The de novo design of antimicrobial therapeutics involves the exploration of a vast chemical repertoire to find compounds with broad-spectrum potency and low toxicity. Here, we report an efficient ...computational method for the generation of antimicrobials with desired attributes. The method leverages guidance from classifiers trained on an informative latent space of molecules modelled using a deep generative autoencoder, and screens the generated molecules using deep-learning classifiers as well as physicochemical features derived from high-throughput molecular dynamics simulations. Within 48 days, we identified, synthesized and experimentally tested 20 candidate antimicrobial peptides, of which two displayed high potency against diverse Gram-positive and Gram-negative pathogens (including multidrug-resistant Klebsiella pneumoniae) and a low propensity to induce drug resistance in Escherichia coli. Both peptides have low toxicity, as validated in vitro and in mice. We also show using live-cell confocal imaging that the bactericidal mode of action of the peptides involves the formation of membrane pores. The combination of deep learning and molecular dynamics may accelerate the discovery of potent and selective broad-spectrum antimicrobials.
The extraction of high-level color descriptors is an increasingly important problem, as these descriptions often provide links to image content. When combined with image segmentation, color naming ...can be used to select objects by color, describe the appearance of the image, and generate semantic annotations. This paper presents a computational model for color categorization and naming and extraction of color composition. In this paper, we start from the National Bureau of Standards' recommendation for color names, and through subjective experiments, we develop our color vocabulary and syntax. To assign a color name from the vocabulary to an arbitrary input color, we then design a perceptually based color-naming metric. The proposed algorithm follows relevant neurophysiological findings and studies on human color categorization. Finally, we extend the algorithm and develop a scheme for extracting the color composition of a complex image. According to our results, the proposed method identifies known color regions in different color spaces accurately, the color names assigned to randomly selected colors agree with human judgments, and the description of the color composition of complex scenes is consistent with human observations.
Proposes a perceptually based system for pattern retrieval and matching. The central idea is that similarity judgment has to be modeled along perceptual dimensions. Hence, we detect basic visual ...categories that people use in their judgment of similarity, and design a computational model that accepts patterns as input and, depending on the query, produces a set of choices that follow human behavior in pattern matching. There are two major research aspects to our work. The first one addresses the issue of how humans perceive and measure similarity within the domain of color patterns. To understand and describe this mechanism, we performed a subjective experiment which yielded five perceptual criteria used in comparison between color patterns (vocabulary), as well as a set of rules governing the use of these criteria in similarity judgment (grammar). The second research aspect is the implementation of the perceptual criteria and rules in an image retrieval system. Following the processing typical for human vision, we design a system to: (1) extract perceptual features from the vocabulary and (2) perform the comparison between the patterns according to the grammar rules. The modeling of human perception of color patterns is new - starting with a new color codebook design, compact color representation, and texture description through multi-scale edge distribution along different directions. Moreover, we propose new color and texture distance functions that correlate with human performance. The performance of the system is illustrated with numerous examples from image databases from different application domains.
We propose a new approach for image segmentation that is based on low-level features for color and texture. It is aimed at segmentation of natural scenes, in which the color and texture of each ...segment does not typically exhibit uniform statistical characteristics. The proposed approach combines knowledge of human perception with an understanding of signal characteristics in order to segment natural scenes into perceptually/semantically uniform regions. The proposed approach is based on two types of spatially adaptive low-level features. The first describes the local color composition in terms of spatially adaptive dominant colors, and the second describes the spatial characteristics of the grayscale component of the texture. Together, they provide a simple and effective characterization of texture that the proposed algorithm uses to obtain robust and, at the same time, accurate and precise segmentations. The resulting segmentations convey semantic information that can be used for content-based retrieval. The performance of the proposed algorithms is demonstrated in the domain of photographic images, including low-resolution, degraded, and compressed images.
•Zika and other mosquito-borne flaviviruses persist in wild primates.•High biodiversity and low data availability prevent targeted surveillance.•Imputation and machine learning confront data sparsity ...to predict primate hosts.•Hosts with highest risk of Zika positivity are in close proximity to humans.•Targeted surveillance of predicted hosts and vectors may mitigate spillover risk.
The recent Zika virus (ZIKV) epidemic in the Americas ranks among the largest outbreaks in modern times. Like other mosquito-borne flaviviruses, ZIKV circulates in sylvatic cycles among primates that can serve as reservoirs of spillover infection to humans. Identifying sylvatic reservoirs is critical to mitigating spillover risk, but relevant surveillance and biological data remain limited for this and most other zoonoses. We confronted this data sparsity by combining a machine learning method, Bayesian multi-label learning, with a multiple imputation method on primate traits. The resulting models distinguished flavivirus-positive primates with 82% accuracy and suggest that species posing the greatest spillover risk are also among the best adapted to human habitations. Given pervasive data sparsity describing animal hosts, and the virtual guarantee of data sparsity in scenarios involving novel or emerging zoonoses, we show that computational methods can be useful in extracting actionable inference from available data to support improved epidemiological response and prevention.
We present an algorithm for frequent item set mining that identifies high-utility item combinations. In contrast to the traditional association rule and frequent item mining techniques, the goal of ...the algorithm is to find segments of data, defined through combinations of few items (rules), which satisfy certain conditions as a group and maximize a predefined objective function. We formulate the task as an optimization problem, present an efficient approximation to solve it through specialized partition trees, called High-Yield Partition Trees, and investigate the performance of different splitting strategies. The algorithm has been tested on “real-world” data sets, and achieved very good results.
We present a methodology for managing outsourcing projects from the vendor's perspective, designed to maximize the value to both the vendor and its clients. The methodology is applicable across the ...outsourcing lifecycle, providing the capability to select and target new clients, manage the existing client portfolio and quantify the realized benefits to the client resulting from the outsourcing agreement. Specifically, we develop a statistical analysis framework to model client behavior at each stage of the outsourcing lifecycle, including: (1) a predictive model and tool for white space client targeting and selection—
opportunity identification (2) a model and tool for client risk assessment and project portfolio management—
client tracking, and (3) a systematic analysis of outsourcing results,
impact analysis, to gain insights into potential benefits of IT outsourcing as a part of a successful management strategy. Our analysis is formulated in a logistic regression framework, modified to allow for non-linear input–output relationships, auxiliary variables, and small sample sizes. We provide examples to illustrate how the methodology has been successfully implemented for targeting, tracking, and assessing outsourcing clients within IBM global services division.
Scope and purpose
The predominant literature on IT outsourcing often examines various aspects of vendor–client relationship, strategies for successful outsourcing from the client perspective, and key sources of risk to the client, generally ignoring the risk to the vendor. However, in the rapidly changing market, a significant share of risks and responsibilities falls on vendor, as outsourcing contracts are often renegotiated, providers replaced, or services brought back in house. With the transformation of outsourcing engagements, the risk on the vendor's side has increased substantially, driving the vendor's financial and business performance and eventually impacting the value delivery to the client. As a result, only well-ran vendor firms with robust processes and tools that allow identification and active management of risk at all stages of the outsourcing lifecycle are able to deliver value to the client. This paper presents a framework and methodology for managing a portfolio of outsourcing projects from the vendor's perspective, throughout the entire outsourcing lifecycle. We address three key stages of the outsourcing process: (1) opportunity identification and qualification (i.e. selection of the most likely new clients), (2) client portfolio risk management during engagement and delivery, and (3) quantification of benefits to the client throughout the life of the deal.
Issue Title: Special Issue on Content-Based Image Retrieval Abstract image semantics resists all forms of modeling, very much like any kind of intelligence does. However, in order to develop more ...satisfying image navigation systems, we need tools to construct a semantic bridge between the user and the database. In this paper we present an image indexing scheme and a query language, which allow the user to introduce cognitive dimension to the search. At an abstract level, this approach consists of: (1) learning the "natural language" that humans speak to communicate their semantic experience of images, (2) understanding the relationships between this language and objective measurable image attributes, and then (3) developing corresponding feature extraction schemes. More precisely, we have conducted a number of subjective experiments in which we asked human subjects to group images, and then explain verbally why they did so. The results of this study indicated that a part of the abstraction involved in image interpretation is often driven by semantic categories, which can be broken into more tangible semantic entities, i.e. objective semantic indicators. By analyzing our experimental data, we have identified some candidate semantic categories (i.e. portraits, people, crowds, cityscapes, landscapes, etc.) and their underlying semantic indicators (i.e. skin, sky, water, object, etc.). These experiments also helped us derive important low-level image descriptors, accounting for our perception of these indicators. We have then used these findings to develop an image feature extraction and indexing scheme. In particular, our feature set has been carefully designed to match the way humans communicate image meaning. This led us to the development of a "semantic-friendly" query language for browsing and searching diverse collections of images. We have implemented our approach into an Internet search engine, and tested it on a large number of images. The results we obtained are very promising.PUBLICATION ABSTRACT
Color descriptors are among the most important features used in image analysis and retrieval. Due to its compact representation and low complexity, direct histogram comparison is a commonly used ...technique for measuring the color similarity. However, it has many serious drawbacks, including a high degree of dependency on color codebook design, sensitivity to quantization boundaries, and inefficiency in representing images with few dominant colors. In this paper, we present a new algorithm for color matching that models behavior of the human visual system in capturing color appearance of an image. We first develop a new method for color codebook design in the Lab space. The method is well suited for creating small fixed color codebooks; for image analysis, matching, and retrieval. Then we introduce a statistical technique to extract perceptually relevant colors. We also propose a new color distance measure that is based on the optimal mapping between two sets of color components representing two images. Experiments comparing the new algorithm to some existing techniques show that these novel elements lead to better match to human perception in judging image similarity in terms of color composition.
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