Computational convergence of the path integral for real dendritic morphologies

Neurons are characterised by a morphological structure unique amongst biological cells, the core of which is the dendritic tree. The vast number of dendritic geometries, combined with heterogeneous properties of the cell membrane, continue to challenge scientists in predicting neuronal input-output relationships, even in the case of sub-threshold dendritic currents. The Green’s function obtained for a given dendritic geometry provides this functional relationship for passive or quasi-active dendrites and can be constructed by a sum-over-trips approach based on a path integral formalism. In this paper, we introduce a number of efficient algorithms for realisation of the sum-over-trips framework and investigate the convergence of these algorithms on different dendritic geometries. We demonstrate that the convergence of the trip sampling methods strongly depends on dendritic morphology as well as the biophysical properties of the cell membrane. For real morphologies, the number of trips to guarantee a small convergence error might become very large and strongly affect computational efficiency. As an alternative, we introduce a highly-efficient matrix method which can be applied to arbitrary branching structures

Numerical analysis of shell and spatial structures

Since the advent of the computer into the engineering field, the application of the numerical methods to the solution of engineering problems has grown very rapidly. Among the different computer methods of structural analysis the Finite Element (FEM) has been predominantly used. Shells and space structures are very attractive and have been constructed to solve a large variety of functional problems (roofs, industrial building, aqueducts, reservoirs, footings etc). In this type of structures aesthetics, structural efficiency and concept play a very important role. This class of structures can be divided into three main groups, namely continuous (concrete) shells, space frames and tension (fabric, pneumatic, cable etc )structures. In the following only the current applications of the FEM to the analysis of continuous shell structures will be discussed. However, some of the comments on this class of shells can be also applied to some extend to the others, but obviously specific computational problems will be restricted to the continuous shells. Different aspects, such as, the type of elements,input-output computational techniques etc, of the analysis of shells by the FEM will be described below. Clearly, the improvements and developments occurring in general for the FEM since its first appearance in the fifties have had a significative impact on the particular class of structures under discussion

How to Explain Miscomputation

Just as theory of representation is deficient if it can’t explain how misrepresentation is possible, a theory of computation is deficient if it can’t explain how miscomputation is possible. Nonetheless, philosophers have generally ignored miscomputation. My primary goal in this paper is to clarify both what miscomputation is and how to adequately explain it. Miscomputation is a special kind of malfunction: a system miscomputes when it computes in a way that it shouldn’t. To explain miscomputation, you must provide accounts of computational behavior, computational norms, and how computational behavior can deviate from computational norms. A secondary goal of this paper is to defend an (quasi-)individualist, mechanistic theory of miscomputation. Computational behavior is narrowly individuated. Computational norms are widely individuated. A system miscomputes when its behavior manifests a narrow computational structure that the widely individuated norms say that it should not have

Recovering non-local dependencies for Chinese

To date, work on Non-Local Dependencies (NLDs) has focused almost exclusively on English and it is an open research question how well these approaches migrate to other languages. This paper surveys non-local dependency constructions in Chinese as represented in the Penn Chinese Treebank (CTB) and provides an approach for generating proper predicate-argument-modifier structures including NLDs from surface contextfree phrase structure trees. Our approach recovers non-local dependencies at the level of Lexical-Functional Grammar f-structures, using automatically acquired subcategorisation frames and f-structure paths linking antecedents and traces in NLDs. Currently our algorithm achieves 92.2% f-score for trace insertion and 84.3% for antecedent recovery evaluating on gold-standard CTB trees, and 64.7% and 54.7%, respectively, on CTBtrained state-of-the-art parser output trees

Topological Data Analysis of Task-Based fMRI Data from Experiments on Schizophrenia

We use methods from computational algebraic topology to study functional brain networks, in which nodes represent brain regions and weighted edges encode the similarity of fMRI time series from each region. With these tools, which allow one to characterize topological invariants such as loops in high-dimensional data, we are able to gain understanding into low-dimensional structures in networks in a way that complements traditional approaches that are based on pairwise interactions. In the present paper, we use persistent homology to analyze networks that we construct from task-based fMRI data from schizophrenia patients, healthy controls, and healthy siblings of schizophrenia patients. We thereby explore the persistence of topological structures such as loops at different scales in these networks. We use persistence landscapes and persistence images to create output summaries from our persistent-homology calculations, and we study the persistence landscapes and images using $k$-means clustering and community detection. Based on our analysis of persistence landscapes, we find that the members of the sibling cohort have topological features (specifically, their 1-dimensional loops) that are distinct from the other two cohorts. From the persistence images, we are able to distinguish all three subject groups and to determine the brain regions in the loops (with four or more edges) that allow us to make these distinctions

Wide-coverage deep statistical parsing using automatic dependency structure annotation

A number of researchers (Lin 1995; Carroll, Briscoe, and Sanfilippo 1998; Carroll et al. 2002; Clark and Hockenmaier 2002; King et al. 2003; Preiss 2003; Kaplan et al. 2004;Miyao and Tsujii 2004) have convincingly argued for the use of dependency (rather than CFG-tree) representations for parser evaluation. Preiss (2003) and Kaplan et al. (2004) conducted a number of experiments comparing “deep” hand-crafted wide-coverage with “shallow” treebank- and machine-learning based parsers at the level of dependencies, using simple and automatic methods to convert tree output generated by the shallow parsers into dependencies. In this article, we revisit the experiments in Preiss (2003) and Kaplan et al. (2004), this time using the sophisticated automatic LFG f-structure annotation methodologies of Cahill et al. (2002b, 2004) and Burke (2006), with surprising results. We compare various PCFG and history-based parsers (based on Collins, 1999; Charniak, 2000; Bikel, 2002) to find a baseline parsing system that fits best into our automatic dependency structure annotation technique. This combined system of syntactic parser and dependency structure annotation is compared to two hand-crafted, deep constraint-based parsers (Carroll and Briscoe 2002; Riezler et al. 2002). We evaluate using dependency-based gold standards (DCU 105, PARC 700, CBS 500 and dependencies for WSJ Section 22) and use the Approximate Randomization Test (Noreen 1989) to test the statistical significance of the results. Our experiments show that machine-learning-based shallow grammars augmented with sophisticated automatic dependency annotation technology outperform hand-crafted, deep, widecoverage constraint grammars. Currently our best system achieves an f-score of 82.73% against the PARC 700 Dependency Bank (King et al. 2003), a statistically significant improvement of 2.18%over the most recent results of 80.55%for the hand-crafted LFG grammar and XLE parsing system of Riezler et al. (2002), and an f-score of 80.23% against the CBS 500 Dependency Bank (Carroll, Briscoe, and Sanfilippo 1998), a statistically significant 3.66% improvement over the 76.57% achieved by the hand-crafted RASP grammar and parsing system of Carroll and Briscoe (2002)

C-structures and f-structures for the British national corpus

We describe how the British National Corpus (BNC), a one hundred million word balanced corpus of British English, was parsed into Lexical Functional Grammar (LFG) c-structures and f-structures, using a treebank-based parsing architecture. The parsing architecture uses a state-of-the-art statistical parser and reranker trained on the Penn Treebank to produce context-free phrase structure trees, and an annotation algorithm to automatically annotate these trees into LFG f-structures. We describe the pre-processing steps which were taken to accommodate the differences between the Penn Treebank and the BNC. Some of the issues encountered in applying the parsing architecture on such a large scale are discussed. The process of annotating a gold standard set of 1,000 parse trees is described. We present evaluation results obtained by evaluating the c-structures produced by the statistical parser against the c-structure gold standard. We also present the results obtained by evaluating the f-structures produced by the annotation algorithm against an automatically constructed f-structure gold standard. The c-structures achieve an f-score of 83.7% and the f-structures an f-score of 91.2%

Evaluation of protein surface roughness index using its heat denatured aggregates

Recent research works on potential of different protein surface describing parameters to predict protein surface properties gained significance for its possible implication in extracting clues on protein's functional site. In this direction, Surface Roughness Index, a surface topological parameter, showed its potential to predict SCOP-family of protein. The present work stands on the foundation of these works where a semi-empirical method for evaluation of Surface Roughness Index directly from its heat denatured protein aggregates (HDPA) was designed and demonstrated successfully. The steps followed consist, the extraction of a feature, Intensity Level Multifractal Dimension (ILMFD) from the microscopic images of HDPA, followed by the mapping of ILMFD into Surface Roughness Index (SRI) through recurrent backpropagation network (RBPN). Finally SRI for a particular protein was predicted by clustering of decisions obtained through feeding of multiple data into RBPN, to obtain general tendency of decision, as well as to discard the noisy dataset. The cluster centre of the largest cluster was found to be the best match for mapping of Surface Roughness Index of each protein in our study. The semi-empirical approach adopted in this paper, shows a way to evaluate protein's surface property without depending on its already evaluated structure