Auto-Fill: Learning to Predict Missing Values Accurately with Specialist Language Models
Authors: Yurong Liu, Yeye He, Haoyu Dong, Junjie Xing, Shi Han, Dongmei Zhang, Surajit Chaudhuri
Organizations: New York University · Microsoft Research
Abstract
Predicting missing cell values in tabular data is a fundamental problem in data cleaning. While state-of-the-art reasoning models show great promise in predicting missing values in tables, by reasoning holistically across rows and columns, they are costly to deploy at scale and tend to be overconfident, often generating hallucinated or false-positive predictions. In this paper, we observe that achieving high-precision missing-value prediction in tables requires a distinct combination of three capabilities: (1) world knowledge, (2) text-based reasoning, and (3) code-based reasoning. We systematically explore design choices for combining these capabilities, and propose an Auto-Fill approach that post-trains three specialist small language models (SLMs), each optimized for one capability. We develop a calibrated ensemble mechanism that either dynamically selects the most confident specialist or abstains, ensuring high accuracy. Extensive experiments on 11 benchmarks with 2200 real tables drawn from diverse domains show that Auto-Fill achieves superior accuracy compared to state-of-the-art reasoning models (e.g., o3-pro, Gemini 3 Pro, and DeepSeek R1), while operating at a fraction (less than 1%) of the cost of these frontier models. Our results highlight the effectiveness of specialization and calibrated abstention in the important domain of tabular data. Auto-Fill is publicly available at https://github.com/lyrain2001/auto-fill.
Every major data modality now has a foundation model that understands it natively: text has language models, images have vision models, audio has audio models. Tabular data, the modality on which many consequential real-world AI decisions are made, does not. Every approach to tabular AI today, from gradient-boosted trees to the latest tabular foundation models, requires a preprocessing pipeline before any model can consume the data. None of them understand tabular data as a modality. We introduce the Data Language Model (DLM), the missing foundation model for tabular data. A DLM understands tables the way a language model understands sentences: natively, without serialization or preprocessing, directly from raw cell values. It is the tabular data layer on which AI models, agents, and vertical AI applications can be built, eliminating the preprocessing pipelines that currently stand between raw data and every AI system that consumes it. We present Schema-1, the first DLM: a 140M parameter model trained on more than 2.3M synthetic and real-world tabular datasets. Schema-1 outperforms gradient-boosted ensembles, AutoML stacks, and the tabular foundation models we evaluate on established row-level prediction benchmarks. On missing value reconstruction it achieves lower reconstruction error than all classical statistical methods and frontier large language models on mean performance across conditions, establishing that structural understanding of a dataset's own distributional geometry is more useful for imputation than world knowledge encoded in language. It identifies the industry sector of any unseen dataset from raw cell values alone, reliably across any domain, a task no prior tabular model can perform. It is the native tabular understanding layer that has been missing from the AI stack.
Multi-step LLM reasoning over structured tables fails because planning and execution share no explicit cell-grounding contract. Existing methods constrain the planner to a left-to-right factorization at odds with table permutation invariance, and score intermediate states by generated content alone, overlooking cell grounding. We conduct a pilot study showing that diffusion language models (DLMs) produce more human-aligned and permutation-stable cell attention on tables than autoregressive models, with a 40.2% median reduction in attention-AUROC variability under row reordering. Motivated by this, we propose TABALIGN, a planned table reasoning framework that operationalizes the contract. TABALIGN pairs a masked DLM planner, whose bidirectional denoising emits plan steps as binary cell masks, with TABATTN, a lightweight verifier trained on 1,600 human-verified attention standards to score each step by its attention overlap with the plan-designated mask. Across eight benchmarks covering table question answering and fact verification, TABALIGN improves average accuracy by 15.76 percentage points over the strongest open-source baseline at comparable 8B-class scale, with a matched-backbone ablation attributing 2.87 percentage points of this gain to the DLM planner over an AR planner on a fixed reasoner. Cleaner DLM plans also accelerate downstream reasoning execution by 44.64%.
While large language models (LLMs) perform well on table tasks, they still make data referencing errors (DREs), i.e., incorrectly citing or omitting table values, despite understanding the table structure. Beyond final-answer accuracy, DREs directly compromise the correctness and reliability of intermediate reasoning steps. Yet prior studies have only offered limited, small-scale analyses. In this work, we present the first systematic evaluation of tabular data referencing errors across different models and tasks. Our results show that DREs occur across all tested models (1.7B to 20B parameters). Furthermore, we demonstrate that incorporating data referencing as a critic significantly improves answer accuracy up to 12.0%, through critic-based filtering and rejection sampling. Finally, we trained a lightweight 4B-parameter critic model that achieves an average F1 score of 78.2% in detecting both in-distribution and out-of-distribution DREs, and effectively assists inference for larger models.