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1. STULL: Unbiased Online Sampling for Visual Exploration of Large Spatiotemporal Data

   https://doi.org/10.1109/VAST50239.2020.00012  

   Wang, Guizhen; Guo, Jingjing; Tang, Mingjie; Queiroz Neto, Jose Florencio; Yau, Calvin; Daghistani, Anas; Karimzadeh, Morteza; Aref, Walid G.; Ebert, David S. (October 2020, 2020 IEEE Conference on Visual Analytics Science and Technology (VAST))

   null (Ed.)

   Online sampling-supported visual analytics is increasingly important, as it allows users to explore large datasets with acceptable approximate answers at interactive rates. However, existing online spatiotemporal sampling techniques are often biased, as most researchers have primarily focused on reducing computational latency. Biased sampling approaches select data with unequal probabilities and produce results that do not match the exact data distribution, leading end users to incorrect interpretations. In this paper, we propose a novel approach to perform unbiased online sampling of large spatiotemporal data. The proposed approach ensures the same probability of selection to every point that qualifies the specifications of a user's multidimensional query. To achieve unbiased sampling for accurate representative interactive visualizations, we design a novel data index and an associated sample retrieval plan. Our proposed sampling approach is suitable for a wide variety of visual analytics tasks, e.g., tasks that run aggregate queries of spatiotemporal data. Extensive experiments confirm the superiority of our approach over a state-of-the-art spatial online sampling technique, demonstrating that within the same computational time, data samples generated in our approach are at least 50% more accurate in representing the actual spatial distribution of the data and enable approximate visualizations to present closer visual appearances to the exact ones. 

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2. HyQE: Ranking Contexts with Hypothetical Query Embeddings

   Zhou, Weichao; Zhang, Jiaxin; Hasson, Hilaf; Singh, Anu; Li, Wenchao (November 2024, The 2024 Conference on Empirical Methods in Natural Language Processing)

   Retrieval-augmented generation (RAG) systems can effectively address user queries by leveraging indexed document corpora to retrieve the relevant contexts. Ranking techniques have been adopted in RAG systems to sort the retrieved contexts by their relevance to the query so that users can select the most useful contexts for their downstream tasks. While many existing ranking methods rely on the similarity between the embedding vectors of the context and query to measure relevance, it is important to note that similarity does not equate to relevance in all scenarios. Some ranking methods use large language models (LLMs) to rank the contexts by putting the query and the candidate contexts in the prompt and asking LLM about their relevance. The scalability of those methods is contingent on the number of candidate contexts and the context window of those LLMs. Also, those methods require fine-tuning the LLMs, which can be computationally expensive and require domain-related data. In this work, we propose a scalable ranking framework that does not involve LLM training. Our framework uses an off-the-shelf LLM to hypothesize the user's query based on the retrieved contexts and ranks the contexts based on the similarity between the hypothesized queries and the user query. Our framework is efficient at inference time and is compatible with many other context retrieval and ranking techniques. Experimental results show that our method improves the ranking performance of retrieval systems in multiple benchmarks. 

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3. Graph Enhanced BERT for Query Understanding

   Li, Juanhui; Zeng, Wei; Cheng, Suqi; Ma, Yao; Tang, Jiliang; Wang, Shuaiqiang; Yin, Dawei (July 2023, International ACM SIGIR Conference on Research and Development in Information Retrieval)

   Query understanding plays a key role in exploring users’ search intents. However, it is inherently challenging since it needs to capture semantic information from short and ambiguous queries and often requires massive task-specific labeled data. In recent years, pre-trained language models (PLMs) have advanced various natural language processing tasks because they can extract general semantic information from large-scale corpora. However, directly applying them to query understanding is sub-optimal because existing strategies rarely consider to boost the search performance. On the other hand, search logs contain user clicks between queries and urls that provide rich users’ search behavioral information on queries beyond their content. Therefore, in this paper, we aim to fill this gap by exploring search logs. In particular, we propose a novel graph-enhanced pre-training framework, GE-BERT, which leverages both query content and the query graph to capture both semantic information and users’ search behavioral information of queries. Extensive experiments on offline and online tasks have demonstrated the effectiveness of the proposed framework. 

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4. Interpretable online network dictionary learning for inferring long-range chromatin interactions

   https://doi.org/10.1371/journal.pcbi.1012095  

   Rana, Vishal; Peng, Jianhao; Pan, Chao; Lyu, Hanbaek; Cheng, Albert; Kim, Minji; Milenkovic, Olgica (May 2024, PLOS Computational Biology)

   Schlick, Tamar (Ed.)

   Dictionary learning (DL), implemented via matrix factorization (MF), is commonly used in computational biology to tackle ubiquitous clustering problems. The method is favored due to its conceptual simplicity and relatively low computational complexity. However, DL algorithms produce results that lack interpretability in terms of real biological data. Additionally, they are not optimized for graph-structured data and hence often fail to handle them in a scalable manner. In order to address these limitations, we propose a novel DL algorithm calledonline convex network dictionary learning(online cvxNDL). Unlike classical DL algorithms, online cvxNDL is implemented via MF and designed to handle extremely large datasets by virtue of its online nature. Importantly, it enables the interpretation of dictionary elements, which serve as cluster representatives, through convex combinations of real measurements. Moreover, the algorithm can be applied to data with a network structure by incorporating specialized subnetwork sampling techniques. To demonstrate the utility of our approach, we apply cvxNDL on 3D-genome RNAPII ChIA-Drop data with the goal of identifying important long-range interaction patterns (long-range dictionary elements). ChIA-Drop probes higher-order interactions, and produces data in the form of hypergraphs whose nodes represent genomic fragments. The hyperedges represent observed physical contacts. Our hypergraph model analysis has the objective of creating an interpretable dictionary of long-range interaction patterns that accurately represent global chromatin physical contact maps. Through the use of dictionary information, one can also associate the contact maps with RNA transcripts and infer cellular functions. To accomplish the task at hand, we focus on RNAPII-enriched ChIA-Drop data fromDrosophila MelanogasterS2 cell lines. Our results offer two key insights. First, we demonstrate that online cvxNDL retains the accuracy of classical DL (MF) methods while simultaneously ensuring unique interpretability and scalability. Second, we identify distinct collections of proximal and distal interaction patterns involving chromatin elements shared by related processes across different chromosomes, as well as patterns unique to specific chromosomes. To associate the dictionary elements with biological properties of the corresponding chromatin regions, we employ Gene Ontology (GO) enrichment analysis and perform multiple RNA coexpression studies. 

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5. Temporal Geo-Social Personalized Keyword Search Over Streaming Data

   https://doi.org/10.1145/3473006  

   Almaslukh, Abdulaziz; Kang, Yunfan; Magdy, Amr (December 2021, ACM Transactions on Spatial Algorithms and Systems)

   The unprecedented rise of social media platforms, combined with location-aware technologies, has led to continuously producing a significant amount of geo-social data that flows as a user-generated data stream. This data has been exploited in several important use cases in various application domains. This article supports geo-social personalized queries in streaming data environments. We define temporal geo-social queries that provide users with real-time personalized answers based on their social graph. The new queries allow incorporating keyword search to get personalized results that are relevant to certain topics. To efficiently support these queries, we propose an indexing framework that provides lightweight and effective real-time indexing to digest geo-social data in real time. The framework distinguishes highly dynamic data from relatively stable data and uses appropriate data structures and a storage tier for each. Based on this framework, we propose a novel geo-social index and adopt two baseline indexes to support the addressed queries. The query processor then employs different types of pruning to efficiently access the index content and provide a real-time query response. The extensive experimental evaluation based on real datasets has shown the superiority of our proposed techniques to index real-time data and provide low-latency queries compared to existing competitors. 

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