Constructing confidence intervals (CIs) for the average treatment effect (ATE) from patient records is crucial to assess the effectiveness and safety of drugs. However, patient records typically come from different hospitals, thus raising the question of how multiple observational datasets can be effectively combined for this purpose. In our paper, we propose a new method that estimates the ATE from multiple observational datasets and provides valid CIs. Our method makes little assumptions about the observational datasets and is thus widely applicable in medical practice. The key idea of our method is that we leverage prediction-powered inferences and thereby essentially `shrink' the CIs so that we offer more precise uncertainty quantification as compared to na\"ive approaches. We further prove the unbiasedness of our method and the validity of our CIs. We confirm our theoretical results through various numerical experiments. Finally, we provide an extension of our method for constructing CIs from combinations of experimental and observational datasets.
Answer Set Programming (ASP), a well-known declarative logic programming paradigm, has recently found practical application in Process Mining. In particular, ASP has been used to model tasks involving declarative specifications of business processes. In this area, Declare stands out as the most widely adopted declarative process modeling language, offering a means to model processes through sets of constraints valid traces must satisfy, that can be expressed in Linear Temporal Logic over Finite Traces (LTLf). Existing ASP-based solutions encode Declare constraints by modeling the corresponding LTLf formula or its equivalent automaton which can be obtained using established techniques. In this paper, we introduce a novel encoding for Declare constraints that directly models their semantics as ASP rules, eliminating the need for intermediate representations. We assess the effectiveness of this novel approach on two Process Mining tasks by comparing it with alternative ASP encodings and a Python library for Declare. Under consideration in Theory and Practice of Logic Programming (TPLP).
In this study, we address causal inference when only observational data and a valid causal ordering from the causal graph are available. We introduce a set of flow models that can recover component-wise, invertible transformation of exogenous variables. Our flow-based methods offer flexible model design while maintaining causal consistency regardless of the number of discretization steps. We propose design improvements that enable simultaneous learning of all causal mechanisms and reduce abduction and prediction complexity to linear O(n) relative to the number of layers, independent of the number of causal variables. Empirically, we demonstrate that our method outperforms previous state-of-the-art approaches and delivers consistent performance across a wide range of structural causal models in answering observational, interventional, and counterfactual questions. Additionally, our method achieves a significant reduction in computational time compared to existing diffusion-based techniques, making it practical for large structural causal models.
Approximating time-varying unobserved heterogeneity by discrete types has become increasingly popular in economics. Yet, provably valid post-clustering inference for target parameters in models that do not impose an exact group structure is still lacking. This paper fills this gap in the leading case of a linear panel data model with nonseparable two-way unobserved heterogeneity. Building on insights from the double machine learning literature, we propose a simple inference procedure based on a bias-reducing moment. Asymptotic theory and simulations suggest excellent performance. In the application on fiscal policy we revisit, the novel approach yields conclusions in line with economic theory.
We consider temporal numeric planning problems $\Pi$ expressed in PDDL2.1 level 3, and show how to produce SMT formulas $(i)$ whose models correspond to valid plans of $\Pi$, and $(ii)$ that extend the recently proposed planning with patterns approach from the numeric to the temporal case. We prove the correctness and completeness of the approach and show that it performs very well on 10 domains with required concurrency.
Being able to reconstruct training data from the parameters of a neural network is a major privacy concern. Previous works have shown that reconstructing training data, under certain circumstances, is possible. In this work, we analyse such reconstructions empirically and propose a new formulation of the reconstruction as a solution to a bilevel optimisation problem. We demonstrate that our formulation as well as previous approaches highly depend on the initialisation of the training images $x$ to reconstruct. In particular, we show that a random initialisation of $x$ can lead to reconstructions that resemble valid training samples while not being part of the actual training dataset. Thus, our experiments on affine and one-hidden layer networks suggest that when reconstructing natural images, yet an adversary cannot identify whether reconstructed images have indeed been part of the set of training samples.
Inverse protein folding generates valid amino acid sequences that can fold into a desired protein structure, with recent deep-learning advances showing significant potential and competitive performance. However, challenges remain in predicting highly uncertain regions, such as those with loops and disorders. To tackle such low-confidence residue prediction, we propose a \textbf{Ma}sk \textbf{p}rior-guided denoising \textbf{Diff}usion (\textbf{MapDiff}) framework that accurately captures both structural and residue interactions for inverse protein folding. MapDiff is a discrete diffusion probabilistic model that iteratively generates amino acid sequences with reduced noise, conditioned on a given protein backbone. To incorporate structural and residue interactions, we develop a graph-based denoising network with a mask prior pre-training strategy. Moreover, in the generative process, we combine the denoising diffusion implicit model with Monte-Carlo dropout to improve uncertainty estimation. Evaluation on four challenging sequence design benchmarks shows that MapDiff significantly outperforms state-of-the-art methods. Furthermore, the in-silico sequences generated by MapDiff closely resemble the physico-chemical and structural characteristics of native proteins across different protein families and architectures.
This paper proposes the automatic Doubly Robust Random Forest (DRRF) algorithm for estimating the conditional expectation of a moment functional in the presence of high-dimensional nuisance functions. DRRF extends the automatic debiasing framework based on the Riesz representer to the conditional setting and enables nonparametric, forest-based estimation (Athey et al., 2019; Oprescu et al., 2019). In contrast to existing methods, DRRF does not require prior knowledge of the form of the debiasing term or impose restrictive parametric or semi-parametric assumptions on the target quantity. Additionally, it is computationally efficient in making predictions at multiple query points. We establish consistency and asymptotic normality results for the DRRF estimator under general assumptions, allowing for the construction of valid confidence intervals. Through extensive simulations in heterogeneous treatment effect (HTE) estimation, we demonstrate the superior performance of DRRF over benchmark approaches in terms of estimation accuracy, robustness, and computational efficiency.
We develop a probabilistic variant of Partial Least Squares (PLS) we call Probabilistic Targeted Factor Analysis (PTFA), which can be used to extract common factors in predictors that are useful to predict a set of predetermined target variables. Along with the technique, we provide an efficient expectation-maximization (EM) algorithm to learn the parameters and forecast the targets of interest. We develop a number of extensions to missing-at-random data, stochastic volatility, factor dynamics, and mixed-frequency data for real-time forecasting. In a simulation exercise, we show that PTFA outperforms PLS at recovering the common underlying factors affecting both features and target variables delivering better in-sample fit, and providing valid forecasts under contamination such as measurement error or outliers. Finally, we provide three applications in Economics and Finance where PTFA outperforms compared with PLS and Principal Component Analysis (PCA) at out-of-sample forecasting.
How can we use the novel capacities of large language models (LLMs) in empirical research? And how can we do so while accounting for their limitations, which are themselves only poorly understood? We develop an econometric framework to answer this question that distinguishes between two types of empirical tasks. Using LLMs for prediction problems (including hypothesis generation) is valid under one condition: no ``leakage'' between the LLM's training dataset and the researcher's sample. No leakage can be ensured by using open-source LLMs with documented training data and published weights. Using LLM outputs for estimation problems to automate the measurement of some economic concept (expressed either by some text or from human subjects) requires the researcher to collect at least some validation data: without such data, the errors of the LLM's automation cannot be assessed and accounted for. As long as these steps are taken, LLM outputs can be used in empirical research with the familiar econometric guarantees we desire. Using two illustrative applications to finance and political economy, we find that these requirements are stringent; when they are violated, the limitations of LLMs now result in unreliable empirical estimates. Our results suggest the excitement around the empirical uses of LLMs is warranted -- they allow researchers to effectively use even small amounts of language data for both prediction and estimation -- but only with these safeguards in place.
This paper introduces M$^{3}$-20M, a large-scale Multi-Modal Molecule dataset that contains over 20 million molecules, with the data mainly being integrated from existing databases and partially generated by large language models. Designed to support AI-driven drug design and discovery, M$^{3}$-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit the training or fine-tuning of models, including large language models for drug design and discovery tasks. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M$^{3}$-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, GPT-4, and Llama3-8b. Our experimental results show that M$^{3}$-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than existing single-modal datasets, which validates the value and potential of M$^{3}$-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.
SMILES, a crucial textual representation of molecular structures, has garnered significant attention as a foundation for pre-trained language models (LMs). However, most existing pre-trained SMILES LMs focus solely on the single-token level supervision during pre-training, failing to fully leverage the substructural information of molecules. This limitation makes the pre-training task overly simplistic, preventing the models from capturing richer molecular semantic information. Moreover, during pre-training, these SMILES LMs only process corrupted SMILES inputs, never encountering any valid SMILES, which leads to a train-inference mismatch. To address these challenges, we propose SMI-Editor, a novel edit-based pre-trained SMILES LM. SMI-Editor disrupts substructures within a molecule at random and feeds the resulting SMILES back into the model, which then attempts to restore the original SMILES through an editing process. This approach not only introduces fragment-level training signals, but also enables the use of valid SMILES as inputs, allowing the model to learn how to reconstruct complete molecules from these incomplete structures. As a result, the model demonstrates improved scalability and an enhanced ability to capture fragment-level molecular information. Experimental results show that SMI-Editor achieves state-of-the-art performance across multiple downstream molecular tasks, and even outperforming several 3D molecular representation models.
We consider the inference for the ranking of large language models (LLMs). Alignment arises as a significant challenge to mitigate hallucinations in the use of LLMs. Ranking LLMs has proven to be an effective tool to improve alignment based on the best-of-$N$ policy. In this paper, we propose a new inferential framework for hypothesis testing among the ranking for language models. Our framework is based on a nonparametric contextual ranking framework designed to assess large language models' domain-specific expertise, leveraging nonparametric scoring methods to account for their sensitivity to the prompts. To characterize the combinatorial complexity of the ranking, we introduce a novel concept of confidence diagram, which leverages a Hasse diagram to represent the entire confidence set of rankings by a single directed graph. We show the validity of the proposed confidence diagram by advancing the Gaussian multiplier bootstrap theory to accommodate the supremum of independent empirical processes that are not necessarily identically distributed. Extensive numerical experiments conducted on both synthetic and real data demonstrate that our approach offers valuable insight into the evaluation for the performance of different LLMs across various medical domains.
The remarkable performance of large language models (LLMs) in content generation, coding, and common-sense reasoning has spurred widespread integration into many facets of society. However, integration of LLMs raises valid questions on their reliability and trustworthiness, given their propensity to generate hallucinations: plausible, factually-incorrect responses, which are expressed with striking confidence. Previous work has shown that hallucinations and other non-factual responses generated by LLMs can be detected by examining the uncertainty of the LLM in its response to the pertinent prompt, driving significant research efforts devoted to quantifying the uncertainty of LLMs. This survey seeks to provide an extensive review of existing uncertainty quantification methods for LLMs, identifying their salient features, along with their strengths and weaknesses. We present existing methods within a relevant taxonomy, unifying ostensibly disparate methods to aid understanding of the state of the art. Furthermore, we highlight applications of uncertainty quantification methods for LLMs, spanning chatbot and textual applications to embodied artificial intelligence applications in robotics. We conclude with open research challenges in uncertainty quantification of LLMs, seeking to motivate future research.
Hyperspectral and Multispectral Image Fusion (HMIF) aims to fuse low-resolution hyperspectral images (LR-HSIs) and high-resolution multispectral images (HR-MSIs) to reconstruct high spatial and high spectral resolution images. Current methods typically apply direct fusion from the two modalities without effective supervision, leading to an incomplete perception of deep modality-complementary information and a limited understanding of inter-modality correlations. To address these issues, we propose a simple yet effective solution for unsupervised HMIF, revealing that modality decoupling is key to improving fusion performance. Specifically, we propose an end-to-end self-supervised \textbf{Mo}dality-Decoupled \textbf{S}patial-\textbf{S}pectral Fusion (\textbf{MossFuse}) framework that decouples shared and complementary information across modalities and aggregates a concise representation of both LR-HSIs and HR-MSIs to reduce modality redundancy. Also, we introduce the subspace clustering loss as a clear guide to decouple modality-shared features from modality-complementary ones. Systematic experiments over multiple datasets demonstrate that our simple and effective approach consistently outperforms the existing HMIF methods while requiring considerably fewer parameters with reduced inference time. The anonymous source code is in \href{https://github.com/dusongcheng/MossFuse}{MossFuse}.
Resolving disagreement in manual annotation typically consists of removing unreliable annotators and using a label aggregation strategy such as majority vote or expert opinion to resolve disagreement. These may have the side-effect of silencing or under-representing minority but equally valid opinions. In this paper, we study the impact of standard label aggregation strategies on minority opinion representation in sexism detection. We investigate the quality and value of minority annotations, and then examine their effect on the class distributions in gold labels, as well as how this affects the behaviour of models trained on the resulting datasets. Finally, we discuss the potential biases introduced by each method and how they can be amplified by the models.
Under a set of assumptions on a family of submanifolds $\subset {\mathbb R}^D$, we derive a series of geometric properties that remain valid after finite-dimensional and almost isometric Diffusion Maps (DM), including almost uniform density, finite polynomial approximation and reach. Leveraging these properties, we establish rigorous bounds on the embedding errors introduced by the DM algorithm is $O\left((\frac{\log n}{n})^{\frac{1}{8d+16}}\right)$. Furthermore, we quantify the error between the estimated tangent spaces and the true tangent spaces over the submanifolds after the DM embedding, $\sup_{P\in \mathcal{P}}\mathbb{E}_{P^{\otimes \tilde{n}}} \max_{1\leq j \angle (T_{Y_{\varphi(M),j}}\varphi(M),\hat{T}_j)\leq \tilde{n}} \leq C \left(\frac{\log n }{n}\right)^\frac{k-1}{(8d+16)k}$, which providing a precise characterization of the geometric accuracy of the embeddings. These results offer a solid theoretical foundation for understanding the performance and reliability of DM in practical applications.
System testing is essential in any software development project to ensure that the final products meet the requirements. Creating comprehensive test cases for system testing from requirements is often challenging and time-consuming. This paper explores the effectiveness of using Large Language Models (LLMs) to generate test case designs from Software Requirements Specification (SRS) documents. In this study, we collected the SRS documents of five software engineering projects containing functional and non-functional requirements, which were implemented, tested, and delivered by respective developer teams. For generating test case designs, we used ChatGPT-4o Turbo model. We employed prompt-chaining, starting with an initial context-setting prompt, followed by prompts to generate test cases for each use case. We assessed the quality of the generated test case designs through feedback from the same developer teams as mentioned above. Our experiments show that about 87 percent of the generated test cases were valid, with the remaining 13 percent either not applicable or redundant. Notably, 15 percent of the valid test cases were previously not considered by developers in their testing. We also tasked ChatGPT with identifying redundant test cases, which were subsequently validated by the respective developers to identify false positives and to uncover any redundant test cases that may have been missed by the developers themselves. This study highlights the potential of leveraging LLMs for test generation from the Requirements Specification document and also for assisting developers in quickly identifying and addressing redundancies, ultimately improving test suite quality and efficiency of the testing procedure.
Linear regressions with endogeneity are widely used to estimate causal effects. This paper studies a framework that involves two common issues: endogeneity of the regressors and heteroskedasticity that depends on endogenous regressors-i.e., endogenous heteroskedasticity. We show that the presence of endogenous heteroskedasticity in the structural regression renders the two-stage least squares estimator inconsistent. To address this issue, we propose sufficient conditions and a control function approach to identify and estimate the causal parameters of interest. We establish the limiting properties of the estimator--namely, consistency and asymptotic normality--and propose inference procedures. Monte Carlo simulations provide evidence on the finite-sample performance of the proposed methods and evaluate different implementation strategies. We revisit an empirical application on job training to illustrate the methods.
We consider the problem of recovering the topology and the edge conductance value, as well as characterizing a set of electrical networks that satisfy the limitedly available Thevenin impedance measurements. The measurements are obtained from an unknown electrical network, which is assumed to belong to a class of circular planar passive electrical network. This class of electrical networks consists of R, RL, and RC networks whose edge impedance values are equal, and the absolute value of the real and the imaginary part of the edge impedances are also equal. To solve the topology reconstruction and the set characterization problem, we establish a simple relation between Thevenin impedance and the Laplacian matrix and leverage this relation to get a system of multivariate polynomial equations, whose solution is a set of all electrical networks satisfying the limited available Thevenin's impedance measurements. To confine the search space and generate valid electrical networks, we impose the triangle and Kalmanson's inequality as constraints. The solution to a constrained system of multivariate polynomial equations is a set of reconstructed valid electrical networks. For simple algorithmic solutions, we use Gr\"obner basis polynomials. This paper shows that the triangle and the Kalmanson's inequality holds for general circular planar passive R, RL, and RC electrical networks if certain boundary conditions lie within a convex cone. Numerical examples illustrate the developed topology reconstruction method.