cystic lesions

Advances in imaging technology have improved the annual detection rate of pancreatic cystic lesions (PCLs), but the preoperative diagnosis of PCLs remains unclear. Thus, the usefulness of single-operator cholangioscopy (SOC) as a diagnostic imaging tool for PCLs is worth investigating. We performed an intracystic visual examination of PCLs using SOC to determine the diagnostic value of SOC for PCLs. In this retrospective observational study, PCLs were confirmed using a diagnostic imaging modality. Patients who underwent an EUS-guided through-the-needle fiberoptic pancreatic cystoscopy and SOC examination and those whose lesion type was definitively diagnosed were included (n= 43). If the cystic fluid was turbid, a physiologic saline solution was injected into the cyst, and a SOC fiberoptic probe was inserted through a 19-gauge needle to observe the wall of the intracystic cavity and its contents. The characteristics were recorded, and the cystic fluid and biopsy specimens were further assessed by performing liquid-based cytologic and histopathologic examinations. Particularly, histopathologic examinations were performed in patients who underwent surgery. Intracystic characteristics of the confirmed cases of PCLs (43 patients) were identified through intracystic visual examination with SOC. The clarity of cyst fluid is a prerequisite for imaging by SOC. The tree-like branching pattern of blood vessel distribution may be a serous cystic neoplasm-specific characteristic. Intracystic papilla-like structure is an important characteristic for diagnosing mucinous cystic neoplasms. The identified imaging characteristics such as blood vessel distribution on the intracystic wall and the contents of different PCLs observed under the SOC probe can provide useful information for diagnosing PCLs. SOC could be an important ancillary imaging test of PCLs by EUS.

Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss.

We analyze patterns of gene presence and absence in a maximum likelihood framework with rate parameters for gene gain and loss. Standard methods allow independent gains and losses in different parts of a tree. While losses of the same gene are likely to be frequent, multiple gains need to be considered carefully. A gene gain could occur by horizontal transfer or by origin of a gene within the lineage being studied. If a gene is gained more than once, then at least one of these gains must be a horizontal transfer. A key parameter is the ratio of gain to loss rates, a/v We consider the limiting case known as the infinitely many genes model, where a/v tends to zero and a gene cannot be gained more than once. The infinitely many genes model is used as a null model in comparison to models that allow multiple gains. Using genome data from cyanobacteria and archaea, it is found that the likelihood is significantly improved by allowing for multiple gains, but the average a/v is very small. The fraction of genes whose presence/absence pattern is best explained by multiple gains is only 15% in the cyanobacteria and 20% and 39% in two data sets of archaea. The distribution of rates of gene loss is very broad, which explains why many genes follow a treelike pattern of vertical inheritance, despite the presence of a significant minority of genes that undergo horizontal transfer.

Temperature affects the silicate morphology in a diatom.

Silica deposition by diatoms, a common component of the phytoplankton, has attracted considerable interest given the importance in ecology and materials science. There has recently been a great deal of research into the biological control of biosilicifcation, yet the in vivo physical and chemical effects have not been quantitatively investigated. We have grown the marine diatom Thalassiosira pseudonana in batch culture at three temperatures (14o, 18o, and 23 °C). We observed three distinct temperature-dependent growth phases. The morphology of silica was investigated using scanning electron microscopy followed by image analysis and supervised learning. The silica in the valves of the same species showed different structures: a mesh-like pattern in silicon-rich cultures and a tree-like pattern in silicon-limited cultures. Moreover, temperature affected this silica pattern, especially in silicon-limited cultures. We conclude that cells grown at 14 °C and 18 °C divide more successfully in Si-limited conditions by developing a tree-like pattern (lower silicification).

Behind Family Trees

Although it has long been recognized that the family tree model is too simplistic to account for historical connections between languages, most computational studies of language history have concentrated on tree-building methods. Here, we employ computational network methods to assess the utility of network models in comparison with tree models in studying the subgrouping of Uralic languages. We also compare basic vocabulary data with words that are more easily borrowed and replaced cross-linguistically (less basic vocabulary) in order to find out how secondary connections affect computational analyses of this language family. In general, the networks support a treelike pattern of diversification, but also provide information about conflicting connections underlying some of the ambiguous divergences in the trees. These are seen as reflections of unclear divergence patterns (either in ancestral protolanguages or between languages closely related at present), which pose problems for a tree model. The networks also show that the relationships of closely related present-day languages are more complex than what the tree models suggest. When comparing less basic with basic vocabulary, we can detect the effect of borrowing between different branches (horizontal transfer) mostly between and within the Finnic and Saami subgroups. We argue that the trees obtained with basic vocabulary provide the primary pattern of the divergence of a language family, whereas networks, especially those constructed with less basic vocabulary, add reality to the picture by showing the effect of more complicated developments affecting the connections between the languages.

Conducting crack propagation driven by electric fields in ferroelectric ceramics

Ferroelectric ceramics are susceptible to fracture under high electric fields, which are commonly generated in the vicinity of electrodes or conducting layers. In the present work, we extend a phase-field model of fracture in ferroelectric single crystals to the simulation of the propagation of conducting cracks under purely electrical loading. This is done by introducing the electrical enthalpy of a diffuse conducting layer into the phase-field formulation. Simulation results show oblique crack propagation and crack branching from a conducting notch, forming a tree-like crack pattern in a ferroelectric sample under positive and negative electric fields. Microstructure evolution indicates the formation of tail-to-tail and head-to-head 90° domains, which results in charge accumulation around the crack. The charge accumulation, in turn, induces a high electric field and hence a high electrostatic energy, further driving the conducting crack. Salient features of the results are compared with experiments.

Cutaneous leishmaniasis: new dermoscopic findings

Cutaneous leishmaniasis (CL) has a worldwide distribution. Delayed and incorrect diagnosis may cause the significant spread of this disease and consequent increases in morbidity and drug resistance. We aimed to determine dermoscopic features of CL that may help to improve the accuracy of clinical diagnosis of the disease. A total of 145 lesions in 102 patients were evaluated dermoscopically. Following the diagnosis of CL, all lesions were evaluated by experienced dermoscopists. A total of 51 papules, 40 nodulo-ulcerative lesions, 31 plaques, and 23 nodules were evaluated by dermoscopy. Generalized erythema appeared in all lesions (100%), yellow tears in 58 lesions, both crust and ulcer in 51 lesions, white starburst-like patterns in 27 lesions, ovoid salmon-colored structures in 19 lesions, and a perilesional hypopigmented halo pattern in four lesions. Various vascular structures were present in 126 lesions. The most common vascular structure observed was an irregular linear pattern in 78 lesions, followed by a tree-like pattern in 53 lesions. The rest of the vascular structures included hairpin vessels in 25 lesions, glomerulus-like vessels in 24 lesions, dotted vessels in 23 lesions, comma-shaped vessels in six lesions, and polymorphous/atypical vessels in four lesions. We did not identify the types of parasite involved. Yellow tears, white starburst-like patterns and salmon-colored ovoid structures seem to appear specifically in CL lesions. In geographical areas in which CL is common, dermoscopy may be utilized as a useful diagnostic tool that is practical and non-invasive.

Chaotic vessels fabricated by fractal gelatin

A novel gelatin patterning technique applied to making capillary vessels with fractal dendrite configuration is presented. Such a chaotic tree-like pattern has been obtained by precipitating among the gelatin matrix that is spin coated on a glass substrate at room temperature. The weight percentage of the original gelatin solution is over saturated. As the temperature decreases, the gelatin crystallises and forms a natural fractal pattern extruding the film surface. The process conditions of spin coating and the gelatine concentration are varied so that the hydraulic diameters of the fractal branches are verified from 0.1 to 23 µm. The authors therefore fabricated hollow vessels by the polydimethylsiloxane (PDMS) de-moulding of the soft lithography. The water filling test of the PDMS vessel chip is done accordingly. The issue of the toxicity is also addressed.

Phylomemetics—Evolutionary Analysis beyond the Gene

Genes are propagated by error-prone copying, and the resulting variation provides the basis for phylogenetic reconstruction of evolutionary relationships. Horizontal gene transfer may be superimposed on a tree-like evolutionary pattern, with some relationships better depicted as networks. The copying of manuscripts by scribes is very similar to the replication of genes, and phylogenetic inference programs can be used directly for reconstructing the copying history of different versions of a manuscript text. Phylogenetic methods have also been used for some time to analyse the evolution of languages and the development of physical cultural artefacts. These studies can help to answer a range of anthropological questions. We propose the adoption of the term “phylomemetics” for phylogenetic analysis of reproducing non-genetic elements.

Comparison of the Network Structure and the Pattern of Network Extension in Intracellular Organelles of Yeast

Large-scale information-spreading processes, such as scale-free networks, mostly follow a smallworld principle. In contrast, the processing of information at a person-to-person level follows a narrow and deep tree-like pattern. This information-spreading style represents a type of local communication dynamic within a small-world social network. We constructed local protein-interaction networks for cytoplasm, mitochondria, nucleus, and endosomes, and then characterized their structural properties and patterns of extension. Although the mitochondrial protein network possessed a scale-free character, similar to the networks of other organelles, it had a relatively large diameter. It was difficult to identify possible narrow, deep-reaching style characteristics because of the small mitochondrial dataset. However, the network structure was clearly distinguishable from that of the other organelles. We characterized diameter extension processes and network evolution by randomly extending the number of nodes or edges, showing that the mitochondrial network extension process was relatively distinct from that of other organelle networks in diameter but not in evolution rate. The network structure and the pattern of extension of the protein-interaction network in mitochondria are distinct from those of the cytoplasm, nucleous, and endosome. These differences may be a reflection of the unique origin and distinct functions of mitochondria.

The public goods hypothesis for the evolution of life on Earth

It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis.

Morphodynamics during air injection into water-saturated movable spherical granulates

Laboratory air injection experiments in a two-dimensional vertically placed cell filled with a water-saturated packing of spherical glass beads show a particular transition of air flow patterns at different length scales, tree-like fingering with pore-scale drainage, a local fluidization of beads with finger-scale channeled air flow, and an oscillating irregular channel with finger-scale air flow, where the channel is formed by pushing beads aside. The tree-like pattern shows a parabola-like growth with vertical height, while both the top and the bottom lateral width of the pattern increase linearly for the small injection rate, then stay more or less constant for further increasing injection rates. By tracing the vertical position of maximum advance of the fluidized pattern with time, the evolution of the fluidized pattern is characterized by two dynamic regimes, the pattern not reaching or reaching the injection orifice, respectively, using small and medium injection rates. As the injection rate increases further, the fluidized pattern shows up immediately after air is injected. Via physical conceptual models using local forces or pressure gradient balances, we derive a series of characteristics that describe the width of the tree-like air plume, the width of a single channel, and the starting vertical position of the fluidized pattern.

Excellent long-term outcome of hepaticojejunostomy for biliary atresia with a hilar cyst

Background Biliary atresia (BA) with hilar cyst is an uncommon variant, which constitutes less than 10% of all types of BA, and the operative procedure for this type of BA remains controversial. Methods We have had 200 cases with BA from 1963 to 2008 in our institute and our branch hospitals, in which 12 cases (6%) were BA with a hilar cyst. The clinical records of all cases were evaluated retrospectively. Results Twelve BA patients with a hilar cyst included 2 boys and 10 girls. The diagnosis of BA was confirmed by intraoperative cholangiography (cloudy or treelike pattern). In all 12 cases, a hepaticojejunostomy was performed at a median age of 71.6 days (range, 24-136 days). The follow-up periods were 1.2 to 23.2 years. The current mean total bilirubin level was 0.8 mg/dL (range, 0.2-3.5 mg/dL), and the mean direct bilirubin level was 0.2 mg/dL (range, 0.0 to 0.8 mg/dL). Methylprednisolone or oral prednisolone was administered in 8 cases after operation, and 10 of 12 cases achieved a jaundice free state. The postoperative complications were cholangitis (n = 10), gastroesophageal varices (n = 7), splenomegaly (n = 3), ileus (n = 1), and pulmonary hypertension (n = 1). The overall survival rate with a native liver was 10 (83.3%) of 12 cases, of which 9 cases were jaundice-free and only 1 case showed recurrent jaundice. The other 2 cases underwent living-donor liver transplantation at age of 2 and 20 years, respectively, and they are currently doing well. Conclusions Most cases of BA with a hilar cyst achieved excellent clinical outcome after a hepaticojejunostomy.

Fractal Pattern Formed in Ag-In Electrodeposits

We investigated pattern formation in Ag-In electrodeposition by constructing a morphology diagram that indicates the presence of pattern at a current density and cathode potential. The patterns that emerge as a fishbone and tree are found to have a fractal property. As the current density increases, the fishbone-like pattern with a fractal dimension of 1.44 changes into the tree-like pattern with a fractal dimension of 1.64. The increase in the fractal dimension is related to an increase in the number of branch in the pattern.

THE ONTOGENY OF SCALE-FREE SYNTAX NETWORKS: PHASE TRANSITIONS IN EARLY LANGUAGE ACQUISITION

Language development in children provides a window to understand the transition from protolanguage to language. Here we present the first analysis of the emergence of syntax in terms of complex networks. A previously unreported, sharp transition is shown to occur around two years of age from a (pre-syntactic) tree-like structure to a scale-free, small world syntax network. The development of these networks thus reveals a nonlinear dynamical pattern where the global topology of syntax graphs shifts from a hierarchical, tree-like pattern, to a scale-free organization. Such change seems difficult to be explained under a self-organization framework. Instead, it actually supports the presence of some underlying innate component, as early suggested by some authors.

Microvascular Architecture of Breast Lesions

The purpose of this study was to evaluate the effectiveness of micro flow imaging (MFI) of the microvascular architecture with contrast-enhanced ultrasonography for classification of breast lesions as benign or malignant and the microvascular architectural patterns. Contrast-enhanced ultrasonography and MFI were performed in 61 women with breast lesions. The microvascular morphologic and distribution features of the breast tumors were evaluated with MFI. Receiver operating characteristic curve analysis was used to evaluate the diagnostic value of MFI, and the microvascular architectural patterns were analyzed. Surgical pathologic analysis showed 29 benign and 32 malignant lesions. For MFI, the area under the receiver operating characteristic curve (A(z)) value for the overall features of the blood vessels for classification of breast lesions was 0.94. The accuracy, sensitivity, and specificity were 90.2% (55/61), 93.8% (30/32), and 86.2% (25/29), respectively. The A(z) value for the morphologic and distribution features of peripheral blood vessels was 0.91, which was significantly higher than the A(z) value for the morphologic and distribution features of interior vessels (P= .019). The microvascular architecture of the 61 lesions was categorized into 3 patterns: treelike, root hair-like, and crab claw-like. Benign lesions mainly displayed the treelike pattern (17 [58.6%]); malignant lesions tended to display the crab claw-like pattern (20 [62.5%]); and the root hair-like pattern was shown in both benign and malignant lesions (11 [37.9%] and 8 [25%], respectively). The microvascular architecture showed significant differences between benign and malignant lesions (P< .001). Micro flow imaging can clearly delineate the microvascular architecture of breast lesions and can aid in discrimination between benign and malignant breast lesions.

Tracing information flow on a global scale using Internet chain-letter data

Although information, news, and opinions continuously circulate in the worldwide social network, the actual mechanics of how any single piece of information spreads on a global scale have been a mystery. Here, we trace such information-spreading processes at a person-by-person level using methods to reconstruct the propagation of massively circulated Internet chain letters. We find that rather than fanning out widely, reaching many people in very few steps according to "small-world" principles, the progress of these chain letters proceeds in a narrow but very deep tree-like pattern, continuing for several hundred steps. This suggests a new and more complex picture for the spread of information through a social network. We describe a probabilistic model based on network clustering and asynchronous response times that produces trees with this characteristic structure on social-network data.

Peritectic reaction and its influences on the microstructures evolution during directional solidification of Fe–Ni alloys

Systematic directional solidification experiments were carried out in Fe–Ni peritectic alloys to investigate the influences of peritectic reaction on the microstructures evolution. Various microstructures were observed in the directionally solidified samples, such as bands, mixed bands, island banding, tree-like oscillatory pattern, coupled and cellular coupled growth structures. It was found that peritectic reaction occurs near the trijunctions during the two-phase growth at different interface morphologies of the primary phase observed as planar, cellular and dendritic. Peritectic reaction makes the liquid/δ/γ trijunctions region quite irregular and makes the trijunctions dynamics quite complicated, and thus plays an important role in the formation of various microstructures.

Pattern pluralism and the Tree of Life hypothesis.

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.