Incorporating Machine Learning into Established Bioinformatics Frameworks

The exponential growth of biomedical data in recent years has urged the application of numerous machine learning techniques to address emerging problems in biology and clinical research. By enabling the automatic feature extraction, selection, and generation of predictive models, these methods can be used to efficiently study complex biological systems. Machine learning techniques are frequently integrated with bioinformatic methods, as well as curated databases and biological networks, to enhance training and validation, identify the best interpretable features, and enable feature and model investigation. Here, we review recently developed methods that incorporate machine learning within the same framework with techniques from molecular evolution, protein structure analysis, systems biology, and disease genomics. We outline the challenges posed for machine learning, and, in particular, deep learning in biomedicine, and suggest unique opportunities for machine learning techniques integrated with established bioinformatics approaches to overcome some of these challenges.     

Evaluation of Face Datasets as Tools for Assessing the Performance of Face Recognition Methods

Face datasets are considered a primary tool for evaluating the efficacy of face recognition methods. Here we show that in many of the commonly used face datasets, face images can be recognized accurately at a rate significantly higher than random even when no face, hair or clothes features appear in the image. The experiments were done by cutting a small background area from each face image, so that each face dataset provided a new image dataset which included only seemingly blank images. Then, an image classification method was used in order to check the classification accuracy. Experimental results show that the classification accuracy ranged between 13.5% (color FERET) to 99% (YaleB). These results indicate that the performance of face recognition methods measured using face image datasets may be biased. Compilable source code used for this experiment is freely available for download via the Internet.     

RL \subseteq SC

We show that any randomized logspace algorithm (running in polynomial time with bounded two-sided error) can be simulated deterministically in polynomial time andO(log² n) space. This puts RL in SC, Steve's Class In particular, we get a polynomial time,O(log² n) space algorithm for thest-connectivity problem on undirected graphs.Subject classifications. 68Q10, 68Q15, 68Q25.     

Learning dataset representation for automatic machine learning algorithm selection

The algorithm selection problem is defined as identifying the best-performing machine learning (ML) algorithm for a given combination of dataset, task, and evaluation measure. The human expertise required to evaluate the increasing number of ML algorithms available has resulted in the need to automate the algorithm selection task. Various approaches have emerged to handle the automatic algorithm selection challenge, including meta-learning. Meta-learning is a popular approach that leverages accumulated experience for future learning and typically involves dataset characterization. Existing meta-learning methods often represent a dataset using predefined features and thus cannot be generalized across different ML tasks, or alternatively, learn a dataset’s representation in a supervised manner and therefore are unable to deal with unsupervised tasks. In this study, we propose a novel learning-based task-agnostic method for producing dataset representations. Then, we introduce TRIO, a meta-learning approach, that utilizes the proposed dataset representations to accurately recommend top-performing algorithms for previously unseen datasets. TRIO first learns graphical representations for the datasets, using four tools to learn the latent interactions among dataset instances and then utilizes a graph convolutional neural network technique to extract embedding representations from the graphs obtained. We extensively evaluate the effectiveness of our approach on 337 datasets and 195 ML algorithms, demonstrating that TRIO significantly outperforms state-of-the-art methods for algorithm selection for both supervised (classification and regression) and unsupervised (clustering) tasks.

     

Enhancing comparison shopping agents through ordering and gradual information disclosure

The plethora of comparison shopping agents (CSAs) in today’s markets enables buyers to query more than a single CSA when shopping, thus expanding the list of sellers whose prices they obtain. This potentially decreases the chance of a purchase within any single interaction between a buyer and a CSA, and consequently decreases each CSAs’ expected revenue per-query. Obviously, a CSA can improve its competence in such settings by acquiring more sellers’ prices, potentially resulting in a more attractive “best price”. In this paper we suggest a complementary approach that improves the attractiveness of the best result returned based on intelligently controlling the order according to which they are presented to the user, in a way that utilizes several known cognitive-biases of human buyers. The advantage of this approach is in its ability to affect the buyer’s tendency to terminate her search for a better price, hence avoid querying further CSAs, without spending valuable resources on finding additional prices to present. The effectiveness of our method is demonstrated using real data, collected from four CSAs for five products. Our experiments confirm that the suggested method effectively influence people in a way that is highly advantageous to the CSA compared to the common method for presenting the prices. Furthermore, we experimentally show that all of the components of our method are essential to its success.     

A theoretical framework and empirical examination of the effects of foreign and translated interface language

Given the increased globalization and popularization of computer applications, translating a system's human interface into the local language has become a major consideration for software vendors and distributors. In this paper, we suggest a theoretical framework for the study of user interface translation. The framework includes recognizing vendors' and users' costs of, and benefits from, software translation. An experiment was conducted, based on this framework, to test user performance and preferences regarding interface translations. The experiment manipulated the translation of two interface components: documentation language and manipulation language. The results indicate that users are sensitive to different combinations of interface translation in a way that is commensurate with the instruction-following process (Terwilliger and Polson 1997). Users performed best when a fully translated interface was used and worst when only the manipulation language was translated. Users' preferences were in line with their performance, indicating that a cost benefit approach can serve as a promising starting point to the study of interface translation.     

Competitive analysis of incentive compatible on-line auctions

This paper studies auctions in a setting where the different bidders arrive at different times and the auction mechanism is required to make decisions about each bid as it is received. Such settings occur in computerized auctions of computational resources as well as in other settings. We call such auctions, on-line auctions.

We first characterize exactly on-line auctions that are incentive compatible, i.e. where rational bidders are always motivated to bid their true valuation. We then embark on a competitive worst-case analysis of incentive compatible on-line auctions. We obtain several results, the cleanest of which is an incentive compatible on-line auction for a large number of identical items. This auction has an optimal competitive ratio, both in terms of seller's revenue and in terms of the total social efficiency obtained.     

Wikiometrics: a Wikipedia based ranking system

We present a new concept—Wikiometrics—the derivation of metrics and indicators from Wikipedia. Wikipedia provides an accurate representation of the real world due to its size, structure, editing policy and popularity. We demonstrate an innovative “mining” methodology, where different elements of Wikipedia – content, structure, editorial actions and reader reviews – are used to rank items in a manner which is by no means inferior to rankings produced by experts or other methods. We test our proposed method by applying it to two real-world ranking problems: top world universities and academic journals. Our proposed ranking methods were compared to leading and widely accepted benchmarks, and were found to be extremely correlative but with the advantage of the data being publically available.