data science teams

Abstract: When providing forecasted probabilities with a predictive model, the ideal model offers perfect calibration: the true probability of the outcome (i.e., the probability that $Y=1$) exactly matches the forecasted probability $f(X)$. In practice, models inevitably exhibit calibration error, and it is therefore important to be able to measure this miscalibration to assess a model's reliability. The Expected Calibration Error (ECE) is the most widely used measure of miscalibration, but is known to be impossible to estimate the ECE with guaranteed accuracy in an assumption-free setting. In this work, we propose an alternative measure, the rankECE, that is based on comparing points with neighboring values of the predicted probability $f(X)$. Our theoretical guarantees and empirical results establish that rankECE provides a better proxy for ECE as compared to binned approximations to ECE, which are the most commonly-used approximations in practice.

Abstract: In practice, various learning scenarios provide access to auxiliary features exclusively during training. Incorporating such data to enhance model performance gave rise to a paradigm known as Learning Using Privileged Information (LUPI). While this extra information is intended to improve the resulting model, establishing a generalized, cohesive understanding of how privileged information (PI) transfers useful knowledge remains a challenge. Vapnik's original theory and subsequent works offer performance guarantees in certain cases, but these results are inherently per-algorithm and rely on setting-specific proof approaches. Consequently, a more general framework explaining how and when PI transfers useful knowledge is still missing. To bridge this gap, we introduce an algorithm-agnostic, information-theoretic approach based on the PAC-Bayes framework. Rather than asking whether a particular algorithm exploits PI, we ask how much value it could offer: comparing the tightest achievable risk bound with and without PI yields its potential - an upper limit on the extractable gain. We introduce a metric that quantifies this potential directly from empirical training risk, bypassing the need for test-time data access, and validate our findings in both supervised and unsupervised settings. The results demonstrate a robust correspondence between our training-time metric and true test-time performance gains. Ultimately, this work takes a necessary step toward an information-theoretic understanding of LUPI, and quantifying the potential of privileged features before committing to a model.

Abstract: Even with a fixed dataset and research question, data analysis involves many defensible decisions. Understanding how these choices influence the results is scientifically important but remains challenging. Crowdsourcing and agentic AI can generate hundreds of end-to-end analyses, but scaling generation alone can create a processing bottleneck and an analytic ``black hole.'' A common workaround is to impose a shared fixed decision taxonomy, which can limit insight and understate uncertainty. We present ForkSCOPE, a human-AI collaboration framework that induces structure bottom-up from the code corpus of end-to-end analyses, without a taxonomy fixed before or after generation, so the organization and evaluation of the garden can scale with the corpus. ForkSCOPE surfaces the charted garden of forking paths through a human-AI collaboration pipeline and an evidence-linked interactive viewer for steering and verification: it spotlights organically identified forks and structures and produces a derived taxonomy and decision map compatible with existing multiverse tools.

Abstract: We study an online sketched Newton method that approximates the Newton direction at each step via a state-of-the-art sketching solver, called the generalized accelerated sketch-and-project solver (GAS), thereby mitigating the computational bottleneck of classical second-order methods. The GAS solver improves upon vanilla, unaccelerated sketch-and-project solvers by achieving accelerated convergence through Nesterov momentum updates, and accommodates a flexible projection metric whose proper choice further reduces computational cost. Building on this design, we establish asymptotic normality of the averaged sketched Newton iterates and characterize their limiting covariance matrix. The resulting covariance recovers that of the unaccelerated sketched Newton method under a specific choice of acceleration parameters, converges more rapidly (in the number of sketching steps) to the minimax-optimal covariance in general, and is smaller than that of the last iterate produced by the accelerated method. Finally, we strengthen these results by establishing a functional central limit theorem for the Newton iterates, which allows us to bypass explicit covariance estimation and develop an online inference procedure based on random scaling. Specifically, we construct a pivotal test statistic by appropriately rescaling the averaged iterates, so that its limiting distribution is free of any unknown parameters, enabling asymptotically valid online inference. Numerical experiments demonstrate superior performance of the proposed inference procedure.

Abstract: Latent embeddings have become a central data abstraction in modern machine learning, especially in biomedicine, where foundation models are increasingly used to encode multimodal data like clinical text, medical images, omics, and physiological signals. However, the utility and value of these representations depends on understanding their quality, structure, and the information they encode. Existing analysis workflows for evaluating representations remain fragmented across custom scripts, isolated metrics, and most importantly lack multimodal analysis, limiting accessibility and reproducibility. We present LatentVerse, a representation analysis resource that combines a web-based visual analytics platform for accessible, report-driven exploration with a command-line interface for scalable technical workflows. LatentVerse unifies diagnostics for various representation quality metrics and extends to multimodal settings by decomposing embeddings into shared and modality-specific components. We evaluate LatentVerse through controlled unimodal and multimodal simulations, discovery-oriented analyses on real biomedical embeddings, and a user study across diverse use cases. By supporting thorough and interpretable evaluation of latent spaces, LatentVerse makes foundation model representations more understandable in biomedical and data science applications.

Abstract: Scientific workflows increasingly use repeated queries, multiple models, and interacting agents. Reliability therefore depends on whether models preserve correct conclusions, accept valid corrections, and contribute errors that a selector can distinguish. Using SycoBench- 600 as a controlled measurement substrate, we evaluate these requirements through selective updating, defined by resistance to misleading suggestions and uptake of correct suggestions. The study covers ten models and 17,055 trajectories. Published models span 13.4 to 71.6 percentage points in selectivity. Under identical local evaluation, Qwen3-4B is selectively adaptive at 45.6 points, Gemma3-4B is destabilized at minus 14.1 points, and SmolLM3-3B follows both correct and wrong explicit suggestions, producing zero selectivity. Matched interventions identify model specific responses to doubt, authority, and explicit advice. Among seven published models, the best reaches 95.3 percent accuracy, plurality reaches 88.6 percent, and the oracle ceiling is 99.8 percent. Mean error correlation of 0.285 reduces seven models to an effective independent count of 2.58. A leave-one-stem-family-out reliability selector reaches 96.2 percent, recovering 67.7 percent of the plurality-to-oracle gap. These results establish selective updating, error diversity, and calibrated adjudication as jointly measurable design targets for multi-model scientific workflows.

Abstract: Reproducibility is essential to scientific progress, yet the growing volume and complexity of scientific publications make exhaustive manual verification increasingly impractical. Although recent advances in large language model (LLM) agents enable automated experiment reproduction, existing evaluations largely focus on final repositories and are typically limited to machine learning (ML). We introduce AgentActionBench, a process-oriented benchmark for evaluating agent-based experiment reproduction across ML and AI4Science domains. Our framework uses an MCP-based Action Recorder to capture agents' behaviour throughout the reproduction process and evaluates the resulting traces with paper-specific rubrics. AgentActionBench contains 150 papers, including 120 ML papers and 30 AI4Science papers. A human-annotated subset covering 10% of the benchmark provides validation data, while model-assisted augmentation expands the full benchmark to more than 10,000 rubric items. Experimental results show that current systems remain limited, with execution as the primary bottleneck. Meanwhile, the strong Pearson and Spearman correlations between model-generated and human-annotated rubrics validate the reliability of our scalable rubric-generation approach.

Abstract: Unlabeled-unlabeled (UU) learning allows us to learn a binary classifier from two sets of unlabeled data with different class-priors. It is a general framework because it includes a wide variety of supervised learning such as positive-unlabeled (PU) learning, noisy label learning, and similarity-based learning. Existing UU learning assumes that the test and training distributions have the same class-conditional densities. However, this assumption rarely holds in practice due to distribution shifts. This paper proposes a distribution shift adaptation method for UU learning that uses UU data in the training distribution and a few UU data in the test distribution. The proposed method is based on the importance weighting, which minimizes the test risk by using training data with estimated importance weights. Although existing importance weighting methods cannot handle UU data, we show that it can be done in a principled manner. Thanks to the generality of UU learning, our method can handle various learning problems such as PU and noisy label learning under distribution shift within a single framework while existing methods are usually tailored to a specific problem. Moreover, it does not require any assumption of the shift types such as covariate shift. We experimentally demonstrate the effectiveness of the proposed method with real-world datasets.

Abstract: We develop an exact almost-sure learning theory for smooth parametric models trained by regularly weighted empirical risk minimization on long-range dependent data. The training observations are generated from a fixed finite window of a stationary Gaussian sequence, and the sample weights are regularly varying. If the loss gradient at the population minimizer has Wiener-chaos rank $m$ and a nonzero low-frequency coefficient, then, in the long-memory interior regime, the finite-lag score reduces on the iterated-logarithm scale to a single weighted Hermite chaos. This yields an almost-sure Bahadur representation, an exact limsup law for the learned parameter, and, for $m\ge2$, the functional cluster set of the complete learning trajectory. The polynomial learning exponent is determined by the memory parameter and the chaos rank and is invariant under the admissible power weighting, whereas the sharp pathwise constant and cluster geometry depend on the weights. In the rank-one case, global optimization over the admissible power exponents shows that every optimizer is positive. Time-series prediction and classification examples illustrate the results.

Abstract: Feature transformation improves predictive performance on tabular data by constructing informative abstractions from raw features. Recent generative approaches encode transformation knowledge into continuous embedding spaces for efficient exploration of candidate strategies, but face three key limitations: (1) overlooking hierarchical relationships between low-level features, operations, and high-level abstractions; (2) enforcing order-sensitive embeddings on inherently permutation-invariant transformation sequences, thereby introducing systematic bias; and (3) relying on gradient-based search, which is ill-suited to non-convex transformation spaces. We propose a framework with two complementary components. First, a permutation-invariant hierarchical module captures interactions across features, operations, and abstraction levels, with a self-attention pooling mechanism that maps semantically equivalent structures to consistent embeddings aligned with downstream performance. Second, a policy-guided multi-objective reinforcement learning strategy initializes the search from empirically strong seeds and jointly optimizes predictive accuracy and transformation efficiency. Extensive experiments on diverse tabular benchmarks demonstrate the effectiveness and robustness of our framework against strong baselines. Our code and data are publicly available at: https://github.com/RayLiu1103/PHER.

Abstract: Large language models (LLMs) increasingly act as research agents, yet their ability to track shifts in research attention is difficult to evaluate because reviews and research ideas lack uniquely verifiable outcomes. We introduce Research Attention Prediction (RAP), a rolling benchmark covering 278 AI/ML fields and 1,390 episodes. At each cut-off, an LLM agent searches a temporally restricted arXiv corpus and predicts the next six months' paper shares across eight frozen research directions. Search generally helps, but all four diagnostic models perform worse than an exact-count exponentially weighted moving average (EWMA) baseline in compositional accuracy. We identify two linked bottlenecks. Under cumulative-history access, State carry-forward outperforms direct Forecast for all four diagnostic models; frozen-evidence replay links a shared component of this reversal to Forecast-oriented policies retrieving a smaller share of recent evidence. Even with exact historical activity, future-specific updating remains limited, with only GPT-5.5 plus reopened Search slightly surpassing EWMA. Fine-tuning on realised outcomes improves Qwen3-4B's forecast Spearman correlation by 0.105 on held-out fields at later origins, with gains also on change-rich episodes.

Abstract: Temporal graph learning models the evolution of dynamic systems, where both structural interactions and semantic states change over time. However, existing benchmarks primarily emphasize structural evolution via temporal link prediction (TLP), while support for semantic evolution remains limited. Although temporal node classification (TNC) is sometimes included, it is typically restricted to simplistic binary settings that fail to capture realistic semantic drift. Moreover, commonly used datasets exhibit high link repetition, leading to inflated performance estimates and obscuring true model capability. To address these limitations, we introduce \textbf{TTGBench}, a new benchmark that jointly evaluates structural and semantic evolution. TTGBench comprises six real-world, text-rich datasets characterized by \emph{Dual Volatility}, enabling rigorous and fair evaluation of existing models. Notably, it is the first benchmark to support both multi-class and multi-label TNC, filling a critical gap in evaluating temporal semantic drift. We conduct a comprehensive evaluation of 17 state-of-the-art methods across Temporal Graph Neural Networks (TGNNs) and Large Language Model (LLM)-based paradigms. The results reveal a clear \emph{capability divide} between the two paradigms: TGNN-based methods excel at structural prediction but fail at semantic tracking, whereas LLM-based predictors show the opposite trend. Through in-depth analysis, we uncover their fundamental limitations and provide insights for developing more comprehensive temporal graph models.

Abstract: This report analyzes Qiushi Engine v0.8 across all 40 test tasks in AstaBench E2E-Bench-Hard, a benchmark that requires autonomous agents to carry a research question through experimental design, code implementation, actual execution, result analysis, and report delivery. Qiushi Engine is model-configurable; this evaluation selected DeepSeek deepseek-v4pro-preview as the model backend. The official AstaBench leaderboard records a score of 0.816 and an average benchmark cost of USD 15.209 per task, while the full-precision local recomputation is $81.59 \pm 1.87$. Four tasks satisfied every rubric item, yielding a full-task completion rate of 4/40 = 10% -- 7 percentage points above, and about 3.3 times, the approximately 3% best rate reported for AstaBench's official agents. Across 507 required rubric items, 416 were satisfied (82.1%). Official scoring archives and 40 Meta-Trace records show sustained production and verification of reports, code, and experimental artifacts; the principal gaps lie in repeated runs, external dependencies, specified metrics, and ablation studies. The report explains the benchmark, system workflow, aggregate results, representative cases, and limits of interpretation.

Abstract: We characterize the sharp structure-agnostic minimax risk for coefficient estimation in the partial linear model when the outcome and treatment nuisances are learned by two distinct black-box learners, which resolves the open problem in double machine learning posed by Gu (2025). For each nuisance \(q\in\{μ,π\}\), we characterize the available learner by an approximation-error budget \(a_q\) and a stochastic-error budget \(s_q\), with the latter controlled through localized Rademacher complexity. Writing \(\mathcal E_n\) for the minimax mean-squared error, we show that \[\mathcal E_n\asymp1\wedge\left\{\frac1n+\left(a_μa_π+\min\left\{a_πs_μ+s_π^2,\,a_μs_π+s_μ^2\right\}\right)^2\right\}.\] The main new ingredient is a novel lower bound for the general two-learner problem. Our proof constructs four finite-mixture testing experiments using orthogonal code functions. Across these experiments, the hidden perturbations are placed outside both learner classes, outside only the treatment learner class, outside only the outcome learner class, or inside both learner classes. These four configurations capture, respectively, the interaction between the two approximation errors, the two asymmetric interactions between one learner's approximation error and the other learner's learning error, and the joint estimation difficulty of learning both nuisances. Combining the four resulting lower bounds yields the displayed rate, which matches the latest upper bound in Gu (2026). Our result shows that standard double machine learning can overstate the intrinsic difficulty of target estimation and provides a target-specific principle for learner selection: approximation error and stochastic complexity must be jointly balanced across the two nuisance learners rather than optimized separately.

Abstract: Graph modeling, a crucial task for representing complex relationships in graph-structured data, has achieved significant success in recent years. However, current graph modeling methods rely on traditional Graph Neural Networks and pre-training approaches to implicitly learn the underlying relational structure of graph data. Thus, these prior methods cannot capture the complex graph structure and correlations among inputs. In this paper, we introduce a novel Attention-based Normalizing Flow-based Approach\footnote{Our implementation and models will be released publicly for research reproducibility.} (ANFA or $α$) that provides an explicit, interpretable, and tractable Graph Modeling ($α$-Graph). In particular, we propose a new Unconditional Graph Normalizing Flow with an Invertible Attention Mechanism to capture the complex relational structure of graph data. To further enhance the expressiveness of the model, we introduce Conditional Graph Normalizing Flow with Learnable Queries that enables efficient modeling of correlations in graph-structured data. We show that our Conditional Graph Normalizing Flows behave similarly to Unconditional Graph Normalizing Flows, enhancing expressiveness while maintaining training stability and efficiency. Our experimental results on three benchmarks will illustrate the effectiveness and the state-of-the-art (SoTA) performance of the proposed $α$-Graph method.

Abstract: Counterfactual explanations formalize "what-if" scenarios by identifying modifications to an input instance that obtain a desired alternative prediction. Traditionally, whether generated via instance-specific optimization or amortized single pass models, these approaches rely on a single, deterministic point-estimate predictor. However, this ignores predictive uncertainty and hypothesis variability, leading to brittle explanations that frequently become invalid if the underlying model is retrained or updated. To address this fragility, we propose the Amortized Variational Counterfactual Generator (AVCG), a generalized optimization framework that formulates counterfactual generation as optimization over an arbitrary distribution of plausible predictive hypotheses rather than a single deterministic predictor. This formulation naturally accommodates Bayesian posteriors, Rashomon-restricted hypothesis spaces, and other uncertainty representations within a unified optimization framework. Evaluation across multiple benchmark datasets demonstrates that the AVCG framework produces counterfactual explanations that remain highly valid under predictive uncertainty and model changes, while maintaining competitive plausibility and single-pass runtime performance.

Abstract: Time series data is very common in many real-world applications and in numerous domains, with increasing interest for automated information extraction using machine learning. One of these subfields is time series clustering, which consists in identifying clusters among a set of time series in an unsupervised fashion. Most time series clustering algorithms suffer from the same balancing act: they trade clustering performance for faster runtimes or vice versa. We present a novel time series clustering algorithm that we call CLUES-WEASEL, which stands for CLustering with the UnsupervisEd Second version of Word ExtrAction for time SEries cLassification. CLUES-WEASEL extracts features using the unsupervised version of the transformation step of WEASEL 2.0, which is a time series classification algorithm, then reduces these features using principal component analysis, and finally performs clustering with the $k$-means algorithm using these reduced extracted features. Through extensive experiments, we prove that CLUES-WEASEL is significantly better than any other existing time series clustering algorithm while being (much) faster than any state-of-the-art one. We also show that the architecture of CLUES-WEASEL can work well with other time series feature extraction algorithms. Our findings highlight the relevance of CLUES-WEASEL for time series clustering.