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Detecting deterioration of visual field sensitivity measurements is important for the diagnosis and management of glaucoma. This review surveys the current methods for assessing progression that are implemented in clinical devices, which have been used in clinical trials, alongside more recent advances proposed in the literature. Advice is also offered to clinicians on what they can do to improve the collection of perimetric data to help analytical progression methods more accurately predict change. This advice includes a discussion of how frequently visual field testing should be undertaken, with a view towards future developments, such as digital healthcare outside the standard clinical setting and more personalised approaches to perimetry. [ABSTRACT FROM AUTHOR]

Describes research conducted at the TREC (Text Retrieval Conference) interactive track that compared Boolean and natural language searching, showing they achieved comparable results; and assessed the validity of batch-oriented retrieval evaluations, showing that the results from batch evaluations were not comparable to those obtained in experiments with real users. (Author/LRW)

We consider the problem of calculating minimum-redundancy codes for alphabets in which there is significant repetition of symbol weights. On a sorted-by-weight alphabet of n symbols and r distinct symbol weights we show that a minimum-redundancy prefix code can be constructed in O (r + r log(n/r)) time, and that a minimum-redundancy L-bit length-limited prefix code can be constructed in O ([L.sub.r] + Lr log(n/r)) time. When r is small relative to n - which is necessarily the case for most practical coding problems on large alphabets - these bounds represent a substantial improvement upon the best previous algorithms for these two problems, which consumed O (n) time and O (nL) time, respectively. The improved algorithms are also space-efficient. Index Terms - Adaptive algorithm, Huffman code, length-limited code, minimum-redundancy code, package-merge algorithm, prefix-free code, text compression.

Minimum redundancy coding (also known as Huffman coding) is one of the enduring techniques of data compression. Many efforts have been made to improve the efficiency of minimum redundancy coding, the majority based on the use of improved representations for explicit Huffman trees. In this paper, we examine how minimum redundancy coding can be implemented efficiently by divorcing coding from a code tree, with emphasis on the situation when n is large, perhaps on the order of [10.sup.6]. We review techniques for devising minimum redundancy codes, and consider in detail how encoding and decoding should be accomplished. In particular, we describe a modified decoding method that allows improved decoding speed, requiring just a few machine operations per output symbol (rather than for each decoded bit), and uses just a few hundred bytes of memory above and beyond the space required to store an enumeration of the source alphabet. Index Terms - Canonical code, Huffman code, length-limited code, minimum redundancy code, prefix code, text compression.

Aims To investigate the effect of fundus tracking perimetry on structure-function relationship in glaucoma. Methods Perimetric data were acquired with the Humphrey Field Analyzer (HFA) and the Compass fundus perimeter (CMP, equipped with fundus tracking). We included data from 696 eyes from 360 healthy people and 711 eyes from 434 patients with glaucoma from the original study, for which the circumpapillary retinal nerve fibre layer optical coherence tomography scan (Cp-RNFL) was available. We explored the structure-function relationship using both global indices (mean deviation and average Cp-RNFL thickness loss) and anatomically defined visual field clusters comparing the R2 values from mixed-effect models. We then measured the diagnostic ability of a combined Structure Function Index (SFI) using perimetric data from either perimeter. The comparisons were based on partial receiver operating characteristic curves with a minimum specificity of 75% and their areas under the curve. Results The R² for the global structure-function relationship was 0.50 for the CMP and 0.48 for the HFA. When visual field clusters were included in the model, the R² was 0.29 for CMP and 0.30 for HFA. Overall, the discrimination ability of the SFI was not significantly higher than the Cp-RNFL for either the CMP (p=0.07) or the HFA (p=0.14). However, it was significantly better in eyes with perimetric damage (p<0.001), in which the CMP-SFI performed significantly better than the HFA-SFI (p=0.03). Conclusions Structure-function relationship is similar between the two perimeters. Fundus tracking might improve discrimination ability with a combined SFI. [ABSTRACT FROM AUTHOR]

In 1990, Manber and Myers proposed suffix arrays as a space-saving alternative to suffix trees and described the first algorithms for suffix array construction and use. Since that time, and especially in the last few years, suffix array construction algorithms have proliferated in bewildering abundance. This survey paper attempts to provide simple high-level descriptions of these numerous algorithms that highlight both their distinctive features and their commonalities, while avoiding as much as possible the complexities of implementation details. New hybrid algorithms are also described. We provide comparisons of the algorithms' worst-case time complexity and use of additional space, together with results of recent experimental test runs on many of their implementations. Categories and Subject Descriptors: E.1 [Data Structures]: Arrays; F.2.2 [Analysis of Algorithms and Problem Complexity]: Nonnumerical Algorithms and Problems; H.3.3 [Information Storage and Retrieval]: Information Search and Retrieval General Terms: Algorithms, Design, Performance Additional Key Words and Phrases: Suffix array, suffix tree, suffix sorting, Burrows--Wheeler transform ACM Reference Format: DOI = 10.1145/1242471.1242472 http://doi.acm.org/ 10.1145/1242471.1242472

Combining information from optical coherence tomography (OCT) imaging and visual field testing is useful in the clinical assessment and monitoring of patients with glaucoma. Measurements of retinal nerve fibre layer thickness or neuroretinal rim width taken around the optic nerve head may be related to the visual field using a structure-function map. In this review, the structure-function mapping methods in clinical use are discussed. Typical clinical maps provide a population average, 'one size fits all' representation, but in recent years methods for customising structure-function maps to individual eyes have been developed and these are reviewed here. In the macula, visual field stimuli stimulate photoreceptors for which associated retinal ganglion cells are peripherally displaced. Recently developed methods that relate OCT measurements to visual field test locations in the macula are therefore also reviewed. The use of structure-function maps to relate OCT measurements to localised visual field sensitivity in new applications is also explored. These new applications include the selection of visual field test locations and stimulus intensities based on OCT data, and the formal post-test combination of results across modalities. Such applications promise to exploit the structure-function relationship in glaucoma to improve disease diagnosis and monitoring of progression. Limitations in the validation and use of current structure-function mapping techniques are discussed. [ABSTRACT FROM AUTHOR]

Semistatic minimum-redundancy prefix (MRP) coding is fast compared with rival coding methods, but requires two passes during encoding. Its adaptive counterpart, dynamic Huffman coding, requires only one pass over the input message for encoding and decoding, and is asymptotically efficient. Dynamic Huffman coding is, however, notoriously slow in practice. By removing the restriction that the code used for each message symbol must have minimum-redundancy and thereby admitting some compression loss, it is possible to improve the speed of adaptive MRP coding. This paper presents a controlled method for trading compression loss for coding speed by approximating symbol frequencies with a geometric distribution. The result is an adaptive MRP coder that is asymptotically efficient and also fast in practice. Index Terms--Adaptive coding, Huffman coding, minimum-redundancy coding (MRP), on-line coding.

We consider the problem of constructing and transmitting the prelude for Huffman coding. With careful organization of the required operations and an appropriate representation for the prelude, it is possible to make semistatic coding efficient even when S, the size of the source alphabet, is of the same magnitude as m, the length of the message being coded. The proposed structures are of direct relevance in applications that mimic one-pass operation through the use of semistatic compression on a block-by-block basis. Index Terms--Adaptive coding, canonical code, Huffman code, minimum-redundancy code, prefix code.

We consider the problem of constructing and transmitting the prelude for Huffman coding. With careful organization of the required operations and an appropriate representation for the prelude, it is possible to make semistatic coding efficient even when S, the size of the source alphabet, is of the same magnitude as m, the length of the message being coded. The proposed structures are of direct relevance in applications that mimic one-pass operation through the use of semistatic compression on a block-by-block basis.

Abstract: Purpose: To determine the extent to which (1) optic nerve tissue is displaced following mild acute elevation of intraocular pressure, and (2) clinically accessible measures at the anterior eye can be used as a surrogate for such displacements. Methods: We imaged the optic disc of 21 healthy subjects before and after intraocular pressure (IOP) elevation of ~10 mmHg delivered by ophthalmodynamometry. Steady‐state tissue displacement during IOP elevation was assessed axially from OCT data, and laterally from SLO data. Recovery from IOP elevation was assessed by tracking a single vertical B‐scan through the cup centre. Anatomical structures were demarcated by three masked clinicians to determine lateral shifts for temporal cup edge and central disc vessels, and axial shifts of disc surface and anterior lamina cribrosa. Spatial maps of deformation were constructed within the demarcated cup and disc to assess within‐tissue displacement. Measured displacements were correlated with corneal hysteresis, corneal thickness, and IOP. Results: The temporal cup edge moved more temporally with higher baseline IOP (R2 = 0.33, p = 0.006) and with lesser elevation of IOP (R2 = 0.43, p = 0.001); it moved more superiorly for thinner corneas (R2 = 0.35, p = 0.007). Thinner corneas also produced less within‐cup deformation, relative to that of the disc (R2 = 0.39, p = 0.004). Axial displacement of the lamina and lateral displacement of vessels were often substantial (lamina 20 ± 15 μm, range 1–60 μm; vessels 37 ± 25 μm, range 2–102 μm) but did not correlate with measured parameters. Recovery from IOP elevation did not take more than 300–400 ms in any subject. Conclusions: Mild acute elevation of IOP produces large and rapidly reversible shifts in optic nerve tissue in young, healthy eyes. The resulting degree, direction and spatial distribution of cup movement are associated with IOP status and corneal thickness, but not corneal hysteresis. [ABSTRACT FROM AUTHOR]

Purpose To explore the potential relationship between optic disc haemorrhage, venous pulsation pressure (VPP), ocular perfusion pressures and visual field change in glaucomatous and glaucoma suspect eyes. Materials and methods This prospective observational study examined 155 open angle glaucoma or glaucoma suspect eyes from 78 patients over 5 years. Patients were followed with 3 monthly non-mydriatic disc photographs, 6 monthly standard automated perimetry and annual ophthalmodynamometry. The number of disc haemorrhages in each hemidisc was counted across the study period. Visual field rate of change was calculated using linear regression on the sensitivity of each location over time, then averaged for the matching hemifield. VPP and central retinal artery diastolic pressure (CRADP) were calculated from the measured ophthalmodynanometric forces (ODF). The difference between brachial artery diastolic pressure (DiastBP) and CRADP was calculated as an index of possible flow pathology along the carotid and ophthalmic arteries. Results Mean age of the cohort was 71.9 ± 7.3 Years. 76 out of 155 eyes (49%) followed for a mean period of 64.2 months had at least 1 disc haemorrhage. 62 (81.6%) of these 76 eyes had recurrent haemorrhages, with a mean of 5.94 recurrences over 64.2 months. Using univariate analysis, rate of visual field change (P<0.0001), VPP (P = 0.0069), alternative ocular perfusion pressure (CRADP–VPP, P = 0.0036), carotid resistance index (DiastBP–CRADP, P = 0.0108) and mean brachial blood pressure (P = 0.0203) were significantly associated with the number of disc haemorrhages. Using multivariate analysis, increased baseline visual field sensitivity (P = 0.0243, coefficient = 0.0275) was significantly associated with disc haemorrhage, in conjunction with higher VPP (P = 0.0029, coefficient = 0.0631), higher mean blood pressure (P = 0.0113, coefficient = 0.0190), higher carotid resistance index (P = 0.0172, coefficient = 0.0566), and rate of visual field loss (P<0.0001, coefficient = -2.0695). Conclusions Higher VPP was associated with disc haemorrhage and implicates the involvement of venous pathology, but the effect size is small. Additionally, a greater carotid resistance index suggests that flow pathology in the ophthalmic or carotid arteries may be associated with disc haemorrhage. [ABSTRACT FROM AUTHOR]

Objective: We propose an effective automatic method for identification of four retinal layer boundaries from the spectral domain optical coherence tomography images in the presence and absence of pathologies and morphological changes due to disease. Methods: The approach first finds an approximate location of three reference layers and then uses these to bound the search space for the actual layers, which is achieved by modeling the problem as a graph and applying Dijkstra's shortest path algorithm. The edge weight between nodes is determined using pixel distance, slope similarity to a reference, and nonassociativity of the layers, which is designed to overcome the distorting effects that pathology can play in the boundary determination. Results: The accuracy of our method was evaluated on three different datasets. It outperforms the current five state-of-the-art methods. On average, the mean and standard deviation of the root-mean-square error in the form of mean $\pm$ standard deviation in pixels for our method is 1.57 $\pm$ 0.69, which is lower than compared to the existing top five methods of 16.17 $\pm$ 22.64, 6.66 $\pm$ 9.11, 5.70 $\pm$ 10.54, 3.69 $\pm$ 2.04, and 2.29 $\pm$ 1.54. Conclusion: Our method is highly accurate, robust, reliable, and consistent. This identification can enable to quantify the biomarkers of the retina in large-scale study for assessing, monitoring disease progression, as well as early detection of retinal diseases. Significance: Identification of these boundaries can help to determine the loss of neuroretinal cells or layers and the presence of retinal pathology, which can be used as features for the automatic determination of the stages of retinal diseases. [ABSTRACT FROM AUTHOR]

Motivation: Next generation sequencing machines produce vast amounts of genomic data. For the data to be useful, it is essential that it can be stored and manipulated efficiently. This work responds to the combined challenge of compressing genomic data, while providing fast access to regions of interest, without necessitating decompression of whole files. Results: We describe CSAM (Compressed SAM format), a compression approach offering lossless and lossy compression for SAM files. The structures and techniques proposed are suitable for representing SAM files, as well as supporting fast access to the compressed information. They generate more compact lossless representations than BAM, which is currently the preferred lossless compressed SAM-equivalent format; and are self-contained, that is, they do not depend on any external resources to compress or decompress SAM files. [ABSTRACT FROM AUTHOR]

Background/aims A recent study has shown that the paracentral upper visual field in the macular region is often affected in glaucoma and suggested that two test locations within the central 10° should be added to the Humphrey 24-2 visual field test pattern to detect such damage. This study employed data collected using a different visual field test pattern to determine whether the same two-test locations are supported as the most informative regarding visual field loss. Methods A data set of 62 patients with glaucoma and 48 controls had visual field assessments on the Medmont perimeter M700 (Central Threshold or Glaucoma test). Twelve 24-2 locations within central 10° of visual field were derived by interpolation of the nearest neighbours of the Medmont data. The remaining 24 Medmont locations in the central 10° of the glaucomatous set were labelled as abnormal if their thresholds fell outside the lower 5th centile of the age-corrected values for the same location from the control group. All possible pairs of the 24 locations were then assessed for diagnostic power by counting the number of patients that had 0, 1 or 2 abnormal locations in a pair. Results Overwhelmingly, pairs of locations in the superior macular region were more often abnormal than pairs in the inferior. About 50 pairs of locations had equivalent ability to detect damage, with the best pair having 74% of patients with at least one of the locations as abnormal, and 52% both. Conclusions Adding a pair of locations to the superior macular region of the Humphrey Visual Field 24-2 pattern increases the number of abnormal locations identified in individuals with glaucoma. [ABSTRACT FROM AUTHOR]

The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix pointers. In this paper, we describe a new two-level suffix array-based index structure that requires significantly less disk space than previous approaches. Key to the saving is the use of disk blocks that are based on prefixes rather than the more usual uniform-sampling approach, allowing reductions between blocks and subparts of other blocks. We also describe a new in-memory structure—the condensed BWT— and show that it allows common patterns to be resolved without access to the text. Experiments using 64 GB of English web text on a computer with 4 GB of main memory demonstrate the speed and versatility of the new approach. For this data, the index is around one-third the size of previous two-level mechanisms; and the memory footprint of as little as 1% of the text size means that queries can be processed more quickly than is possible with a compact FM-INDEX. [ABSTRACT FROM PUBLISHER]

The success of an enterprise information retrieval system is determined by interactions among three key entities: the search engine employed; the service provider who delivers, modifies, and maintains the engine; and the users of the service within the organization. Evaluations of an enterprise search have predominately focused on the effectiveness and efficiency of the engine, with very little analysis of user involvement in the process, and none on the role of service providers. We propose and evaluate a model of costs and benefits to a service provider when investing in enhancements to the ranking of documents returned by their search engine. We demonstrate the model through a case study to analyze the potential impact of using domain experts to provide enhanced mediated search results. By demonstrating how to quantify the cost and benefit of an improved information retrieval system to the service provider, our case study shows that using the relevance assessments of domain experts to rerank original search results can significantly improve the accuracy of ranked lists. Moreover, the service provider gains substantial return on investment and a higher search success rate by investing in the relevance assessments of domain experts. Our cost and benefit analysis results are contrasted with standard modes of effectiveness analysis, including quantitative (using measures such as precision) and qualitative (through user preference surveys) approaches. Modeling costs and benefits explicitly can provide useful insights that the other approaches do not convey. [ABSTRACT FROM AUTHOR]

SUMMARY Attributing authorship of documents with unknown creators has been studied extensively for natural language text such as essays and literature, but less so for non-natural languages such as computer source code. Previous attempts at attributing authorship of source code can be categorised by two attributes: the software features used for the classification, either strings of n tokens/bytes ( n-grams) or software metrics; and the classification technique that exploits those features, either information retrieval ranking or machine learning. The results of existing studies, however, are not directly comparable as all use different test beds and evaluation methodologies, making it difficult to assess which approach is superior. This paper summarises all previous techniques to source code authorship attribution, implements feature sets that are motivated by the literature, and applies information retrieval ranking methods or machine classifiers for each approach. Importantly, all approaches are tested on identical collections from varying programming languages and author types. Our conclusions are as follows: (i) ranking and machine classifier approaches are around 90% and 85% accurate, respectively, for a one-in-10 classification problem; (ii) the byte-level n-gram approach is best used with different parameters to those previously published; (iii) neural networks and support vector machines were found to be the most accurate machine classifiers of the eight evaluated; (iv) use of n-gram features in combination with machine classifiers shows promise, but there are scalability problems that still must be overcome; and (v) approaches based on information retrieval techniques are currently more accurate than approaches based on machine learning. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Past work suggests that anchor text is a good source of evidence that can be used to improve web searching. Two approaches for making use of this evidence include fusing search results from an anchor text representation and the original text representation based on a document's relevance score or rank position, and combining term frequency from both representations during the retrieval process. Although these approaches have each been tested and compared against baselines, different evaluations have used different baselines; no consistent work enables rigorous cross-comparison between these methods. The purpose of this work is threefold. First, we survey existing fusion methods of using anchor text in search. Second, we compare these methods with common testbeds and web search tasks, with the aim of identifying the most effective fusion method. Third, we try to correlate search performance with the characteristics of a test collection. Our experimental results show that the best performing method in each category can significantly improve search results over a common baseline. However, there is no single technique that consistently outperforms competing approaches across different collections and search tasks. [ABSTRACT FROM AUTHOR]

Searchers on the Web often aim to find key resources about a topic. Finding such results is called topic distillation. Previous research has shown that the use of sources of evidence such as page indegree and URL structure can significantly improve search performance on interconnected collections such as the Web, beyond the use of simple term distribution statistics. This article presents a new approach to improve topic distillation by exploring the use of external sources of evidence: link structure, including query dependent indegree and outdegree; and web page characteristics, such as the density of anchor links. Our experiments with the TREC .GOV collection, an 18GB crawl of the US .gov domain from 2002, show that using such evidence can significantly improve search effectiveness, with combinations of evidence leading to significant performance gains over both full-text and anchor-text baselines. Moreover, we demonstrate that, at a different scope level, both local query-dependent outdegree and query-dependent indegree out-performed their global query-independent counterparts; and at the same scope level, outdegree out-performed indegree. Adding query-dependent indegree or page characteristics to query-dependent outdegree could have a small, but not significant, improvement. [ABSTRACT FROM AUTHOR]

Machine transliteration is the process of automatically transforming the script of a word from a source language to a target language, while preserving pronunciation. The development of algorithms specifically for machine transliteration began over a decade ago based on the phonetics of source and target languages, followed by approaches using statistical and language-specific methods. In this survey, we review the key methodologies introduced in the transliteration literature. The approaches are categorized based on the resources and algorithms used, and the effectiveness is compared. [ABSTRACT FROM AUTHOR]

Given a string x = x[1..n], a repetition of period p in x is a substring ur = x[i..i+rp-1], p = ∣u∣, r ≥ 2, where neither u = x[i..i+p-1] nor x[i..i+(r+1)p-1] is a repetition. The maximum number of repetitions in any string x is well known to be ϴ(n log n). A run or maximal periodicity of period p in x is a substring urt = x[i..i+rp+∣t∣-1] of x, where ur is a repetition, t is a proper prefix of u, and no repetition of period p begins at position i-1 of x or ends at position i+rp+∣t∣. In 2000 Kolpakov and Kucherov [J. Discrete Algorithms, 1 (2000), pp. 159–186] showed that the maximum number ρ(n) of runs in any string x is O(n), but their proof was nonconstructive and provided no specific constant of proportionality. At the same time, they presented experimental data strongly suggesting that ρ(n) < n. Related work by Fraenkel and Simpson [J. Combin. Theory Ser. A., 82 (1998), pp. 112–120] showed that the maximum number σ(n) of distinct squares in any string x satisfies σ(n) < 2n, while experiment again encourages the belief that in fact σ(n) < n. In this paper, as a first step toward proving these conjectures, we present a periodicity lemma that establishes limitations on the number and range of periodicities that can occur over a specified range of positions in x. We then apply this result to specify corresponding limitations on the occurrence of runs. [ABSTRACT FROM AUTHOR]