Algorithms to Explore the Structure and Evolution of Biological Networks

High-throughput experimental protocols have revealed thousands of relationships amongst genes and proteins under various conditions. These putative associations are being aggressively mined to decipher the structural and functional architecture of the cell. One useful tool for exploring this data has been computational network analysis. In this thesis, we propose a collection of novel algorithms to explore the structure and evolution of large, noisy, and sparsely annotated biological networks. We first introduce two information-theoretic algorithms to extract interesting patterns and modules embedded in large graphs. The first, graph summarization, uses the minimum description length principle to find compressible parts of the graph. The second, VI-Cut, uses the variation of information to non-parametrically find groups of topologically cohesive and similarly annotated nodes in the network. We show that both algorithms find structure in biological data that is consistent with known biological processes, protein complexes, genetic diseases, and operational taxonomic units. We also propose several algorithms to systematically generate an ensemble of near-optimal network clusterings and show how these multiple views can be used together to identify clustering dynamics that any single solution approach would miss. To facilitate the study of ancient networks, we introduce a framework called ``network archaeology'') for reconstructing the node-by-node and edge-by-edge arrival history of a network. Starting with a present-day network, we apply a probabilistic growth model backwards in time to find high-likelihood previous states of the graph. This allows us to explore how interactions and modules may have evolved over time. In experiments with real-world social and biological networks, we find that our algorithms can recover significant features of ancestral networks that have long since disappeared. Our work is motivated by the need to understand large and complex biological systems that are being revealed to us by imperfect data. As data continues to pour in, we believe that computational network analysis will continue to be an essential tool towards this end

The power of protein interaction networks for associating genes with diseases

Motivation: Understanding the association between genetic diseases and their causal genes is an important problem concerning human health. With the recent influx of high-throughput data describing interactions between gene products, scientists have been provided a new avenue through which these associations can be inferred. Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques

Summarisation of weighted networks

Networks often contain implicit structure. We introduce novel problems and methods that look for structure in networks, by grouping nodes into supernodes and edges to superedges, and then make this structure visible to the user in a smaller generalised network. This task of finding generalisations of nodes and edges is formulated as network Summarisation'. We propose models and algorithms for networks that have weights on edges, on nodes or on both, and study three new variants of the network summarisation problem. In edge-based weighted network summarisation, the summarised network should preserve edge weights as well as possible. A wider class of settings is considered in path-based weighted network summarisation, where the resulting summarised network should preserve longer range connectivities between nodes. Node-based weighted network summarisation in turn allows weights also on nodes and summarisation aims to preserve more information related to high weight nodes. We study theoretical properties of these problems and show them to be NP-hard. We propose a range of heuristic generalisation algorithms with different trade-offs between complexity and quality of the result. Comprehensive experiments on real data show that weighted networks can be summarised efficiently with relatively little error.Peer reviewe

Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure

Conspiracy in the Time of Corona: Automatic detection of Emerging Covid-19 Conspiracy Theories in Social Media and the News

Abstract Rumors and conspiracy theories thrive in environments of low confi- dence and low trust. Consequently, it is not surprising that ones related to the Covid-19 pandemic are proliferating given the lack of scientific consensus on the virus’s spread and containment, or on the long term social and economic ramifications of the pandemic. Among the stories currently circulating are ones suggesting that the 5G telecommunication network activates the virus, that the pandemic is a hoax perpetrated by a global cabal, that the virus is a bio-weapon released deliberately by the Chinese, or that Bill Gates is using it as cover to launch a broad vaccination program to facilitate a global surveillance regime. While some may be quick to dismiss these stories as having little impact on real-world behavior, recent events including the destruction of cell phone towers, racially fueled attacks against Asian Americans, demonstrations espousing resistance to public health orders, and wide-scale defiance of scientifically sound public mandates such as those to wear masks and practice social distancing, countermand such conclusions. Inspired by narrative theory, we crawl social media sites and news reports and, through the application of automated machine-learning methods, discover the underlying narrative frame- works supporting the generation of rumors and conspiracy theories. We show how the various narrative frameworks fueling these stories rely on the alignment of otherwise disparate domains of knowledge, and consider how they attach to the broader reporting on the pandemic. These alignments and attachments, which can be monitored in near real-time, may be useful for identifying areas in the news that are particularly vulnerable to reinterpretation by conspiracy theorists. Understanding the dynamics of storytelling on social media and the narrative frameworks that provide the generative basis for these stories may also be helpful for devising methods to disrupt their spread

Foundations and Recent Trends in Multimodal Machine Learning: Principles, Challenges, and Open Questions

Multimodal machine learning is a vibrant multi-disciplinary research field that aims to design computer agents with intelligent capabilities such as understanding, reasoning, and learning through integrating multiple communicative modalities, including linguistic, acoustic, visual, tactile, and physiological messages. With the recent interest in video understanding, embodied autonomous agents, text-to-image generation, and multisensor fusion in application domains such as healthcare and robotics, multimodal machine learning has brought unique computational and theoretical challenges to the machine learning community given the heterogeneity of data sources and the interconnections often found between modalities. However, the breadth of progress in multimodal research has made it difficult to identify the common themes and open questions in the field. By synthesizing a broad range of application domains and theoretical frameworks from both historical and recent perspectives, this paper is designed to provide an overview of the computational and theoretical foundations of multimodal machine learning. We start by defining two key principles of modality heterogeneity and interconnections that have driven subsequent innovations, and propose a taxonomy of 6 core technical challenges: representation, alignment, reasoning, generation, transference, and quantification covering historical and recent trends. Recent technical achievements will be presented through the lens of this taxonomy, allowing researchers to understand the similarities and differences across new approaches. We end by motivating several open problems for future research as identified by our taxonomy

Analisa dan Implementasi Graph Summarization dengan metode CANAL

Pemodelan data menggunakan graph telah diterapkan oleh banyak aplikasi dan sistem berskala besar dalam berbagai bidang. Data tersebut direpresentasikan sebagai graph dengan node yang mewakili sebuah objek dan edge menandakan hubungan antara dua objek. Untuk memahami karakteristik sebuah graph, maka dibutuhkan teknik graph summarization. Pada tugas akhir ini, digunakan metode CANAL (Categorization of Attributes with Numerical Values based on Attribute Values and Link Structures of Nodes) untuk meringkas graph. Metode ini merupakan pengembangan dari metode Aggregation-Based Graph summarization yang melakukan peringkasan dengan mengelompokkan serta menggabung node kedalam sebuah super node dengan mengggali pengetahuan dari data untuk menemukan cutoff yang digunakan dalam pengelompokan node secara otomatis. Metode CANAL memperbaiki metode graph summarization SNAP dan k-SNAP yang masih mempunyai kelemahan dalam menangani data dengan atribut numerik. Kedua metode tersebut hanya dapat menangani categorical node attribute, sehingga ketika dihadapkan dengan atribut numerik pengguna masih harus melakukan pengelompokan secara manual berdasarkan pengetahuan mereka terhadap data yang digunakan. Hasil dari sistem yang akan dibangun merupakan sebuah graph summary yang merepresentasikan pattern hubungan antar kelompok dalam ringkasan. Pattern tersebut dapat digunakan untuk membantu memahami informasi yang tersembunyi didalam graph asli. Dari ringkasan yang dihasilkan oleh metode CANAL kemudian dinilai kualitasnya dan dibandingkan dengan kualitasnya dengan ringkasan yang berasal dari cutoff manual. Perbandingan tersebut menunjukkan bahwa kualitas ringkasan dari CANAL memiliki kualitas baik yang setara dengan kualitas ringkasan dengan cutoff manual. Kata kunci: graph summarization, Aggregation-Based Graph summarization, node attribute, link structure, interestingness measur