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Mucahid Kutlu

dblp:27/7658 · also Mücahid Kutlu · DBLP profile ↗
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33ranked-venue papers
12as first author
9since 2021 · last 2026
0000-0002-5660-4992ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Databases, data management, data science and information retrieval · 18 · 3 first-author · 5 since 2021Artificial intelligence and machine learning · 8 · 3 first-author · 1 since 2021Systems, architecture and hardware · 6 · 6 first-authorApplied, interdisciplinary, general and emerging computing · 6 · 1 first-author · 4 since 2021Human-computer interaction and ubiquitous computing · 4 · 2 since 2021Security and privacy · 1 · 1 since 2021Graphics, computer vision, multimedia, augmented reality and games · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Databases, data mining, and information retrieval
7 papers
Information retrieval · 77% Graph data management · 12% Web and social media mining · 12%
Computer architecture, parallel and distributed computing, and storage systems
2 papers
Distributed systems · 46% Hardware reliability and fault tolerance · 27% High-performance computing · 27%

Topics — the 17 heaviest of 17, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Information retrieval
evaluation
1.242019
Constructing Test Collections using Multi-armed Bandits and Active Learning · WWW 2019
Crowd vs. Expert: What Can Relevance Judgment Rationales Teach Us About Assessor Disagreement? · SIGIR 2018
The Many Benefits of Annotator Rationales for Relevance Judgments · IJCAI 2017
Information retrieval › evaluation
relevance judgment
1.132020
ArTest: The First Test Collection for Arabic Web Search with Relevance Rationales · SIGIR 2020
Crowd vs. Expert: What Can Relevance Judgment Rationales Teach Us About Assessor Disagreement? · SIGIR 2018
The Many Benefits of Annotator Rationales for Relevance Judgments · IJCAI 2017
Information retrieval › evaluation
test collection
0.722020
ArTest: The First Test Collection for Arabic Web Search with Relevance Rationales · SIGIR 2020
ArabicWeb16: A New Crawl for Today's Arabic Web · SIGIR 2016
Web and social media mining › bot detection
social bot detection
0.712023
Deep Learning Based Social Bot Detection on Twitter · IEEE Trans. Inf. Forensics Secur. 2023
Information retrieval › evaluation › test collection
test collection construction
0.412019
Constructing Test Collections using Multi-armed Bandits and Active Learning · WWW 2019
Information retrieval › evaluation › relevance judgment
assessor disagreement
0.312018
Crowd vs. Expert: What Can Relevance Judgment Rationales Teach Us About Assessor Disagreement? · SIGIR 2018
Information retrieval › evaluation › relevance judgment
crowdsourced relevance judgment
0.312018
Crowd vs. Expert: What Can Relevance Judgment Rationales Teach Us About Assessor Disagreement? · SIGIR 2018
Graph data management
distributed graph processing
0.312018
LA3: A Scalable Link- and Locality-Aware Linear Algebra-Based Graph Analytics System · Proc. VLDB Endow. 2018
Graph data management
graph analytics
0.312018
LA3: A Scalable Link- and Locality-Aware Linear Algebra-Based Graph Analytics System · Proc. VLDB Endow. 2018
Information retrieval › search engines
web crawling
0.212016
ArabicWeb16: A New Crawl for Today's Arabic Web · SIGIR 2016
Hardware reliability and fault tolerance › software fault tolerance
algorithm-based fault tolerance
0.112012
Fault tolerant parallel data-intensive algorithms · HPDC 2012
High-performance computing
data-intensive computing
0.112012
Fault tolerant parallel data-intensive algorithms · HPDC 2012
Distributed systems
fault tolerance
0.112012
Fault tolerant parallel data-intensive algorithms · HPDC 2012
Distributed systems
distributed graph processing
0.112018
LA3: A Scalable Link- and Locality-Aware Linear Algebra-Based Graph Analytics System · Proc. VLDB Endow. 2018
Collaborative and social computing
crowdsourcing
0.112017
The Many Benefits of Annotator Rationales for Relevance Judgments · IJCAI 2017
Information retrieval › cross-language information retrieval
arabic retrieval
0.112016
ArabicWeb16: A New Crawl for Today's Arabic Web · SIGIR 2016
Information retrieval
cross-language information retrieval
0.112016
ArabicWeb16: A New Crawl for Today's Arabic Web · SIGIR 2016

Methods — techniques the papers use, named apart from their topics

crowdsourcing · 0.8pseudo-asynchronous computation · 0.7linear algebra-based graph processing · 0.7deep learning · 0.7communication filtering · 0.7LSTM · 0.7multi-armed bandit · 0.4active learning · 0.4quantitative analysis · 0.3qualitative analysis · 0.3cost-benefit analysis · 0.3re-execution · 0.1data replication · 0.1
YearPublicationVenuePosition
2026 Measuring Political Stance and Consistency in Large Language Models
Salah Feras Alali, Mohammad Nashat Maasfeh, Mucahid Kutlu, Saban Kardas
ECIR (3)3
2024 How you describe procurement calls matters: Predicting outcome of public procurement using call descriptions
abstract
Abstract A competitive and cost-effective public procurement (PP) process is essential for the effective use of public resources. In this work, we explore whether descriptions of procurement calls can be used to predict their outcomes. In particular, we focus on predicting four well-known economic metrics: (i) the number of offers, (ii) whether only a single offer is received, (iii) whether a foreign firm is awarded the contract, and (iv) whether the contract price exceeds the expected price. We extract the European Union’s multilingual PP notices, covering 22 different languages. We investigate fine-tuning multilingual transformer models and propose two approaches: (1) multilayer perceptron (MLP) models with transformer embeddings for each business sector in which the training data are filtered based on the procurement category and (2) a k-nearest neighbor (KNN)-based approach fine-tuned using triplet networks. The fine-tuned MBERT model outperforms all other models in predicting calls with a single offer and foreign contract awards, whereas our MLP-based filtering approach yields state-of-the-art results in predicting contracts in which the contract price exceeds the expected price. Furthermore, our KNN-based approach outperforms all the baselines in all tasks and our other proposed models in predicting the number of offers. Moreover, we investigate cross-lingual and multilingual training for our tasks and observe that multilingual training improves prediction accuracy in all our tasks. Overall, our experiments suggest that notice descriptions play an important role in the outcomes of PP calls.
Utku Umur Acikalin, Mustafa Kaan Gorgun, Mucahid Kutlu, Bedri Kamil Onur Tas
Nat. Lang. Eng.3
2023 New Metrics to Encourage Innovation and Diversity in Information Retrieval Approaches
Mehmet Deniz Türkmen, Matthew Lease, Mucahid Kutlu
ECIR (2)3
2023 Catch Me If You Can: Deceiving Stance Detection and Geotagging Models to Protect Privacy of Individuals on Twitter
abstract
The recent advances in natural language processing have yielded many exciting developments in text analysis and language understanding models; however, these models can also be used to track people, bringing severe privacy concerns. In this work, we investigate what individuals can do to avoid being detected by those models while using social media platforms. We ground our investigation in two exposure-risky tasks, stance detection and geotagging. We explore a variety of simple techniques for modifying text, such as inserting typos in salient words, paraphrasing, and adding dummy social media posts. Our experiments show that the performance of BERT-based models fine-tuned for stance detection decreases significantly due to typos, but it is not affected by paraphrasing. Moreover, we find that typos have minimal impact on state-of-the-art geotagging models due to their increased reliance on social networks; however, we show that users can deceive those models by interacting with different users, reducing their performance by almost 50%.
Dilara Dogan, Bahadir Altun, Muhammed Said Zengin, Mucahid Kutlu, Tamer Elsayed
ICWSM4
2023 Predicting Election Results Via Social Media: A Case Study for 2018 Turkish Presidential Election
abstract
Social media platforms provide massive amounts of data that can be used to analyze social issues and forecast events in the future. However, it is a challenging task due to the biased and noisy nature of the data. In this work, we propose a method to predict election results via Twitter. In particular, we first detect the stance of social media accounts using their retweets. Subsequently, we develop four different counting methods for our prediction task. In the simple user counting (SC) method, we count labeled users without taking any further steps to reduce bias. In the city-based weighted counting (CBWC) method, we apply a weighted counting based on the number of electorate in each city. The closest-city-based prediction (CCBP) method utilizes sociological similarity between cities to predict results for cities with limited sample sizes. The using former election results (UFERs) method compares predictions for each city against former election results to detect data bias and uses them accordingly. We evaluate our proposed methods with the data collected for the presidential election of Turkey held in 2018. In our extensive evaluation, we show that utilizing domain-specific information and location-based weighted counting is effective in reducing bias. CBWC, CCBP, and UFER methods outperform tweet-counting-based baseline methods. Furthermore, UFER and CCBP outperform almost all traditional polls, suggesting that social media platforms are alternative mediums for conducting election polls.
Cansin Bayrak, Mucahid Kutlu
IEEE Trans. Comput. Soc. Syst.2
2023 Re-Think Before You Share: A Comprehensive Study on Prioritizing Check-Worthy Claims
abstract
The massive amount of misinformation spreading on the internet on a daily basis has enormous negative impacts on societies. Therefore, we need systems to help fact-checkers to combat misinformation and to raise public awareness of this important problem. In this article, we propose a hybrid model which combines bidirectional encoder representations from transformer (BERT) model with various features to prioritize claims based on their check-worthiness. Features we use include domain-specific controversial topics (CT), word embeddings (WE), part-of-speech (POS) tags, and others. In addition, we explore various ways of increasing labeled data size to effectively train the models, such as increasing positive (IncPos) samples, active learning (AL), and utilizing labeled data in other languages. In our extensive experiments, we show that our model outperforms all state-of-the-art models in test collections of Conference and Labs of Evaluation Forum (CLEF) CheckThat! Lab (CTL) 2018 and 2019. In addition, when positive samples are increased in the training set, our model achieves the best mean average precision (MAP) score reported so far for the test collection of CTL 2020. Furthermore, we show that cross-lingual training is effective for prioritizing Arabic and Turkish claims, but not for English.
Yavuz Selim Kartal, Mucahid Kutlu
IEEE Trans. Comput. Soc. Syst.2
2023 Deep Learning Based Social Bot Detection on Twitter
abstract
While social bots can be used for various good causes, they can also be utilized to manipulate people and spread malware. Therefore, it is crucial to detect bots running on social media platforms. However, social bots are increasingly successful in creating human-like messages with the recent developments in artificial intelligence. Thus, we need more sophisticated solutions to detect them. In this study, we propose a novel deep learning architecture in which three long short-term memory (LSTM) models and a fully connected layer are utilized to capture complex social media activity of humans and bots. Since our architecture involves many components connected at different levels, we explore three learning schemes to train each component effectively. In our extensive experiments, we analyze the impact of each component of our architecture on classification accuracy using four different datasets. Furthermore, we show that our proposed architecture outperforms all baselines used in our experiments.
Efe Arin, Mucahid Kutlu
IEEE Trans. Inf. Forensics Secur.2
2022 The CLEF-2022 CheckThat! Lab on Fighting the COVID-19 Infodemic and Fake News Detection
Preslav Nakov, Alberto Barrón-Cedeño, Giovanni Da San Martino, Firoj Alam, Julia Maria Struß, Thomas Mandl 0001, Rubén Míguez, Tommaso Caselli, Mucahid Kutlu, Wajdi Zaghouani, Chengkai Li 0001, Shaden Shaar, Gautam Kishore Shahi, Hamdy Mubarak, Alex Nikolov, Nikolay Babulkov, Yavuz Selim Kartal, Javier Beltrán
ECIR (2)9
2021 Embeddings-Based Clustering for Target Specific Stances: The Case of a Polarized Turkey
Ammar Rashed, Mucahid Kutlu, Kareem Darwish, Tamer Elsayed, Cansin Bayrak
ICWSM2
2020 Building Test Collections using Bandit Techniques: A Reproducibility Study
abstract
The high cost of constructing test collections led many researchers to develop intelligent document selection methods to find relevant documents with fewer judgments than the standard pooling method requires. In this paper, we conduct a comprehensive set of experiments to evaluate six bandit-based document selection methods, in terms of evaluation reliability, fairness, and reusability of the resultant test collections. In our experiments, the best performing method varies across test collections, showing the importance of using diverse test collections for an accurate performance analysis. Our experiments with six test collections also show that Move-To-Front is the most robust method among the ones we investigate.
Bahadir Altun, Mucahid Kutlu
CIKM2
2020 TrClaim-19: The First Collection for Turkish Check-Worthy Claim Detection with Annotator Rationales
abstract
Massive misinformation spread over Internet has many negative impacts on our lives.While spreading a claim is easy, investigating its veracity is hard and time consuming, Therefore, we urgently need systems to help human factcheckers.However, available data resources to develop effective systems are limited and the vast majority of them is for English.In this work, we introduce TrClaim-19, which is the very first labeled dataset for Turkish checkworthy claims.TrClaim-19 consists of labeled 2287 Turkish tweets with annotator rationales, enabling us to better understand the characteristics of check-worthy claims.The rationales we collected suggest that claims' topics and their possible negative impacts are the main factors affecting their check-worthiness.
Yavuz Selim Kartal, Mucahid Kutlu
CoNLL2
2020 ArTest: The First Test Collection for Arabic Web Search with Relevance Rationales
abstract
The scarcity of Arabic test collections has long hindered information retrieval (IR) research over the Arabic Web. In this work, we present ArTest, the first large-scale test collection designed for the evaluation of ad-hoc search over the Arabic Web. ArTest uses ArabicWeb16, a collection of around 150M Arabic Web pages as the document collection, and includes 50 topics, 10,529 relevance judgments, and (more importantly) a rationale behind each judgment. To our knowledge, this is also the first IR test collection that includes rationales of primary assessors (i.e., topic developers) for their relevance judgments, exhibiting a useful resource for understanding the relevance phenomena. Finally, ArTest is made publicly-available for the research community.
Maram Hasanain, Yassmine Barkallah, Reem Suwaileh, Mucahid Kutlu, Tamer Elsayed
SIGIR4
2020 Annotator Rationales for Labeling Tasks in Crowdsourcing
abstract
When collecting item ratings from human judges, it can be difficult to measure and enforce data quality due to task subjectivity and lack of transparency into how judges make each rating decision. To address this, we investigate asking judges to provide a specific form of rationale supporting each rating decision. We evaluate this approach on an information retrieval task in which human judges rate the relevance of Web pages for different search topics. Cost-benefit analysis over 10,000 judgments collected on Amazon’s Mechanical Turk suggests a win-win. Firstly, rationales yield a multitude of benefits: more reliable judgments, greater transparency for evaluating both human raters and their judgments, reduced need for expert gold, the opportunity for dual-supervision from ratings and rationales, and added value from the rationales themselves. Secondly, once experienced in the task, crowd workers provide rationales with almost no increase in task completion time. Consequently, we can realize the above benefits with minimal additional cost.
Mucahid Kutlu, Tyler McDonnell, Tamer Elsayed, Matthew Lease
J. Artif. Intell. Res.1
2019 Correlation, Prediction and Ranking of Evaluation Metrics in Information Retrieval
Soumyajit Gupta, Mucahid Kutlu, Vivek Khetan, Matthew Lease
ECIR (1)2
2019 Constructing Test Collections using Multi-armed Bandits and Active Learning
abstract
While test collections provide the cornerstone of system-based evaluation in information retrieval, human relevance judging has become prohibitively expensive as collections have grown ever larger. Consequently, intelligently deciding which documents to judge has become increasingly important. We propose a two-phase approach to intelligent judging across topics which does not require document rankings from a shared task. In the first phase, we dynamically select the next topic to judge via a multi-armed bandit method. In the second phase, we employ active learning to select which document to judge next for that topic. Experiments on three TREC collections (varying scarcity of relevant documents) achieve t 0.90 correlation for [email protected] ranking and find 90% of the relevant documents at 48% of the original budget. To support reproducibility and follow-on work, we have shared our code online1.
Mucahid Kutlu, Matthew Lease
WWW2
2018 When Rank Order Isn't Enough: New Statistical-Significance-Aware Correlation Measures
abstract
Because it is expensive to construct test collections for Cranfield-based evaluation of information retrieval systems, a variety of lower-cost methods have been proposed. The reliability of these methods is often validated by measuring rank correlation (e.g., Kendall's tau) between known system rankings on the full test collection vs. observed system rankings on the lower-cost one. However, existing rank correlation measures do not consider the statistical significance of score differences between systems in the observed rankings. To address this, we propose two statistical-significance-aware rank correlation measures, one of which is a head-weighted version of the other. We first show empirical differences between our proposed measures and existing ones. We then compare the measures while benchmarking four system evaluation methods: pooling, crowdsourcing, evaluation with incomplete judgments, and automatic system ranking. We show that use of our measures can lead to different experimental conclusions regarding reliability of alternative low-cost evaluation methods.
Mucahid Kutlu, Tamer Elsayed, Maram Hasanain, Matthew Lease
CIKM1
2018 Re-ranking Web Search Results for Better Fact-Checking: A Preliminary Study
abstract
Even though Web search engines play an important role in finding documents relevant to user queries, there is little to no attention given to how they perform in terms of usefulness for fact-checking claims. In this paper, we introduce a new research problem that addresses the ability of fact-checking systems to distinguish Web search results that are useful in discovering the veracity of claims from the ones that are not.We also propose a re-ranking method to improve ranking of search results for fact-checking. To evaluate our proposed method, we conducted a preliminary study for which we have developed a test collection that includes 22 claims and 20 manually-annotated Web search results for each. Our experiments show that the proposed method outperforms the baseline represented by the original ranking of search results. The contributions this improvement brings to real-world applications is two-fold: it will help human fact-checkers find useful documents for their task faster, and it will help automated fact-checking systems by pointing out which documents are useful and which are not.
Khaled Yasser, Mucahid Kutlu, Tamer Elsayed
CIKM2
2018 Your Behavior Signals Your Reliability: Modeling Crowd Behavioral Traces to Ensure Quality Relevance Annotations
abstract
While peer-agreement and gold checks are well-established methods for ensuring quality in crowdsourced data collection, we explore a relatively new direction for quality control: estimating work quality directly from workers’ behavioral traces collected during annotation. We propose three behavior-based models to predict label correctness and worker accuracy, then further apply model predictions to label aggregation and optimization of label collection. As part of this work, we collect and share a new Mechanical Turk dataset of behavioral signals judging the relevance of search results. Results show that behavioral data can be effectively used to predict work quality, which could be especially useful with single labeling or in a cold start scenario in which individuals’ prior work history is unavailable. We further show improvement in label aggregation and reducing labeling cost while ensuring data quality.
Tanya Goyal, Tyler McDonnell, Mucahid Kutlu, Tamer Elsayed, Matthew Lease
HCOMP3
2018 Crowd vs. Expert: What Can Relevance Judgment Rationales Teach Us About Assessor Disagreement?
abstract
While crowdsourcing offers a low-cost, scalable way to collect relevance judgments, lack of transparency with remote crowd work has limited understanding about the quality of collected judgments. In prior work, we showed a variety of benefits from asking crowd workers to provide \em rationales for each relevance judgment \citemcdonnell2016relevant. In this work, we scale up our rationale-based judging design to assess its reliability on the 2014 TREC Web Track, collecting roughly 25K crowd judgments for 5K document-topic pairs. We also study having crowd judges perform topic-focused judging, rather than across topics, finding this improves quality. Overall, we show that crowd judgments can be used to reliably rank IR systems for evaluation. We further explore the potential of rationales to shed new light on reasons for judging disagreement between experts and crowd workers. Our qualitative and quantitative analysis distinguishes subjective vs.\ objective forms of disagreement, as well as the relative importance of each disagreement cause, and we present a new taxonomy for organizing the different types of disagreement we observe. We show that many crowd disagreements seem valid and plausible, with disagreement in many cases due to judging errors by the original TREC assessors. We also share our WebCrowd25k dataset, including: (1) crowd judgments with rationales, and (2) taxonomy category labels for each judging disagreement analyzed.
Mucahid Kutlu, Tyler McDonnell, Yassmine Barkallah, Tamer Elsayed, Matthew Lease
SIGIR1
2018 Intelligent topic selection for low-cost information retrieval evaluation: A New perspective on deep vs. shallow judging
Mucahid Kutlu, Tamer Elsayed, Matthew Lease
Inf. Process. Manag.1
2018 EveTAR: building a large-scale multi-task test collection over Arabic tweets
Maram Hasanain, Reem Suwaileh, Tamer Elsayed, Mucahid Kutlu, Hind A. Al-Merekhi
Inf. Retr. J.4
2018 LA3: A Scalable Link- and Locality-Aware Linear Algebra-Based Graph Analytics System
abstract
This paper presents LA3 , a scalable distributed system for graph analytics. LA3 couples a vertex-based programming model with a highly optimized linear algebra-based engine. It translates any vertex-centric program into an iteratively executed sparse matrix-vector multiplication (SpMV). To reduce communication and enhance scalability, the adjacency matrix representing an input graph is partitioned into locality-aware 2D tiles distributed across multiple processes. Alongside, three major optimizations are incorporated to preclude redundant computations and minimize communication. First, the link-based structure of the input graph is exploited to classify vertices into different types. Afterwards, vertices of special types are factored out of the main loop of the graph application to avoid superfluous computations. We refer to this novel optimization as computation filtering. Second, a communication filtering mechanism is involved to optimize for the high sparsity of the input matrix due to power-law distributions, common in real-world graphs. This optimization ensures that each process receives only the messages that pertain to non-zero entries in its tiles, substantially reducing communication traffic since most tiles are highly sparse. Lastly, a pseudo-asynchronous computation and communication optimization is proposed, whereby processes progress and communicate asynchronously, consume messages as soon as they become available, and block otherwise. We implemented and extensively tested LA3 on private and public clouds. Results show that LA3 outperforms six related state-of-the-art and popular distributed graph analytics systems by an average of 10X.
Muhammad Yousuf Ahmad, Omar Khattab, Arsal Malik, Ahmad Musleh, Mohammad Hammoud, Mucahid Kutlu, Mostafa Shehata, Tamer Elsayed
Proc. VLDB Endow.6
2017 The Many Benefits of Annotator Rationales for Relevance Judgments
abstract
When collecting subjective human ratings of items, it can be difficult to measure and enforce data quality due to task subjectivity and lack of insight into how judges arrive at each rating decision. To address this, we propose requiring judges to provide a specific type of rationale underlying each rating decision. We evaluate this approach in the domain of Information Retrieval, where human judges rate the relevance of Webpages. Cost-benefit analysis over 10,000 judgments collected on Mechanical Turk suggests a win-win: experienced crowd workers provide rationales with no increase in task completion time while providing further benefits, including more reliable judgments and greater transparency.
Tyler McDonnell, Mucahid Kutlu, Tamer Elsayed, Matthew Lease
IJCAI2
2016 Why Is That Relevant? Collecting Annotator Rationales for Relevance Judgments
abstract
When collecting subjective human ratings of items, it can be difficult to measure and enforce data quality due to task subjectivity and lack of insight into how judges’ arrive at each rating decision. To address this, we propose requiring judges to provide a specific type of rationale underlying each rating decision. We evaluate this approach in the domain of Information Retrieval, where human judges rate the relevance of Webpages to search queries. Cost-benefit analysis over 10,000 judgments collected on Mechanical Turk suggests a win-win: experienced crowd workers provide rationales with almost no increase in task completion time while providing a multitude of further benefits, including more reliable judgments and greater transparency for evaluating both human raters and their judgments. Further benefits include reduced need for expert gold, the opportunity for dual-supervision from ratings and rationales, and added value from the rationales themselves.
Tyler McDonnell, Matthew Lease, Mucahid Kutlu, Tamer Elsayed
HCOMP3
2016 ArabicWeb16: A New Crawl for Today's Arabic Web
abstract
Web crawls provide valuable snapshots of the Web which enable a wide variety of research, be it distributional analysis to characterize Web properties or use of language, content analysis in social science, or Information Retrieval (IR) research to develop and evaluate effective search algorithms. While many English-centric Web crawls exist, existing public Arabic Web crawls are quite limited, limiting research and development. To remedy this, we present ArabicWeb16, a new public Web crawl of roughly 150M Arabic Web pages with significant coverage of dialectal Arabic as well as Modern Standard Arabic. For IR researchers, we expect ArabicWeb16 to support various research areas: ad-hoc search, question answering, filtering, cross-dialect search, dialect detection, entity search, blog search, and spam detection. Combined use with a separate Arabic Twitter dataset we are also collecting may provide further value.
Reem Suwaileh, Mucahid Kutlu, Nihal Fathima, Tamer Elsayed, Matthew Lease
SIGIR2
2015 RE-PAGE: Domain-Specific REplication and PArallel Processing of GEnomic Data
abstract
As development of high-throughput and low-cost sequencing technologies is leading to massive volumes of genomic data, new solutions for handling data-intensive applications on parallel platforms are urgently required. Particularly, the nature of processing leads to both load balancing and I/O contention challenges. In this paper, we have developed a novel middleware system, RE-PAGE, which allows parallelization of applications that process genomic data with a simple, high-level API. To address load balancing and I/O contention, the features of the middleware include: 1) use of domain-specific information in the formation of data chunks (which can be of non-uniform sizes), 2) replication and placement of each chunk on a small number of nodes, performed in an intelligent way, and 3) scheduling schemes for achieving load balance, when data movement costs out-weigh processing costs and the chunks are of non-uniform sizes. We have evaluated our framework using three genomic applications, which are VarScan, Unified Genotyper, and Coverage Analyzer. We show that our approach leads to better performance than conventional MapReduce scheduling approaches and systems that access data from a centralized store. We also compare against popular frameworks, Hadoop and GATK, and show that our middleware outperforms both, achieving high parallel efficiency and scalability.
Mucahid Kutlu, Gagan Agrawal
CLUSTER1
2015 GEM: A Framework for Developing Shared-Memory Parallel Genomic Applications on Memory Constrained Architectures
abstract
Amount of available genomic data is increasing rapidly with the recent developments in sequencing technologies. Analysis of such data can potentially lead significant advancements in medical research and even practice. However, it is imperative to exploit parallelism and utilize computational resources effectively to handle large scale genomic data. At the same time, the trends in computing technologies are towards architectures with large number of cores and smaller memory size per core (e.g. Intel Xeon Phi). Innovative solutions that meet the requirements of parallel genomic data processing with the constraints of the new computational architectures are urgently needed. In this work, we develop a novel middleware system, GEM, for developing shared-memory parallel genomic applications with memory constraint architectures. We propose load-map-reduce approach and a novel scheduling scheme to decrease I/O contention and prevent over-consumption of the limited memory. We also use domain specific knowledge to decrease the memory requirements of the tasks. In our experiments, we show that GEM has high scalability on Intel Xeon Phi architecture. We also compare GEM against two other frameworks for genomic data processing, GATK and PAGE, and show that our middleware outperforms both.
Mucahid Kutlu, Gagan Agrawal
ICPP1
2014 Cluster-Based SNP Calling on Large-Scale Genome Sequencing Data
abstract
The available genetic data is increasing rapidly, with new high-throughput and low-cost technologies. While this data has enormous potential to impact scientific and medical advances, such data volumes cannot be processed without the use of parallelism. Most of the existing work on analysis of this data has focused on the accuracy of the analyses, and not performance, i.e. either the algorithms are serial and/or very simple and non-scalable parallelization techniques have been used. In this paper, we address the problem of identification of variants in large-scale genome sequencing data. After examining different possible approaches, we identify one which does not require any communication. However, achieving load-balance is non-trivial, because of the data-dependent nature of the processing. We develop three scheduling schemes including a dynamic scheme, which reduces scheduling overheads by using two different chunk sizes, a static scheme, which uses a pre-processing step to estimate workloads, and a combined scheme. In evaluating our schemes, we find that use of a pre-processing step (histogram computation) to estimate workloads is very effective, and thus, our combined scheme gives the best results. With a 32× increase in the number of cores, approximately a 24× performance improvement is seen, establishing that scalable processing of genomic data is possible. We also perform a comparison against an implementation based on Hadoop, and show that with our combined scheme, our implementation outperforms the one using Hadoop.
Mucahid Kutlu, Gagan Agrawal
CCGRID1
2014 PAGE: A Framework for Easy PArallelization of GEnomic Applications
abstract
With the availability of high-throughput and low-cost sequencing technologies, an increasing amount of genetic data is becoming available to researchers. There is clearly a potential for significant new scientific and medical advances by analysis of such data, however, it is imperative to exploit parallelism and achieve effective utilization of the computing resources to be able to handle massive datasets. Thus, frameworks that can help researchers develop parallel applications without dealing with low-level details of parallel coding are very important for advances in genetic research. In this study, we develop a middleware, PAGE, which supports 'map reduce-like' processing, but with significant differences from a system like Hadoop, to be useful and effective for parallelizing analysis of genomic data. Particularly, it can work with map functions written in any language, thus allowing utilization of existing serial tools (even those for which only an executable is available) as map functions. Thus, it can greatly simplify parallel application development for scenarios where complex data formats and/or nuanced serial algorithms are involved, as is often the case for genomic data. It allows parallelization by partitioning by-locus or partitioning by-chromosome, provides different scheduling schemes, and execution models, to match the nature of algorithms common in genetic research. We have evaluated the middleware system using four popular genomic applications, including VarScan, Unified Genotyper, Realigner Target Creator, and Indel Realigner, and compared the achieved performance against with two popular frameworks (Hadoop and GATK). We show that our middleware outperforms GATK and Hadoop and it is able to achieve high parallel efficiency and scalability.
Mucahid Kutlu, Gagan Agrawal
IPDPS1
2013 A Hybrid Morphological Disambiguation System for Turkish
Mucahid Kutlu, Ilyas Cicekli
IJCNLP1
2012 Fault tolerant parallel data-intensive algorithms
abstract
Fault-tolerance is rapidly becoming a crucial issue in high-end and distributed computing, as increasing number of cores are decreasing the mean-time to failure of the systems. While checkpointing, including checkpointing of parallel programs like MPI applications, provides a general solution, the overhead of this approach is becoming increasingly unacceptable. Thus, algorithm-based fault-tolerance provides a nice practical alternative, though it is less general. Although this approach has been studied for many applications, there is no existing work for algorithm-based fault-tolerance for the growing class of data-intensive parallel applications. In this paper, we present an algorithm-based fault tolerance solution that handles fail-stop failures for a class of data intensive algorithms. We divide the dataset into smaller data blocks and in replication step, we distribute the replicated blocks with the aim of keeping the maximum data intersection between any two processors minimum. This allows us to have minimum data loss when multiple failures occur. In addition, our approach enables better load balance after failure, and decreases the amount of re-processing of the lost data. We have evaluated our approach by using two popular parallel data mining algorithms, which are k-means and apriori. We show that our approach has negligible overhead when there are no failures, and allows us to gracefully handle different number of failures, and failures at different points of processing. We also provide the comparison of our approach with the MapReduce based solution for fault tolerance, and show that we outperform Hadoop both in absence and presence of failures.
Mucahid Kutlu, Gagan Agrawal, Oguz Kurt
HiPC1
2012 Fault tolerant parallel data-intensive algorithms
abstract
Fault-tolerance is rapidly becoming a crucial issue in high-end and distributed computing, as increasing number of cores are decreasing the mean-time to failure of the systems. In this work, we present an algorithm-based fault tolerance solution that handles fail-stop failures for a class of iterative data intensive algorithms. We intelligently replicate the data to minimize data loss in multiple failures and decrease re-execution in recovery by little modifications in the algorithms. We evaluate our approach by using two data mining algorithms, kmeans and Apriori. We show that our approach has negligible overhead and allows us to gracefully handle different number of failures. In addition, our approach outperforms Hadoop both in absence and presence of failures.
Mucahid Kutlu, Gagan Agrawal, Oguz Kurt
HPDC1
2010 Generic Text Summarization for Turkish
abstract
In this paper, we propose a generic text summarization method that generates summaries of Turkish texts by ranking sentences according to their scores. Sentence scores are calculated using their surface-level features, and summaries are created by extracting the highest ranked sentences from the original documents. To extract sentences which form a summary with an extensive coverage of the main content of the text and less redundancy, we use features such as term frequency, key phrase (KP), centrality, title similarity and sentence position. The sentence rank is computed using a score function that uses its feature values and the weights of the features. The best feature weights are learned using machine-learning techniques with the help of human-constructed summaries. Performance evaluation is conducted by comparing summarization outputs with manual summaries of two newly created Turkish data sets. This paper presents one of the first Turkish summarization systems, and its results are promising. We introduce the usage of KP as a surface-level feature in text summarization, and we show the effectiveness of the centrality feature in text summarization. The effectiveness of the features in Turkish text summarization is also analyzed in detail.
Mucahid Kutlu, Celal Cigir, Ilyas Cicekli
Comput. J.1