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From Top-1 to Top-K: A Reproducibility Study and Benchmarking of Counterfactual Explanations for Recommender Systems Impact of large language models on peer review opinions from a fine-grained perspective: Evidence from top conference proceedings in AI Diagnosable ColBERT: Debugging Late-Interaction Retrieval Models Using a Learned Latent Space as Reference Enhancing Unsupervised Keyword Extraction in Academic Papers through Integrating Highlights with Abstract CAST: Modeling Semantic-Level Transitions for Complementary-Aware Sequential Recommendation IndiaFinBench: An Evaluation Benchmark for Large Language Model Performance on Indian Financial Regulatory Text Think Before Writing: Feature-Level Multi-Objective Optimization for Generative Citation Visibility RARE: Redundancy-Aware Retrieval Evaluation Framework for High-Similarity Corpora Personalized Benchmarking: Evaluating LLMs by Individual Preferences Modular Representation Compression: Adapting LLMs for Efficient and Effective Recommendations JFinTEB: Japanese Financial Text Embedding Benchmark UsefulBench: Towards Decision-Useful Information as a Target for Information Retrieval SIMMER: Cross-Modal Food Image--Recipe Retrieval via MLLM-Based Embedding Rethinking the Necessity of Adaptive Retrieval-Augmented Generation through the Lens of Adaptive Listwise Ranking BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labels Learning Behaviorally Grounded Item Embeddings via Personalized Temporal Contexts Collaborative Filtering Through Weighted Similarities of User and Item Embeddings IG-Search: Step-Level Information Gain Rewards for Search-Augmented Reasoning Metric-agnostic Learning-to-Rank via Boosting and Rank Approximation GenRec: A Preference-Oriented Generative Framework for Large-Scale Recommendation Uncertainty-aware Generative Learning Path Recommendation with Cognition-Adaptive Diffusion CPGRec+: A Balance-oriented Framework for Personalized Video Game Recommendations Don't Retrieve, Navigate: Distilling Enterprise Knowledge into Navigable Agent Skills for QA and RAG NewsTorch: A PyTorch-based Toolkit for Learner-oriented News Recommendation Controlling Authority Retrieval: A Missing Retrieval Objective for Authority-Governed Knowledge APEX-MEM: Agentic Semi-Structured Memory with Temporal Reasoning for Long-Term Conversational AI ID and Graph View Contrastive Learning with Multi-View Attention Fusion for Sequential Recommendation Large Language Models to Enhance Business Process Modeling: Past, Present, and Future Trends Dual-Enhancement Product Bundling: Bridging Interactive Graph and Large Language Model Evaluation of Agents under Simulated AI Marketplace Dynamics
IDentity with Locality: An ideal hash for gene sequence s...
Aditya Desai, Gaurav Gupta, Tianyi Zhang, Anshumali Shrivastava · 2024-06-21 · via cs.IR updates on arXiv.org

Gene sequence search is a fundamental operation in computational genomics. Due to the petabyte scale of genome archives, most gene search systems now use hashing-based data structures such as Bloom Filters (BF). The state-of-the-art systems such as Compact bit-slicing signature index (COBS) and Repeated And Merged Bloom filters (RAMBO) use BF with Random Hash (RH) functions for gene representation and identification. The standard recipe is to cast the gene search problem as a sequence of membership problems testing if each subsequent gene substring (called kmer) of Q is present in the set of kmers of the entire gene database D. We observe that RH functions, which are crucial to the memory and the computational advantage of BF, are also detrimental to the system performance of gene-search systems. While subsequent kmers being queried are likely very similar, RH, oblivious to any similarity, uniformly distributes the kmers to different parts of potentially large BF, thus triggering excessive cache misses and causing system slowdown. We propose a novel hash function called the Identity with Locality (IDL) hash family, which co-locates the keys close in input space without causing collisions. This approach ensures both cache locality and key preservation. IDL functions can be a drop-in replacement for RH functions and help improve the performance of information retrieval systems. We give a simple but practical construction of IDL function families and show that replacing the RH with IDL functions reduces cache misses by a factor of 5x, thus improving query and indexing times of SOTA methods such as COBS and RAMBO by factors up to 2x without compromising their quality. We also provide a theoretical analysis of the false positive rate of BF with IDL functions. Our hash function is the first study that bridges Locality Sensitive Hash (LSH) and RH to obtain cache efficiency.