004 Datenverarbeitung; Informatik
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PC2P
(2021)
Motivation:
Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction.
Results:
To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75% and 100% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks.
In recent years, many efforts have been made to apply image processing techniques for plant leaf identification. However, categorizing leaf images at the cultivar/variety level, because of the very low inter-class variability, is still a challenging task. In this research, we propose an automatic discriminative method based on convolutional neural networks (CNNs) for classifying 12 different cultivars of common beans that belong to three various species. We show that employing advanced loss functions, such as Additive Angular Margin Loss and Large Margin Cosine Loss, instead of the standard softmax loss function for the classification can yield better discrimination between classes and thereby mitigate the problem of low inter-class variability. The method was evaluated by classifying species (level I), cultivars from the same species (level II), and cultivars from different species (level III), based on images from the leaf foreside and backside. The results indicate that the performance of the classification algorithm on the leaf backside image dataset is superior. The maximum mean classification accuracies of 95.86, 91.37 and 86.87% were obtained at the levels I, II and III, respectively. The proposed method outperforms the previous relevant works and provides a reliable approach for plant cultivars identification.
High annotation costs are a substantial bottleneck in applying deep learning architectures to clinically relevant use cases, substantiating the need for algorithms to learn from unlabeled data.
In this work, we propose employing self-supervised methods. To that end, we trained with three self-supervised algorithms on a large corpus of unlabeled dental images, which contained 38K bitewing radiographs (BWRs). We then applied the learned neural network representations on tooth-level dental caries classification, for which we utilized labels extracted from electronic health records (EHRs). Finally, a holdout test-set was established, which consisted of 343 BWRs and was annotated by three dental professionals and approved by a senior dentist.
This test-set was used to evaluate the fine-tuned caries classification models. Our experimental results demonstrate the obtained gains by pretraining models using self-supervised algorithms. These include improved caries classification performance (6 p.p. increase in sensitivity) and, most importantly, improved label-efficiency.
In other words, the resulting models can be fine-tuned using few labels (annotations).
Our results show that using as few as 18 annotations can produce >= 45% sensitivity, which is comparable to human-level diagnostic performance.
This study shows that self-supervision can provide gains in medical image analysis, particularly when obtaining labels is costly and expensive.
We study the classical, two-sided stable marriage problem under pairwise preferences. In the most general setting, agents are allowed to express their preferences as comparisons of any two of their edges, and they also have the right to declare a draw or even withdraw from such a comparison. This freedom is then gradually restricted as we specify six stages of orderedness in the preferences, ending with the classical case of strictly ordered lists. We study all cases occurring when combining the three known notions of stability-weak, strong, and super-stability-under the assumption that each side of the bipartite market obtains one of the six degrees of orderedness. By designing three polynomial algorithms and two NP-completeness proofs, we determine the complexity of all cases not yet known and thus give an exact boundary in terms of preference structure between tractable and intractable cases.
Our input is a complete graph G on n vertices where each vertex has a strict ranking of all other vertices in G. The goal is to construct a matching in G that is popular. A matching M is popular if M does not lose a head-to-head election against any matching M ': here each vertex casts a vote for the matching in {M,M '} in which it gets a better assignment. Popular matchings need not exist in the given instance G and the popular matching problem is to decide whether one exists or not. The popular matching problem in G is easy to solve for odd n. Surprisingly, the problem becomes NP-complete for even n, as we show here. This is one of the few graph theoretic problems efficiently solvable when n has one parity and NP-complete when n has the other parity.
Local laws on urban policy, i.e., ordinances directly affect our daily life in various ways (health, business etc.), yet in practice, for many citizens they remain impervious and complex. This article focuses on an approach to make urban policy more accessible and comprehensible to the general public and to government officials, while also addressing pertinent social media postings. Due to the intricacies of the natural language, ranging from complex legalese in ordinances to informal lingo in tweets, it is practical to harness human judgment here. To this end, we mine ordinances and tweets via reasoning based on commonsense knowledge so as to better account for pragmatics and semantics in the text. Ours is pioneering work in ordinance mining, and thus there is no prior labeled training data available for learning. This gap is filled by commonsense knowledge, a prudent choice in situations involving a lack of adequate training data. The ordinance mining can be beneficial to the public in fathoming policies and to officials in assessing policy effectiveness based on public reactions. This work contributes to smart governance, leveraging transparency in governing processes via public involvement. We focus significantly on ordinances contributing to smart cities, hence an important goal is to assess how well an urban region heads towards a smart city as per its policies mapping with smart city characteristics, and the corresponding public satisfaction.
VLDB 2021
(2021)
The 47th International Conference on Very Large Databases (VLDB'21) was held on August 16-20, 2021 as a hybrid conference. It attracted 180 in-person attendees in Copenhagen and 840 remote attendees. In this paper, we describe our key decisions as general chairs and program committee chairs and share the lessons we learned.
Modern data analysis tasks often involve control flow statements, such as the iterations in PageRank and K-means. To achieve scalability, developers usually implement these tasks in distributed dataflow systems, such as Spark and Flink. Designers of such systems have to choose between providing imperative or functional control flow constructs to users. Imperative constructs are easier to use, but functional constructs are easier to compile to an efficient dataflow job. We propose Mitos, a system where control flow is both easy to use and efficient. Mitos relies on an intermediate representation based on the static single assignment form. This allows us to abstract away from specific control flow constructs and treat any imperative control flow uniformly both when building the dataflow job and when coordinating the distributed execution.
Nowadays, production planning and control must cope with mass customization, increased fluctuations in demand, and high competition pressures. Despite prevailing market risks, planning accuracy and increased adaptability in the event of disruptions or failures must be ensured, while simultaneously optimizing key process indicators. To manage that complex task, neural networks that can process large quantities of high-dimensional data in real time have been widely adopted in recent years. Although these are already extensively deployed in production systems, a systematic review of applications and implemented agent embeddings and architectures has not yet been conducted. The main contribution of this paper is to provide researchers and practitioners with an overview of applications and applied embeddings and to motivate further research in neural agent-based production. Findings indicate that neural agents are not only deployed in diverse applications, but are also increasingly implemented in multi-agent environments or in combination with conventional methods — leveraging performances compared to benchmarks and reducing dependence on human experience. This not only implies a more sophisticated focus on distributed production resources, but also broadening the perspective from a local to a global scale. Nevertheless, future research must further increase scalability and reproducibility to guarantee a simplified transfer of results to reality.
Algorithmic management
(2022)