Mojo is an emerging programming language built on MLIR (Multi-Level Intermediate Representation) and supports JIT (Just-in-Time) compilation. It enables transparent hardware-specific optimizations (e.g., for CPUs and GPUs), while allowing users to express their logic using Python-like user-friendly syntax. Mojo has demonstrated strong performance on tensor operations; however, its capabilities for relational operations (e.g., filtering, join, and group-by aggregation) common in data science workflows, remain unexplored. To date, no dataframe implementation exists in the Mojo ecosystem. In this paper, we introduce the first Mojo-native dataframe library, called MojoFrame, that supports core relational operations and user-defined functions (UDFs). MojoFrame is built on top of Mojo's tensor to achieve fast operations on numeric columns, while utilizing a cardinality-aware approach to effectively integrate non-numeric columns for flexible data representation. To achieve high efficiency, MojoFrame takes significantly different approaches than existing libraries. We show that MojoFrame supports all operations for TPC-H queries and a selection of TPC-DS queries with promising performance, achieving up to 4.60x speedup versus existing dataframe libraries in other programming languages. Nevertheless, there remain optimization opportunities for MojoFrame (and the Mojo language), particularly in in-memory data representation and dictionary operations.

Real-world tasks such as recommending videos tagged kids can be reduced to finding similar vectors associated with hard predicates. This task, filtered vector search , is challenging as prior state-of-the-art graph-based (unfiltered) similarity search techniques degenerate when hard constraints are considered: effective graph-based filtered similarity search relies on sufficient connectivity for reaching similar items within a few hops. To consider predicates, recent works propose modifying graph traversal to visit only items that satisfy predicates. However, they fail to offer the just-a-few-hops property for a wide range of predicates: they must restrict predicates significantly or lose efficiency if only few items satisfy predicates. We propose an opposite approach: instead of constraining traversal, we build many indexes each serving different predicate forms. For effective construction, we devise a three-dimensional analytical model capturing relationships among index size, search time, and recall, with which we follow a workload-aware approach to pack as many useful indexes as possible into a collection. At query time, the analytical model is employed yet again to discern the one that offers the fastest search at a given recall. We show superior performance and support on datasets with varying selectivities and forms: our approach achieves up to 8.06× speedup while having as low as 1% build time versus other indexes, with less than 2.15× memory of a standard HNSW graph and modest knowledge of past workloads.

Computational notebooks (e.g., Jupyter, Google Colab) are widely used by data scientists. A key feature of notebooks is the interactive computing model of iteratively executing cells (i.e., a set of statements) and observing the result (e.g., model or plot). Unfortunately, existing notebook systems do not offer time-traveling to past states : when the user executes a cell, the notebook session state consisting of user-defined variables can be irreversibly modified —e.g., the user cannot 'un-drop' a dataframe column. This is because, unlike DBMS, existing notebook systems do not keep track of the session state. Existing techniques for checkpointing and restoring session states, such as OS-level memory snapshot or application-level session dump, are insufficient: checkpointing can incur prohibitive storage costs and may fail, while restoration can only be inefficiently performed from scratch by fully loading checkpoint files. In this paper, we introduce a new notebook system, Kishu, that offers time-traveling to and from arbitrary notebook states using an efficient and fault-tolerant incremental checkpoint and checkout mechanism. Kishu creates incremental checkpoints that are small and correctly preserve complex inter-variable dependencies at a novel Co-variable granularity. Then, to return to a previous state, Kishu accurately identifies the state difference between the current and target states to perform incremental checkout at sub-second latency with minimal data loading. Kishu is compatible with 146 object classes from popular data science libraries (e.g., Ray, Spark, PyTorch), and reduces checkpoint size and checkout time by up to 4.55× and 9.02×, respectively, on a variety of notebooks.

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high dimensional, sparse, and heterogeneous and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

With data pipeline tools and the expressiveness of SQL, managing interdependent materialized views (MVs) are becoming increasingly easy. These MVs are updated repeatedly upon new data ingestion (e.g., daily), from which database admins can observe performance metrics (e.g., refresh time of each MV, size on disk) in a consistent way for different types of updates (full vs. incremental) and for different systems (single node, distributed, cloud-hosted). One missed opportunity is that existing data systems treat those MV updates as independent SQL statements without fully exploiting their dependency information and performance metrics. However, if we know that the result of a SQL statement will be consumed immediately after for subsequent operations, those subsequent operations do not have to wait until the early results are fully materialized on storage because the results are already readily available in memory. Of course, this may come at a cost because keeping those results in memory (even temporarily) will reduce the amount of available memory; thus, our decision should be careful.In this paper, we introduce a new system, called S/C, which tackles this problem through efficient creation and update of a set of MVs with acyclic dependencies among them. S/C judiciously uses bounded memory to reduce the end-to-end MV refresh time by short-circuiting expensive reads and writes; S/C’s objective function accurately estimates the time savings from keeping intermediate data in memory for particular periods. Our solution jointly optimizes an MV refresh order, what data to keep in memory, and when to release the data from memory. At a high level, S/C still materializes all data exactly as defined in MV definitions; thus, it does not impact any service-level agreements. In our experiments with TPC-DS datasets (up to 1TB), we show that S/C's optimization can speedup end-to-end runtime by 1.04×–5.08× with (only) 1.6GB memory.

Computational notebooks (e.g., Jupyter, Google Colab) are widely used for interactive data science and machine learning. In those frameworks, users can start a session , then execute cells (i.e., a set of statements) to create variables, train models, visualize results, etc. Unfortunately, existing notebook systems do not offer live migration: when a notebook launches on a new machine, it loses its state , preventing users from continuing their tasks from where they had left off. This is because, unlike DBMS, the sessions directly rely on underlying kernels (e.g., Python/R interpreters) without an additional data management layer. Existing techniques for preserving states, such as copying all variables or OS-level checkpointing, are unreliable (often fail), inefficient, and platform-dependent. Also, re-running code from scratch can be highly time-consuming. In this paper, we introduce a new notebook system, Elastic-Notebook, that offers live migration via checkpointing/restoration using a novel mechanism that is reliable, efficient, and platform-independent. Specifically, by observing all cell executions via transparent, lightweight monitoring, ElasticNotebook can find a reliable and efficient way (i.e., replication plan ) for reconstructing the original session state, considering variable-cell dependencies, observed runtime, variable sizes, etc. To this end, our new graph-based optimization problem finds how to reconstruct all variables (efficiently) from a subset of variables that can be transferred across machines. We show that ElasticNotebook reduces end-to-end migration and restoration times by 85%-98% and 94%-99%, respectively, on a variety (i.e., Kaggle, JWST, and Tutorial) of notebooks with negligible runtime and memory overheads of <2.5% and <10%.

Subteam Replacement: given a team of people embedded in a social network to complete a certain task, and a subset of members (i.e., subteam) in this team which have become unavailable, find another set of people who can perform the subteam’s role in the larger team. We conjecture that a good candidate subteam should have high skill and structural similarity with the replaced subteam while sharing a similar connection with the larger team as a whole. Based on this conjecture, we propose a novel graph kernel which evaluates the goodness of candidate subteams in this holistic way freely adjustable to the need of the situation. To tackle the significant computational difficulties, we equip our kernel with a fast approximation algorithm which (a) employs effective pruning strategies, (b) exploits the similarity between candidate team structures to reduce kernel computations, and (c) features a solid theoretical bound on the quality of the obtained solution. We extensively test our solution on both synthetic and real datasets to demonstrate its effectiveness and efficiency. Our proposed graph kernel outputs more human-agreeable recommendations compared to metrics used in previous work, and our algorithm consistently outperforms alternative choices by finding nearoptimal solutions while scaling linearly with the size of the replaced subteam.

In settings such as corporate management where team structure is highly volatile and large-scale personnel changes are commonplace, the ability to simultaneously replace multiple team members in a team is highly appreciated. We define the problem of Subteam Replacement to address this observation: given a team of people embedded in a social network to complete a certain task, and a subset of members - subteam - in this team which has become unavailable, find another set of people which can perform the subteam's role in the larger team. We propose a holistic evaluation metric and scalable solution for Subteam Replacement with strong theoretical guarantees and perform quantitative evaluations on both generated and real datasets.