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Patrick Emami

Publications and source records attributed to Patrick Emami.

At least 19 recordsLinked to original sources
arXiv2026

Position: AI Agents in Scientific Teams Should Be Studied as Human-Agent Systems

Large language model-based agents are increasingly deployed as collaborators in scientific discovery yet most current work focuses on the autonomous capabilities of "AI Scientists". We argue that this overlooks the social aspects of scientific teamwork, and that studying AI Scientists as human-agent systems (HAS)--where the unit of analysis is the human-agent pair--is both underexplored and undervalued. We establish these points through literature and empirical analysis, and highlight recent incidences and studies which show that deploying agents in science without accounting for human-agent dynamics introduces near-term risks, including reduced diversity of scientific inquiry. Through analysis of real-world case studies, we show that scientists and agents can augment each other's capabilities. We call for new research that adopts the HAS lens to develop mathematical frameworks for understanding and fostering human-AI synergy in scientific discovery.

cs.AI↗
arXiv2026

A Close Look At World Model Recovery In Supervised Fine-Tuned LLM Planners

Supervised fine-tuning (SFT) improves end-to-end classical planning in large language models (LLMs), but do these models also learn to represent and reason about the planning problems they are solving? Due to the relative complexity of classical planning problems and the challenge that end-to-end plan generation poses for LLMs, it has been difficult to explore this question. In our work, we devise and perform a series of interpretability experiments that holistically interrogate world model recovery by examining both internal representations and generative capabilities of fine-tuned LLMs. We find that: a) Supervised fine-tuning on valid action sequences enables LLMs to linearly encode action validity and some state predicates. b) Models that struggle to use output probabilities for classifying action validity may still learn internal representations that separate valid from invalid actions. c) Broader state space coverage during fine-tuning, such as from random walk data, yields more accurate recovery of the underlying world model. In summary, this work contributes a recipe for applying interpretability techniques to planning LLMs and generates insights that shed light on open questions about how knowledge is represented in LLMs.

cs.LG↗
arXiv2026

SCICONVBENCH: Benchmarking LLMs on Multi-Turn Clarification for Task Formulation in Computational Science

Large Language Models (LLMs) are increasingly deployed as scientific AI as- sistants, and a growing body of benchmarks evaluates their capabilities across knowledge retrieval, reasoning, code generation, and tool use. These evaluations, however, typically assume the scientific problem is already well-posed, whereas practical scientific assistance often begins with an ill-posed user request that must be refined through dialogue before any computation, analysis, or experiment can be carried out reliably. We introduce SCICONVBENCH, a benchmark for multi- turn clarification in scientific task formulation across four computational science problem domains: fluid mechanics, solid mechanics, materials science, and par- tial differential equations (PDEs). SCICONVBENCH targets two complementary capabilities: eliciting missing information (disambiguation) and detecting and correcting erroneous requests containing internally contradictory information (in- consistency resolution). Our benchmark pairs a structured task ontology with a rubric-based evaluation framework, enabling systematic measurement of LLM per- formance across three dimensions: clarification behavior, conversational grounding, and final-specification fidelity. Current frontier models perform relatively well on inconsistency resolution, but even the best model resolves only 52.7% of the disambiguation cases in fluid mechanics. We further find that frontier LLMs fre- quently make silent assumptions and perform implicit specification repairs that are not grounded in the conversation with users. SCICONVBENCH establishes a foundation for evaluating the upstream conversational reasoning that a reliable computational science assistant requires. The code and data can be found at https://github.com/csml-rpi/SciConvBench.

cs.AI↗
arXiv2026

Evaluating Memory Condensation Strategies for Coding Agents in Data-Driven Scientific Discovery

Coding agents accumulate extensive context during long-running tasks, yet fixed context windows force practitioners to choose between truncation and task failure. While numerous memory condensation strategies have been proposed, from simple sliding windows to LLM-generated summaries, no systematic comparison exists to guide strategy selection, especially in scientific discovery tasks. We evaluate eight memory condensation strategies using GPT-4o on sixty DiscoveryBench tasks spanning six scientific domains (480 total evaluations). We find that no condenser significantly alters hypothesis quality, while LLM-based condensers increase token costs by 24-94 percent, and masking tool-call outputs achieves an 8.6 percent net savings. We also observe that the optimal condenser for data-driven scientific discovery varies by scientific domain and task length.

cs.LG↗
arXiv2026

Born-Qualified: An Autonomous Framework for Deploying Advanced Energy and Electronic Materials

Autonomous science is transforming how we discover materials and chemical systems for advanced energy technologies. However, many initially promising systems never reach deployment. This "valley of death" stems from optimization that prioritizes laboratory metrics over industrial viability. We propose a new strategy: "born-qualified" autonomous development, which embeds manufacturability, cost, and durability constraints from the outset. This approach is enabled by four pillars, including the development of multi-objective metrics, causal models, a modular infrastructure, and embedding manufacturing in the discovery loop. Realizing this vision will require sustained, community-wide commitment, but the potential return on that investment is commensurate with the scale of the challenge.

cond-mat.mtrl-sci↗
arXiv2025

Conditional Distribution Estimation of Building Characteristics with Diffusion Models for Urban Energy Modeling

Understanding current energy consumption behavior in communities is critical for informing future energy use decisions and enabling efficient energy management. Urban energy models, which are used to simulate these energy use patterns, require large datasets with detailed building characteristics for accurate outcomes. However, such detailed characteristics at the individual building level are often unknown and costly to acquire, or unavailable. Through this work, we propose using a generative modeling approach to generate realistic building attributes to fill in the data gaps and finally provide complete characteristics as inputs to energy models. Our model learns complex, building-level patterns from training on a large-scale residential building stock model containing 2.2 million buildings. We employ a tabular diffusion-based framework that is designed to handle heterogeneous (discrete and continuous) features in tabular building data, such as occupancy, floor area, heating, cooling, and other equipment details. We develop a capability for conditional diffusion, enabling the imputation of missing building characteristics conditioned on known attributes. We conduct a comprehensive validation of our conditional diffusion model, firstly by comparing the generated conditional distributions against the underlying data distribution, and secondly, by performing a case study for a Baltimore residential region, showing the practical utility of our approach. Our work is one of the first to demonstrate the potential of generative modeling to accelerate building energy modeling workflows.

cs.CE↗
arXiv2025

CFDLLMBench: A Benchmark Suite for Evaluating Large Language Models in Computational Fluid Dynamics

Large Language Models (LLMs) have demonstrated strong performance across general NLP tasks, but their utility in automating numerical experiments of complex physical system -- a critical and labor-intensive component -- remains underexplored. As the major workhorse of computational science over the past decades, Computational Fluid Dynamics (CFD) offers a uniquely challenging testbed for evaluating the scientific capabilities of LLMs. We introduce CFDLLMBench, a benchmark suite comprising three complementary components -- CFDQuery, CFDCodeBench, and FoamBench -- designed to holistically evaluate LLM performance across three key competencies: graduate-level CFD knowledge, numerical and physical reasoning of CFD, and context-dependent implementation of CFD workflows. Grounded in real-world CFD practices, our benchmark combines a detailed task taxonomy with a rigorous evaluation framework to deliver reproducible results and quantify LLM performance across code executability, solution accuracy, and numerical convergence behavior. CFDLLMBench establishes a solid foundation for the development and evaluation of LLM-driven automation of numerical experiments for complex physical systems. Code and data are available at https://github.com/NREL-Theseus/cfdllmbench/.

cs.CL↗
arXiv2024

On the Effectiveness of Neural Operators at Zero-Shot Weather Downscaling

Machine learning (ML) methods have shown great potential for weather downscaling. These data-driven approaches provide a more efficient alternative for producing high-resolution weather datasets and forecasts compared to physics-based numerical simulations. Neural operators, which learn solution operators for a family of partial differential equations (PDEs), have shown great success in scientific ML applications involving physics-driven datasets. Neural operators are grid-resolution-invariant and are often evaluated on higher grid resolutions than they are trained on, i.e., zero-shot super-resolution. Given their promising zero-shot super-resolution performance on dynamical systems emulation, we present a critical investigation of their zero-shot weather downscaling capabilities, which is when models are tasked with producing high-resolution outputs using higher upsampling factors than are seen during training. To this end, we create two realistic downscaling experiments with challenging upsampling factors (e.g., 8x and 15x) across data from different simulations: the European Centre for Medium-Range Weather Forecasts Reanalysis version 5 (ERA5) and the Wind Integration National Dataset Toolkit (WTK). While neural operator-based downscaling models perform better than interpolation and a simple convolutional baseline, we show the surprising performance of an approach that combines a powerful transformer-based model with parameter-free interpolation at zero-shot weather downscaling. We find that this Swin-Transformer-based approach mostly outperforms models with neural operator layers in terms of average error metrics, whereas an Enhanced Super-Resolution Generative Adversarial Network (ESRGAN)-based approach is better than most models in terms of capturing the physics of the ground truth data. We suggest their use in future work as strong baselines.

cs.CE↗
arXiv2024

SysCaps: Language Interfaces for Simulation Surrogates of Complex Systems

Surrogate models are used to predict the behavior of complex energy systems that are too expensive to simulate with traditional numerical methods. Our work introduces the use of language descriptions, which we call ``system captions'' or SysCaps, to interface with such surrogates. We argue that interacting with surrogates through text, particularly natural language, makes these models more accessible for both experts and non-experts. We introduce a lightweight multimodal text and timeseries regression model and a training pipeline that uses large language models (LLMs) to synthesize high-quality captions from simulation metadata. Our experiments on two real-world simulators of buildings and wind farms show that our SysCaps-augmented surrogates have better accuracy on held-out systems than traditional methods while enjoying new generalization abilities, such as handling semantically related descriptions of the same test system. Additional experiments also highlight the potential of SysCaps to unlock language-driven design space exploration and to regularize training through prompt augmentation.

cs.LG↗
arXiv2024

Three Pathways to Neurosymbolic Reinforcement Learning with Interpretable Model and Policy Networks

Neurosymbolic AI combines the interpretability, parsimony, and explicit reasoning of classical symbolic approaches with the statistical learning of data-driven neural approaches. Models and policies that are simultaneously differentiable and interpretable may be key enablers of this marriage. This paper demonstrates three pathways to implementing such models and policies in a real-world reinforcement learning setting. Specifically, we study a broad class of neural networks that build interpretable semantics directly into their architecture. We reveal and highlight both the potential and the essential difficulties of combining logic, simulation, and learning. One lesson is that learning benefits from continuity and differentiability, but classical logic is discrete and non-differentiable. The relaxation to real-valued, differentiable representations presents a trade-off; the more learnable, the less interpretable. Another lesson is that using logic in the context of a numerical simulation involves a non-trivial mapping from raw (e.g., real-valued time series) simulation data to logical predicates. Some open questions this note exposes include: What are the limits of rule-based controllers, and how learnable are they? Do the differentiable interpretable approaches discussed here scale to large, complex, uncertain systems? Can we truly achieve interpretability? We highlight these and other themes across the three approaches.

cs.AI↗
arXiv2023

Non-Stationary Policy Learning for Multi-Timescale Multi-Agent Reinforcement Learning

In multi-timescale multi-agent reinforcement learning (MARL), agents interact across different timescales. In general, policies for time-dependent behaviors, such as those induced by multiple timescales, are non-stationary. Learning non-stationary policies is challenging and typically requires sophisticated or inefficient algorithms. Motivated by the prevalence of this control problem in real-world complex systems, we introduce a simple framework for learning non-stationary policies for multi-timescale MARL. Our approach uses available information about agent timescales to define a periodic time encoding. In detail, we theoretically demonstrate that the effects of non-stationarity introduced by multiple timescales can be learned by a periodic multi-agent policy. To learn such policies, we propose a policy gradient algorithm that parameterizes the actor and critic with phase-functioned neural networks, which provide an inductive bias for periodicity. The framework's ability to effectively learn multi-timescale policies is validated on a gridworld and building energy management environment.

cs.LG↗
arXiv2023

BuildingsBench: A Large-Scale Dataset of 900K Buildings and Benchmark for Short-Term Load Forecasting

Short-term forecasting of residential and commercial building energy consumption is widely used in power systems and continues to grow in importance. Data-driven short-term load forecasting (STLF), although promising, has suffered from a lack of open, large-scale datasets with high building diversity. This has hindered exploring the pretrain-then-fine-tune paradigm for STLF. To help address this, we present BuildingsBench, which consists of: 1) Buildings-900K, a large-scale dataset of 900K simulated buildings representing the U.S. building stock; and 2) an evaluation platform with over 1,900 real residential and commercial buildings from 7 open datasets. BuildingsBench benchmarks two under-explored tasks: zero-shot STLF, where a pretrained model is evaluated on unseen buildings without fine-tuning, and transfer learning, where a pretrained model is fine-tuned on a target building. The main finding of our benchmark analysis is that synthetically pretrained models generalize surprisingly well to real commercial buildings. An exploration of the effect of increasing dataset size and diversity on zero-shot commercial building performance reveals a power-law with diminishing returns. We also show that fine-tuning pretrained models on real commercial and residential buildings improves performance for a majority of target buildings. We hope that BuildingsBench encourages and facilitates future research on generalizable STLF. All datasets and code can be accessed from https://github.com/NREL/BuildingsBench.

cs.LG↗
arXiv2022

Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC

A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast MCMC sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

cs.LG↗
arXiv2022

Learning Canonical Embeddings for Unsupervised Shape Correspondence with Locally Linear Transformations

We present a new approach to unsupervised shape correspondence learning between pairs of point clouds. We make the first attempt to adapt the classical locally linear embedding algorithm (LLE) -- originally designed for nonlinear dimensionality reduction -- for shape correspondence. The key idea is to find dense correspondences between shapes by first obtaining high-dimensional neighborhood-preserving embeddings of low-dimensional point clouds and subsequently aligning the source and target embeddings using locally linear transformations. We demonstrate that learning the embedding using a new LLE-inspired point cloud reconstruction objective results in accurate shape correspondences. More specifically, the approach comprises an end-to-end learnable framework of extracting high-dimensional neighborhood-preserving embeddings, estimating locally linear transformations in the embedding space, and reconstructing shapes via divergence measure-based alignment of probabilistic density functions built over reconstructed and target shapes. Our approach enforces embeddings of shapes in correspondence to lie in the same universal/canonical embedding space, which eventually helps regularize the learning process and leads to a simple nearest neighbors approach between shape embeddings for finding reliable correspondences. Comprehensive experiments show that the new method makes noticeable improvements over state-of-the-art approaches on standard shape correspondence benchmark datasets covering both human and nonhuman shapes.

cs.CV↗
arXiv2022

Towards Improving the Generation Quality of Autoregressive Slot VAEs

Unconditional scene inference and generation are challenging to learn jointly with a single compositional model. Despite encouraging progress on models that extract object-centric representations (''slots'') from images, unconditional generation of scenes from slots has received less attention. This is primarily because learning the multi-object relations necessary to imagine coherent scenes is difficult. We hypothesize that most existing slot-based models have a limited ability to learn object correlations. We propose two improvements that strengthen object correlation learning. The first is to condition the slots on a global, scene-level variable that captures higher-order correlations between slots. Second, we address the fundamental lack of a canonical order for objects in images by proposing to learn a consistent order to use for the autoregressive generation of scene objects. Specifically, we train an autoregressive slot prior to sequentially generate scene objects following a learned order. Ordered slot inference entails first estimating a randomly ordered set of slots using existing approaches for extracting slots from images, then aligning those slots to ordered slots generated autoregressively with the slot prior. Our experiments across three multi-object environments demonstrate clear gains in unconditional scene generation quality. Detailed ablation studies are also provided that validate the two proposed improvements.

cs.CV↗
arXiv2022

Self-Supervised Robust Scene Flow Estimation via the Alignment of Probability Density Functions

In this paper, we present a new self-supervised scene flow estimation approach for a pair of consecutive point clouds. The key idea of our approach is to represent discrete point clouds as continuous probability density functions using Gaussian mixture models. Scene flow estimation is therefore converted into the problem of recovering motion from the alignment of probability density functions, which we achieve using a closed-form expression of the classic Cauchy-Schwarz divergence. Unlike existing nearest-neighbor-based approaches that use hard pairwise correspondences, our proposed approach establishes soft and implicit point correspondences between point clouds and generates more robust and accurate scene flow in the presence of missing correspondences and outliers. Comprehensive experiments show that our method makes noticeable gains over the Chamfer Distance and the Earth Mover's Distance in real-world environments and achieves state-of-the-art performance among self-supervised learning methods on FlyingThings3D and KITTI, even outperforming some supervised methods with ground truth annotations.

cs.CV↗
arXiv2021

Learning Scene Dynamics from Point Cloud Sequences

Understanding 3D scenes is a critical prerequisite for autonomous agents. Recently, LiDAR and other sensors have made large amounts of data available in the form of temporal sequences of point cloud frames. In this work, we propose a novel problem -- sequential scene flow estimation (SSFE) -- that aims to predict 3D scene flow for all pairs of point clouds in a given sequence. This is unlike the previously studied problem of scene flow estimation which focuses on two frames. We introduce the SPCM-Net architecture, which solves this problem by computing multi-scale spatiotemporal correlations between neighboring point clouds and then aggregating the correlation across time with an order-invariant recurrent unit. Our experimental evaluation confirms that recurrent processing of point cloud sequences results in significantly better SSFE compared to using only two frames. Additionally, we demonstrate that this approach can be effectively modified for sequential point cloud forecasting (SPF), a related problem that demands forecasting future point cloud frames. Our experimental results are evaluated using a new benchmark for both SSFE and SPF consisting of synthetic and real datasets. Previously, datasets for scene flow estimation have been limited to two frames. We provide non-trivial extensions to these datasets for multi-frame estimation and prediction. Due to the difficulty of obtaining ground truth motion for real-world datasets, we use self-supervised training and evaluation metrics. We believe that this benchmark will be pivotal to future research in this area. All code for benchmark and models will be made accessible.

cs.CV↗
arXiv2021

Efficient Iterative Amortized Inference for Learning Symmetric and Disentangled Multi-Object Representations

Unsupervised multi-object representation learning depends on inductive biases to guide the discovery of object-centric representations that generalize. However, we observe that methods for learning these representations are either impractical due to long training times and large memory consumption or forego key inductive biases. In this work, we introduce EfficientMORL, an efficient framework for the unsupervised learning of object-centric representations. We show that optimization challenges caused by requiring both symmetry and disentanglement can in fact be addressed by high-cost iterative amortized inference by designing the framework to minimize its dependence on it. We take a two-stage approach to inference: first, a hierarchical variational autoencoder extracts symmetric and disentangled representations through bottom-up inference, and second, a lightweight network refines the representations with top-down feedback. The number of refinement steps taken during training is reduced following a curriculum, so that at test time with zero steps the model achieves 99.1% of the refined decomposition performance. We demonstrate strong object decomposition and disentanglement on the standard multi-object benchmark while achieving nearly an order of magnitude faster training and test time inference over the previous state-of-the-art model.

cs.CV↗