Zhaoheng Li

Dylan Molho, Jiayuan Ding, Zhaoheng Li et al.

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, 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 through 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.

Shengya Huang, Zhaoheng Li, Derek Warner et al.

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.

Banghao Chi, Yining Xie, Mingyuan Wu et al.

Spreadsheet systems (e.g., Microsoft Excel, Google Sheets) play a central role in modern data-centric workflows. As AI agents grow increasingly capable of automating complex tasks, such as controlling computers and generating presentations, building an AI-driven spreadsheet agent has emerged as a promising research direction. Most existing spreadsheet agents rely on specialized prompting over general-purpose LLMs; while this design has potentials on simple spreadsheet operations, it struggles to manage the complex, multi-step workflows typical of real-world applications. We introduce Spreadsheet-RL, a reinforcement learning (RL) fine-tuning framework designed to train specialized spreadsheet agents within a realistic Microsoft Excel environment. Spreadsheet-RL features an automated pipeline for scalable collection of paired start-goal spreadsheets from online forums, as well as domain-specific evaluation tasks in areas such as finance and supply chain management, which we compile into the new Domain-Spreadsheet benchmark dataset. It also includes a Spreadsheet Gym environment designed for multi-turn RL: Spreadsheet Gym exposes extensive Excel functionality through a Python sandbox, along with a refined harness that incorporates a comprehensive tool set and carefully designed tool-routing rules for spreadsheet tasks. Through comprehensive experiments, we show that Spreadsheet-RL substantially enhances AI agent's performance on both general and domain-specific spreadsheet tasks: it improves Qwen3-4B-Thinking-2507's Pass@1 on SpreadsheetBench from 12.0% to 23.4%, and raises Pass@1 from 8.4% to 17.2% on our curated Domain-Spreadsheet dataset. These results highlight Spreadsheet-RL's strong potential for generalization and real-world adoption in spreadsheet automation, and broadly, its promise for advancing LLM-based interactions with data interfaces in everyday work.

Mingyuan Wu, Jize Jiang, Haozhen Zheng et al.

Vision Language Models (VLMs) have achieved remarkable success in a wide range of vision applications of increasing complexity and scales, yet choosing the right VLM model size involves a trade-off between response quality and cost. While smaller VLMs are cheaper to run, they typically produce responses only marginally better than random guessing on benchmarks such as MMMU. In this paper, we propose Cache of Thought (CoT), a master apprentice framework for collaborative inference between large and small VLMs. CoT manages high quality query results from large VLMs (master) in a cache, which are then selected via a novel multi modal retrieval and in-context learning to aid the performance of small VLMs (apprentice). We extensively evaluate CoT on various widely recognized and challenging general reasoning benchmarks, and show that CoT increases overall reasoning performance by up to 7.7% under the same budget, and specifically boosts the performance of apprentice VLMs by up to 36.6%. Our code is available at https://github.com/UIUC-MONET/Cache-of-Thoughts

Mingyuan Wu, Meitang Li, Jingcheng Yang et al.

Inference-time techniques such as decoding-time scaling and self-refinement have been shown to substantially improve reasoning in large language models (LLMs), driven by emergent self-correction and self-verification behaviors often elicited through reinforcement learning (RL). In this work, we investigate whether these inference-time scaling methods similarly benefit vision-language models (VLMs), especially those fine-tuned with RL. Through extensive evaluation, we find that while strategies like majority vote and best-of-N with self-verification enhance VLM performance, majority vote significantly outperforms verification-centric ones. Furthermore, inference time scaling behaviors commonly associated with RL-tuned models, such as the 'A-ha moment,' do not yield consistent performance gains. Our analysis identifies a key limitation: current RL-trained VLMs exhibit weak self-verification across both visual and textual modalities, limiting the effectiveness of inference-time scaling.

Supawit Chockchowwat, Zhaoheng Li, Yongjoo Park

In machine learning (ML), Python serves as a convenient abstraction for working with key libraries such as PyTorch, scikit-learn, and others. Unlike DBMS, however, Python applications may lose important data, such as trained models and extracted features, due to machine failures or human errors, leading to a waste of time and resources. Specifically, they lack four essential properties that could make ML more reliable and user-friendly -- durability, atomicity, replicability, and time-versioning (DART). This paper presents our vision of Transactional Python that provides DART without any code modifications to user programs or the Python kernel, by non-intrusively monitoring application states at the object level and determining a minimal amount of information sufficient to reconstruct a whole application. Our evaluation of a proof-of-concept implementation with public PyTorch and scikit-learn applications shows that DART can be offered with overheads ranging 1.5%--15.6%.

Ruolin Wang, Zixuan Chen, Mingrui "Ray" Zhang et al.

Online shopping has become a valuable modern convenience, but blind or low vision (BLV) users still face significant challenges using it, because of: 1) inadequate image descriptions and 2) the inability to filter large amounts of information using screen readers. To address those challenges, we propose Revamp, a system that leverages customer reviews for interactive information retrieval. Revamp is a browser integration that supports review-based question-answering interactions on a reconstructed product page. From our interview, we identified four main aspects (color, logo, shape, and size) that are vital for BLV users to understand the visual appearance of a product. Based on the findings, we formulated syntactic rules to extract review snippets, which were used to generate image descriptions and responses to users' queries. Evaluations with eight BLV users showed that Revamp 1) provided useful descriptive information for understanding product appearance and 2) helped the participants locate key information efficiently.