arXiv subjects

David Carlson

Publications and source records attributed to David Carlson.

At least 19 recordsLinked to original sources

arXiv2025

Synergizing Deconfounding and Temporal Generalization For Time-series Counterfactual Outcome Estimation

Estimating counterfactual outcomes from time-series observations is crucial for effective decision-making, e.g. when to administer a life-saving treatment, yet remains significantly challenging because (i) the counterfactual trajectory is never observed and (ii) confounders evolve with time and distort estimation at every step. To address these challenges, we propose a novel framework that synergistically integrates two complementary approaches: Sub-treatment Group Alignment (SGA) and Random Temporal Masking (RTM). Instead of the coarse practice of aligning marginal distributions of the treatments in latent space, SGA uses iterative treatment-agnostic clustering to identify fine-grained sub-treatment groups. Aligning these fine-grained groups achieves improved distributional matching, thus leading to more effective deconfounding. We theoretically demonstrate that SGA optimizes a tighter upper bound on counterfactual risk and empirically verify its deconfounding efficacy. RTM promotes temporal generalization by randomly replacing input covariates with Gaussian noises during training. This encourages the model to rely less on potentially noisy or spuriously correlated covariates at the current step and more on stable historical patterns, thereby improving its ability to generalize across time and better preserve underlying causal relationships. Our experiments demonstrate that while applying SGA and RTM individually improves counterfactual outcome estimation, their synergistic combination consistently achieves state-of-the-art performance. This success comes from their distinct yet complementary roles: RTM enhances temporal generalization and robustness across time steps, while SGA improves deconfounding at each specific time point.

cs.LG↗

arXiv2025

CARE: Turning LLMs Into Causal Reasoning Expert

Large language models (LLMs) have recently demonstrated impressive capabilities across a range of reasoning and generation tasks. However, research studies have shown that LLMs lack the ability to identify causal relationships, a fundamental cornerstone of human intelligence. We first conduct an exploratory investigation of LLMs' behavior when asked to perform a causal-discovery task and find that they mostly rely on the semantic meaning of variable names, ignoring the observation data. This is unsurprising, given that LLMs were never trained to process structural datasets. To first tackle this challenge, we prompt the LLMs with the outputs of established causal discovery algorithms designed for observational datasets. These algorithm outputs effectively serve as the sufficient statistics of the observation data. However, quite surprisingly, we find that prompting the LLMs with these sufficient statistics decreases the LLMs' performance in causal discovery. To address this current limitation, we propose CARE, a framework that enhances LLMs' causal-reasoning ability by teaching them to effectively utilize the outputs of established causal-discovery algorithms through supervised fine-tuning. Experimental results show that a finetuned Qwen2.5-1.5B model produced by CARE significantly outperforms both traditional causal-discovery algorithms and state-of-the-art LLMs with over a thousand times more parameters, demonstrating effective utilization of its own knowledge and the external algorithmic clues.

cs.LG↗

arXiv2025

ClinStructor: AI-Powered Structuring of Unstructured Clinical Texts

Clinical notes contain valuable, context-rich information, but their unstructured format introduces several challenges, including unintended biases (e.g., gender or racial bias), and poor generalization across clinical settings (e.g., models trained on one EHR system may perform poorly on another due to format differences) and poor interpretability. To address these issues, we present ClinStructor, a pipeline that leverages large language models (LLMs) to convert clinical free-text into structured, task-specific question-answer pairs prior to predictive modeling. Our method substantially enhances transparency and controllability and only leads to a modest reduction in predictive performance (a 2-3% drop in AUC), compared to direct fine-tuning, on the ICU mortality prediction task. ClinStructor lays a strong foundation for building reliable, interpretable, and generalizable machine learning models in clinical environments.

cs.CL↗

arXiv2025

Additive Large Language Models for Semi-Structured Text

Large Language Models have advanced clinical text classification, but their opaque predictions remain a critical barrier to practical adoption in research and clinical settings where investigators and physicians need to understand which parts of a patient's record drive risk signals. To address this challenge, we introduce \textbf{CALM}, short for \textbf{Classification with Additive Large Language Models}, an interpretable framework for semi-structured text where inputs are composed of semantically meaningful components, such as sections of an admission note or question-answer fields from an intake form. CALM predicts outcomes as the additive sum of each component's contribution, making these contributions part of the forward computation itself and enabling faithful explanations at both the patient and population level. The additive structure also enables clear visualizations, such as component-level risk curves similar to those used in generalized additive models, making the learned relationships easier to inspect and communicate. Although CALM expects semi-structured inputs, many clinical documents already have this form, and similar structure can often be automatically extracted from free-text notes. CALM achieves performance comparable to conventional LLM classifiers while improving trust, supporting quality-assurance checks, and revealing clinically meaningful patterns during model development and auditing.

cs.CL↗

arXiv2025

Generating Hypotheses of Dynamic Causal Graphs in Neuroscience: Leveraging Generative Factor Models of Observed Time Series

The field of hypothesis generation promises to reduce costs in neuroscience by narrowing the range of interventional studies needed to study various phenomena. Existing machine learning methods can generate scientific hypotheses from complex datasets, but many approaches assume causal relationships are static over time, limiting their applicability to systems with dynamic, state-dependent behavior, such as the brain. While some techniques attempt dynamic causal discovery through factor models, they often restrict relationships to linear patterns or impose other simplifying assumptions. We propose a novel method that models dynamic graphs as a conditionally weighted superposition of static graphs, where each static graph can capture nonlinear relationships. This approach enables the detection of complex, time-varying interactions between variables beyond linear limitations. Our method improves f1-scores of predicted dynamic causal patterns by roughly 22-28% on average over baselines in some of our experiments, with some improvements reaching well over 60%. A case study on real brain data demonstrates our method's ability to uncover relationships linked to specific behavioral states, offering valuable insights into neural dynamics.

cs.LG↗

arXiv2024

Deep Causal Inference for Point-referenced Spatial Data with Continuous Treatments

Causal reasoning is often challenging with spatial data, particularly when handling high-dimensional inputs. To address this, we propose a neural network (NN) based framework integrated with an approximate Gaussian process to manage spatial interference and unobserved confounding. Additionally, we adopt a generalized propensity-score-based approach to address partially observed outcomes when estimating causal effects with continuous treatments. We evaluate our framework using synthetic, semi-synthetic, and real-world data inferred from satellite imagery. Our results demonstrate that NN-based models significantly outperform linear spatial regression models in estimating causal effects. Furthermore, in real-world case studies, NN-based models offer more reasonable predictions of causal effects, facilitating decision-making in relevant applications.

cs.LG↗

arXiv2024

Benchmarking with Supernovae: A Performance Study of the FLASH Code

Astrophysical simulations are computation, memory, and thus energy intensive, thereby requiring new hardware advances for progress. Stony Brook University recently expanded its computing cluster "SeaWulf" with an addition of 94 new nodes featuring Intel Sapphire Rapids Xeon Max series CPUs. We present a performance and power efficiency study of this hardware performed with FLASH: a multi-scale, multi-physics, adaptive mesh-based software instrument. We extend this study to compare performance to that of Stony Brook's Ookami testbed which features ARM-based A64FX-700 processors, and SeaWulf's AMD EPYC Milan and Intel Skylake nodes. Our application is a stellar explosion known as a thermonuclear (Type Ia) supernova and for this 3D problem, FLASH includes operators for hydrodynamics, gravity, and nuclear burning, in addition to routines for the material equation of state. We perform a strong-scaling study with a 220 GB problem size to explore both single- and multi-node performance. Our study explores the performance of different MPI mappings and the distribution of processors across nodes. From these tests, we determined the optimal configuration to balance runtime and energy consumption for our application.

cs.DC↗

arXiv2024

Assessing the Potential of PlanetScope Satellite Imagery to Estimate Particulate Matter Oxidative Potential

Oxidative potential (OP), which measures particulate matter's (PM) capacity to induce oxidative stress in the lungs, is increasingly recognized as an indicator of PM toxicity. Since OP is not routinely monitored, it can be challenging to estimate exposure and health impacts. Remote sensing data are commonly used to estimate PM mass concentration, but have never been used to estimate OP. In this study, we evaluate the potential of satellite images to estimate OP as measured by acellular ascorbic acid (OP AA) and dithiothreitol (OP DTT) assays of 24-hour PM10 sampled periodically over five years at three locations around Grenoble, France. We use a deep convolutional neural network to extract features of daily 3 m/pixel PlanetScope satellite images and train a multilayer perceptron to estimate OP at a 1 km spatial resolution based on the image features and common meteorological variables. The model captures more than half of the variation in OP AA and almost half of the variation in OP DTT (test set R2 = 0.62 and 0.48, respectively), with relative mean absolute error (MAE) of about 32%. Using only satellite images, the model still captures about half of the variation in OP AA and one third of the variation in OP DTT (test set R2 = 0.49 and 0.36, respectively) with relative MAE of about 37%. If confirmed in other areas, our approach could represent a low-cost method for expanding the temporal or spatial coverage of OP estimates.

cs.CV↗

arXiv2024

The bandgap-detuned excitation regime in photonic-crystal resonators

Control of nonlinear interactions in microresonators enhances access to classical and quantum field states across nearly limitless bandwidth. A recent innovation has been to leverage coherent scattering of the intraresonator pump as a control of group-velocity dispersion and nonlinear frequency shifts, which are precursors for the dynamical evolution of new field states. A uniform periodicity nanostructure addresses backscattering with one resonator mode, and pumping that mode enables universal phase-matching for four-wave mixing with control by the bandgap. Yet, since nonlinear-resonator phenomena are intrinsically multimode and exhibit complex modelocking, here we demonstrate a new approach to controlling nonlinear interactions by creating bandgap modes completely separate from the pump laser. We explore this bandgap-detuned excitation regime through generation of benchmark optical parametric oscillators (OPOs) and soliton microcombs. Indeed, we show that mode-locked states are phase matched more effectively in the bandgap-detuned regime in which we directly control the modal Kerr shift with the bandgaps without perturbing the pump field. In particular, bandgap-detuned excitation enables an arbitrary control of backscattering as a versatile tool for mode-locked state engineering. Our experiments leverage nanophotonic resonators for phase matching of OPOs and solitons, leading to control over threshold power, conversion efficiency, and emission direction that enable application advances in high-capacity signaling and computing, signal generation, and quantum sensing.

physics.optics↗

arXiv2024

Augmenting Ground-Level PM2.5 Prediction via Kriging-Based Pseudo-Label Generation

Fusing abundant satellite data with sparse ground measurements constitutes a major challenge in climate modeling. To address this, we propose a strategy to augment the training dataset by introducing unlabeled satellite images paired with pseudo-labels generated through a spatial interpolation technique known as ordinary kriging, thereby making full use of the available satellite data resources. We show that the proposed data augmentation strategy helps enhance the performance of the state-of-the-art convolutional neural network-random forest (CNN-RF) model by a reasonable amount, resulting in a noteworthy improvement in spatial correlation and a reduction in prediction error.

cs.LG↗

arXiv2023

Annealing reduces Si$_3$N$_4$ microwave-frequency dielectric loss in superconducting resonators

The dielectric loss of silicon nitride (Si$_3$N$_4$) limits the performance of microwave-frequency devices that rely on this material for sensing, signal processing, and quantum communication. Using superconducting resonant circuits, we measure the cryogenic loss tangent of either as-deposited or high-temperature annealed stoichiometric Si$_3$N$_4$ as a function of drive strength and temperature. The internal loss behavior of the electrical resonators is largely consistent with the standard tunneling model of two-level systems (TLS), including damping caused by resonant energy exchange with TLS and by the relaxation of non-resonant TLS. We further supplement the TLS model with a self-heating effect to explain an increase in the loss observed in as-deposited films at large drive powers. Critically, we demonstrate that annealing remedies this anomalous power-induced loss, reduces the relaxation-type damping by more than two orders of magnitude, and reduces the resonant-type damping by a factor of three. Employing infrared absorption spectroscopy, we find that annealing reduces the concentration of hydrogen in the Si$_3$N$_4$, suggesting that hydrogen impurities cause substantial dissipation.

quant-ph↗

arXiv2023

Causal Mediation Analysis with Multi-dimensional and Indirectly Observed Mediators

Causal mediation analysis (CMA) is a powerful method to dissect the total effect of a treatment into direct and mediated effects within the potential outcome framework. This is important in many scientific applications to identify the underlying mechanisms of a treatment effect. However, in many scientific applications the mediator is unobserved, but there may exist related measurements. For example, we may want to identify how changes in brain activity or structure mediate an antidepressant's effect on behavior, but we may only have access to electrophysiological or imaging brain measurements. To date, most CMA methods assume that the mediator is one-dimensional and observable, which oversimplifies such real-world scenarios. To overcome this limitation, we introduce a CMA framework that can handle complex and indirectly observed mediators based on the identifiable variational autoencoder (iVAE) architecture. We prove that the true joint distribution over observed and latent variables is identifiable with the proposed method. Additionally, our framework captures a disentangled representation of the indirectly observed mediator and yields accurate estimation of the direct and mediated effects in synthetic and semi-synthetic experiments, providing evidence of its potential utility in real-world applications.

cs.LG↗

arXiv2023

Domain Adaptation via Rebalanced Sub-domain Alignment

Unsupervised domain adaptation (UDA) is a technique used to transfer knowledge from a labeled source domain to a different but related unlabeled target domain. While many UDA methods have shown success in the past, they often assume that the source and target domains must have identical class label distributions, which can limit their effectiveness in real-world scenarios. To address this limitation, we propose a novel generalization bound that reweights source classification error by aligning source and target sub-domains. We prove that our proposed generalization bound is at least as strong as existing bounds under realistic assumptions, and we empirically show that it is much stronger on real-world data. We then propose an algorithm to minimize this novel generalization bound. We demonstrate by numerical experiments that this approach improves performance in shifted class distribution scenarios compared to state-of-the-art methods.

cs.LG↗

arXiv2023

Estimating Causal Effects using a Multi-task Deep Ensemble

A number of methods have been proposed for causal effect estimation, yet few have demonstrated efficacy in handling data with complex structures, such as images. To fill this gap, we propose Causal Multi-task Deep Ensemble (CMDE), a novel framework that learns both shared and group-specific information from the study population. We provide proofs demonstrating equivalency of CDME to a multi-task Gaussian process (GP) with a coregionalization kernel a priori. Compared to multi-task GP, CMDE efficiently handles high-dimensional and multi-modal covariates and provides pointwise uncertainty estimates of causal effects. We evaluate our method across various types of datasets and tasks and find that CMDE outperforms state-of-the-art methods on a majority of these tasks.

cs.LG↗

arXiv2022

Universal visible emitters in nanoscale integrated photonics

Visible wavelengths of light control the quantum matter of atoms and molecules and are foundational for quantum technologies, including computers, sensors, and clocks. The development of visible integrated photonics opens the possibility for scalable circuits with complex functionalities, advancing both the scientific and technological frontiers. We experimentally demonstrate an inverse design approach based on superposition of guided-mode sources, allowing the generation and full control of free-space radiation directly from within a single 150 nm layer Ta2O5, showing low loss across visible and near-infrared spectra. We generate diverging circularly-polarized beams at the challenging 461 nm wavelength that can be directly used for magneto-optical traps of strontium atoms, constituting a fundamental building block for a range of atomic-physics-based quantum technologies. Our generated topological vortex beams and spatially-varying polarization emitters could open unexplored light-matter interaction pathways, enabling a broad new photonic-atomic paradigm. Our platform highlights the generalizability of nanoscale devices for visible-laser emission and will be critical for scaling quantum technologies.

physics.optics↗

arXiv2022

Incorporating Prior Knowledge into Neural Networks through an Implicit Composite Kernel

It is challenging to guide neural network (NN) learning with prior knowledge. In contrast, many known properties, such as spatial smoothness or seasonality, are straightforward to model by choosing an appropriate kernel in a Gaussian process (GP). Many deep learning applications could be enhanced by modeling such known properties. For example, convolutional neural networks (CNNs) are frequently used in remote sensing, which is subject to strong seasonal effects. We propose to blend the strengths of deep learning and the clear modeling capabilities of GPs by using a composite kernel that combines a kernel implicitly defined by a neural network with a second kernel function chosen to model known properties (e.g., seasonality). We implement this idea by combining a deep network and an efficient mapping based on the Nystrom approximation, which we call Implicit Composite Kernel (ICK). We then adopt a sample-then-optimize approach to approximate the full GP posterior distribution. We demonstrate that ICK has superior performance and flexibility on both synthetic and real-world data sets. We believe that ICK framework can be used to include prior information into neural networks in many applications.

cs.LG↗

arXiv2022

Multiple Domain Causal Networks

Observational studies are regarded as economic alternatives to randomized trials, often used in their stead to investigate and determine treatment efficacy. Due to lack of sample size, observational studies commonly combine data from multiple sources or different sites/centers. Despite the benefits of an increased sample size, a naive combination of multicenter data may result in incongruities stemming from center-specific protocols for generating cohorts or reactions towards treatments distinct to a given center, among other things. These issues arise in a variety of other contexts, including capturing a treatment effect related to an individual's unique biological characteristics. Existing methods for estimating heterogeneous treatment effects have not adequately addressed the multicenter context, but rather treat it simply as a means to obtain sufficient sample size. Additionally, previous approaches to estimating treatment effects do not straightforwardly generalize to the multicenter design, especially when required to provide treatment insights for patients from a new, unobserved center. To address these shortcomings, we propose Multiple Domain Causal Networks (MDCN), an approach that simultaneously strengthens the information sharing between similar centers while addressing the selection bias in treatment assignment through learning of a new feature embedding. In empirical evaluations, MDCN is consistently more accurate when estimating the heterogeneous treatment effect in new centers compared to benchmarks that adjust solely based on treatment imbalance or general center differences. Finally, we justify our approach by providing theoretical analyses that demonstrate that MDCN improves on the generalization bound of the new, unobserved target center.

stat.ML↗

arXiv2022

AugmentedPCA: A Python Package of Supervised and Adversarial Linear Factor Models

Deep autoencoders are often extended with a supervised or adversarial loss to learn latent representations with desirable properties, such as greater predictivity of labels and outcomes or fairness with respects to a sensitive variable. Despite the ubiquity of supervised and adversarial deep latent factor models, these methods should demonstrate improvement over simpler linear approaches to be preferred in practice. This necessitates a reproducible linear analog that still adheres to an augmenting supervised or adversarial objective. We address this methodological gap by presenting methods that augment the principal component analysis (PCA) objective with either a supervised or an adversarial objective and provide analytic and reproducible solutions. We implement these methods in an open-source Python package, AugmentedPCA, that can produce excellent real-world baselines. We demonstrate the utility of these factor models on an open-source, RNA-seq cancer gene expression dataset, showing that augmenting with a supervised objective results in improved downstream classification performance, produces principal components with greater class fidelity, and facilitates identification of genes aligned with the principal axes of data variance with implications to development of specific types of cancer.

stat.ML↗