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Apr 13

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 million DFT calculations on molecules and geometries. This dataset covers the most common elements in bio- and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) as well as charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformers benchmark set, OrbNet Denali has a median correlation coefficient of R^2=0.90 compared to the reference DLPNO-CCSD(T) calculation, and R^2=0.97 compared to the method used to generate the training data (wB97X-D3/def2-TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for non-covalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of wB97X-D3/def2-TZVP with an average MAE of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

  • 11 authors
·
Jul 1, 2021

Accurate and scalable exchange-correlation with deep learning

Density Functional Theory (DFT) is the most widely used electronic structure method for predicting the properties of molecules and materials. Although DFT is, in principle, an exact reformulation of the Schr\"odinger equation, practical applications rely on approximations to the unknown exchange-correlation (XC) functional. Most existing XC functionals are constructed using a limited set of increasingly complex, hand-crafted features that improve accuracy at the expense of computational efficiency. Yet, no current approximation achieves the accuracy and generality for predictive modeling of laboratory experiments at chemical accuracy -- typically defined as errors below 1 kcal/mol. In this work, we present Skala, a modern deep learning-based XC functional that bypasses expensive hand-designed features by learning representations directly from data. Skala achieves chemical accuracy for atomization energies of small molecules while retaining the computational efficiency typical of semi-local DFT. This performance is enabled by training on an unprecedented volume of high-accuracy reference data generated using computationally intensive wavefunction-based methods. Notably, Skala systematically improves with additional training data covering diverse chemistry. By incorporating a modest amount of additional high-accuracy data tailored to chemistry beyond atomization energies, Skala achieves accuracy competitive with the best-performing hybrid functionals across general main group chemistry, at the cost of semi-local DFT. As the training dataset continues to expand, Skala is poised to further enhance the predictive power of first-principles simulations.

microsoft Microsoft
·
Jun 17, 2025

Canonical and DLPNO-based G4(MP2)XK-inspired composite wavefunction methods parametrized against large and chemically diverse training sets: Are they more accurate and/or robust than double hybrid DFT?

The large and chemically diverse GMTKN55 benchmark was used as a training set for parametrizing composite wave function thermochemistry protocols akin to G4(MP2)XK theory (Chan et al, JCTC 2019, 15, 4478-4484). Even after reparametrization, the GMTKN55 WTMAD2 (weighted mean absolute deviation, type 2) for G4(MP2)-XK is actually inferior to that of the best rung-4 DFT functional, wB97M-V. By increasing the basis set for the MP2 part to def2-QZVPPD, we were able to substantially improve performance at modest cost (if an RI-MP2 approximation is made), with WTMAD2 for this G4(MP2)-XK-D method now comparable to the better rung-5 functionals (albeit at greater cost). A three-tier approach with a scaled MP3/def2-TZVPP intermediate step, however, leads to a G4(MP3)-D method that is markedly superior to even the best double hybrids wB97M(2) and revDSD-PBEP86-D4. Evaluating the CCSD(T) component with a triple-zeta, rather than split-valence, basis set yields only a modest further improvement that is incommensurate with the drastic increase in computational cost. G4(MP3)-D and G4(MP2)- XK-D have about 40% better WTMAD2, at similar or lower computational cost, than their counterparts G4 and G4(MP2), respectively: detailed comparison reveals that the difference lies in larger molecules due to basis set incompleteness error. An E2/ {T,Q} extrapolation and a CCSD(T)/def2-TZVP step provided the G4-T method of high accuracy and with just three fitted parameters. Using KS orbitals in MP2 leads to the G4(MP3|KS)-D method, which entirely eliminates the CCSD(T) step and has no steps costlier than scaled MP3; this shows a path forward to further improvements in double-hybrid density functional methods. G4-T-DLPNO, a variant in which post-MP2 corrections are evaluated at the DLPNO- CCSD(T) level, achieves nearly the accuracy of G4-T but is applicable to much larger systems.

  • 2 authors
·
Jun 8, 2020

Neuro-inspired Ensemble-to-Ensemble Communication Primitives for Sparse and Efficient ANNs

The structure of biological neural circuits-modular, hierarchical, and sparsely interconnected-reflects an efficient trade-off between wiring cost, functional specialization, and robustness. These principles offer valuable insights for artificial neural network (ANN) design, especially as networks grow in depth and scale. Sparsity, in particular, has been widely explored for reducing memory and computation, improving speed, and enhancing generalization. Motivated by systems neuroscience findings, we explore how patterns of functional connectivity in the mouse visual cortex-specifically, ensemble-to-ensemble communication, can inform ANN design. We introduce G2GNet, a novel architecture that imposes sparse, modular connectivity across feedforward layers. Despite having significantly fewer parameters than fully connected models, G2GNet achieves superior accuracy on standard vision benchmarks. To our knowledge, this is the first architecture to incorporate biologically observed functional connectivity patterns as a structural bias in ANN design. We complement this static bias with a dynamic sparse training (DST) mechanism that prunes and regrows edges during training. We also propose a Hebbian-inspired rewiring rule based on activation correlations, drawing on principles of biological plasticity. G2GNet achieves up to 75% sparsity while improving accuracy by up to 4.3% on benchmarks, including Fashion-MNIST, CIFAR-10, and CIFAR-100, outperforming dense baselines with far fewer computations.

  • 3 authors
·
Aug 19, 2025

Neural Tangent Kernel: Convergence and Generalization in Neural Networks

At initialization, artificial neural networks (ANNs) are equivalent to Gaussian processes in the infinite-width limit, thus connecting them to kernel methods. We prove that the evolution of an ANN during training can also be described by a kernel: during gradient descent on the parameters of an ANN, the network function f_theta (which maps input vectors to output vectors) follows the kernel gradient of the functional cost (which is convex, in contrast to the parameter cost) w.r.t. a new kernel: the Neural Tangent Kernel (NTK). This kernel is central to describe the generalization features of ANNs. While the NTK is random at initialization and varies during training, in the infinite-width limit it converges to an explicit limiting kernel and it stays constant during training. This makes it possible to study the training of ANNs in function space instead of parameter space. Convergence of the training can then be related to the positive-definiteness of the limiting NTK. We prove the positive-definiteness of the limiting NTK when the data is supported on the sphere and the non-linearity is non-polynomial. We then focus on the setting of least-squares regression and show that in the infinite-width limit, the network function f_theta follows a linear differential equation during training. The convergence is fastest along the largest kernel principal components of the input data with respect to the NTK, hence suggesting a theoretical motivation for early stopping. Finally we study the NTK numerically, observe its behavior for wide networks, and compare it to the infinite-width limit.

  • 3 authors
·
Jun 20, 2018

Functional Bayesian Tucker Decomposition for Continuous-indexed Tensor Data

Tucker decomposition is a powerful tensor model to handle multi-aspect data. It demonstrates the low-rank property by decomposing the grid-structured data as interactions between a core tensor and a set of object representations (factors). A fundamental assumption of such decomposition is that there are finite objects in each aspect or mode, corresponding to discrete indexes of data entries. However, real-world data is often not naturally posed in this setting. For example, geographic data is represented as continuous indexes of latitude and longitude coordinates, and cannot fit tensor models directly. To generalize Tucker decomposition to such scenarios, we propose Functional Bayesian Tucker Decomposition (FunBaT). We treat the continuous-indexed data as the interaction between the Tucker core and a group of latent functions. We use Gaussian processes (GP) as functional priors to model the latent functions. Then, we convert each GP into a state-space prior by constructing an equivalent stochastic differential equation (SDE) to reduce computational cost. An efficient inference algorithm is developed for scalable posterior approximation based on advanced message-passing techniques. The advantage of our method is shown in both synthetic data and several real-world applications. We release the code of FunBaT at https://github.com/xuangu-fang/Functional-Bayesian-Tucker-Decomposition.

  • 6 authors
·
Nov 8, 2023

DiffuMatch: Category-Agnostic Spectral Diffusion Priors for Robust Non-rigid Shape Matching

Deep functional maps have recently emerged as a powerful tool for solving non-rigid shape correspondence tasks. Methods that use this approach combine the power and flexibility of the functional map framework, with data-driven learning for improved accuracy and generality. However, most existing methods in this area restrict the learning aspect only to the feature functions and still rely on axiomatic modeling for formulating the training loss or for functional map regularization inside the networks. This limits both the accuracy and the applicability of the resulting approaches only to scenarios where assumptions of the axiomatic models hold. In this work, we show, for the first time, that both in-network regularization and functional map training can be replaced with data-driven methods. For this, we first train a generative model of functional maps in the spectral domain using score-based generative modeling, built from a large collection of high-quality maps. We then exploit the resulting model to promote the structural properties of ground truth functional maps on new shape collections. Remarkably, we demonstrate that the learned models are category-agnostic, and can fully replace commonly used strategies such as enforcing Laplacian commutativity or orthogonality of functional maps. Our key technical contribution is a novel distillation strategy from diffusion models in the spectral domain. Experiments demonstrate that our learned regularization leads to better results than axiomatic approaches for zero-shot non-rigid shape matching. Our code is available at: https://github.com/daidedou/diffumatch/

  • 4 authors
·
Jul 31, 2025

Cost-of-Pass: An Economic Framework for Evaluating Language Models

The widespread adoption of AI systems in the economy hinges on their ability to generate economic value that outweighs their inference costs. Evaluating this tradeoff requires metrics that account for both performance and costs. We propose a framework grounded in production theory for evaluating language models by combining accuracy and inference cost. We introduce "cost-of-pass", the expected monetary cost of generating a correct solution. We then define the "frontier cost-of-pass" as the minimum cost-of-pass achievable across available models or the "human-expert, using the approximate cost of hiring an expert. Our analysis reveals distinct economic insights. First, lightweight models are most cost-effective for basic quantitative tasks, large models for knowledge-intensive ones, and reasoning models for complex quantitative problems, despite higher per-token costs. Second, tracking this frontier cost-of-pass over the past year reveals significant progress, particularly for complex quantitative tasks where the cost has roughly halved every few months. Third, to trace key innovations driving this progress, we examine counterfactual frontiers: estimates of cost-efficiency without specific model classes. We find that innovations in lightweight, large, and reasoning models have been essential for pushing the frontier in basic quantitative, knowledge-intensive, and complex quantitative tasks, respectively. Finally, we assess the cost-reductions afforded by common inference-time techniques like majority voting and self-refinement, finding that their marginal accuracy gains rarely justify their costs. Our findings underscore that complementary model-level innovations are the primary drivers of cost-efficiency, and our economic framework provides a principled tool for measuring this progress and guiding deployment.

  • 5 authors
·
Apr 17, 2025 2

CostNav: A Navigation Benchmark for Real-World Economic-Cost Evaluation of Physical AI Agents

While current navigation benchmarks prioritize task success in simplified settings, they neglect the multidimensional economic constraints essential for the real-world commercialization of autonomous delivery systems. We introduce CostNav, an Economic Navigation Benchmark that evaluates physical AI agents through comprehensive economic cost-revenue analysis aligned with real-world business operations. By integrating industry-standard data - such as SEC filings and AIS injury reports - with Isaac Sim's detailed collision and cargo dynamics, CostNav transcends simple task completion to accurately evaluate business value in complex, real-world scenarios. To our knowledge, CostNav is the first work to quantitatively expose the gap between navigation research metrics and commercial viability, revealing that optimizing for task success on a simplified task fundamentally differs from optimizing for real-world economic deployment. Our evaluation of rule-based Nav2 navigation shows that current approaches are not economically viable: the contribution margin is -22.81/run (AMCL) and -12.87/run (GPS), resulting in no break-even point. We challenge the community to develop navigation policies that achieve economic viability on CostNav. We remain method-agnostic, evaluating success solely on the metric of cost rather than the underlying architecture. All resources are available at https://github.com/worv-ai/CostNav.

  • 24 authors
·
Nov 25, 2025

The Price Reversal Phenomenon: When Cheaper Reasoning Models End Up Costing More

Developers and consumers increasingly choose reasoning language models (RLMs) based on their listed API prices. However, how accurately do these prices reflect actual inference costs? We conduct the first systematic study of this question, evaluating 8 frontier RLMs across 9 diverse tasks covering competition math, science QA, code generation, and multi-domain reasoning. We uncover the pricing reversal phenomenon: in 21.8% of model-pair comparisons, the model with a lower listed price actually incurs a higher total cost, with reversal magnitude reaching up to 28x. For example, Gemini 3 Flash's listed price is 78% cheaper than GPT-5.2's, yet its actual cost across all tasks is 22% higher. We trace the root cause to vast heterogeneity in thinking token consumption: on the same query, one model may use 900% more thinking tokens than another. In fact, removing thinking token costs reduces ranking reversals by 70% and raises the rank correlation (Kendall's τ ) between price and cost rankings from 0.563 to 0.873. We further show that per-query cost prediction is fundamentally difficult: repeated runs of the same query yield thinking token variation up to 9.7x, establishing an irreducible noise floor for any predictor. Our findings demonstrate that listed API pricing is an unreliable proxy for actual cost, calling for cost-aware model selection and transparent per-request cost monitoring.

  • 6 authors
·
Mar 24

Target-based Surrogates for Stochastic Optimization

We consider minimizing functions for which it is expensive to compute the (possibly stochastic) gradient. Such functions are prevalent in reinforcement learning, imitation learning and adversarial training. Our target optimization framework uses the (expensive) gradient computation to construct surrogate functions in a target space (e.g. the logits output by a linear model for classification) that can be minimized efficiently. This allows for multiple parameter updates to the model, amortizing the cost of gradient computation. In the full-batch setting, we prove that our surrogate is a global upper-bound on the loss, and can be (locally) minimized using a black-box optimization algorithm. We prove that the resulting majorization-minimization algorithm ensures convergence to a stationary point of the loss. Next, we instantiate our framework in the stochastic setting and propose the SSO algorithm, which can be viewed as projected stochastic gradient descent in the target space. This connection enables us to prove theoretical guarantees for SSO when minimizing convex functions. Our framework allows the use of standard stochastic optimization algorithms to construct surrogates which can be minimized by any deterministic optimization method. To evaluate our framework, we consider a suite of supervised learning and imitation learning problems. Our experiments indicate the benefits of target optimization and the effectiveness of SSO.

  • 5 authors
·
Feb 6, 2023

SimulCost: A Cost-Aware Benchmark and Toolkit for Automating Physics Simulations with LLMs

Evaluating LLM agents for scientific tasks has focused on token costs while ignoring tool-use costs like simulation time and experimental resources. As a result, metrics like pass@k become impractical under realistic budget constraints. To address this gap, we introduce SimulCost, the first benchmark targeting cost-sensitive parameter tuning in physics simulations. SimulCost compares LLM tuning cost-sensitive parameters against traditional scanning approach in both accuracy and computational cost, spanning 2,916 single-round (initial guess) and 1,900 multi-round (adjustment by trial-and-error) tasks across 12 simulators from fluid dynamics, solid mechanics, and plasma physics. Each simulator's cost is analytically defined and platform-independent. Frontier LLMs achieve 46--64% success rates in single-round mode, dropping to 35--54% under high accuracy requirements, rendering their initial guesses unreliable especially for high accuracy tasks. Multi-round mode improves rates to 71--80%, but LLMs are 1.5--2.5x slower than traditional scanning, making them uneconomical choices. We also investigate parameter group correlations for knowledge transfer potential, and the impact of in-context examples and reasoning effort, providing practical implications for deployment and fine-tuning. We open-source SimulCost as a static benchmark and extensible toolkit to facilitate research on improving cost-aware agentic designs for physics simulations, and for expanding new simulation environments. Code and data are available at https://github.com/Rose-STL-Lab/SimulCost-Bench.

  • 15 authors
·
Mar 11

Towards Automated Formal Verification of Backend Systems with LLMs

Software testing plays a critical role in ensuring that systems behave as intended. However, existing automated testing approaches struggle to match the capabilities of human engineers due to key limitations such as test locality, lack of general reliability, and business logic blindness. In this work, we propose a novel framework that leverages functional programming and type systems to translate Scala backend code into formal Lean representations. Our pipeline automatically generates theorems that specify the intended behavior of APIs and database operations, and uses LLM-based provers to verify them. When a theorem is proved, the corresponding logic is guaranteed to be correct and no further testing is needed. If the negation of a theorem is proved instead, it confirms a bug. In cases where neither can be proved, human intervention is required. We evaluate our method on realistic backend systems and find that it can formally verify over 50% of the test requirements, which suggests that half of a testing engineer's workload can be automated. Additionally, with an average cost of only $2.19 per API, LLM-based verification is significantly more cost-effective than manual testing and can be scaled easily through parallel execution. Our results indicate a promising direction for scalable, AI-powered software testing, with the potential to greatly improve engineering productivity as models continue to advance.

  • 4 authors
·
Apr 13, 2025

M-FAC: Efficient Matrix-Free Approximations of Second-Order Information

Efficiently approximating local curvature information of the loss function is a key tool for optimization and compression of deep neural networks. Yet, most existing methods to approximate second-order information have high computational or storage costs, which can limit their practicality. In this work, we investigate matrix-free, linear-time approaches for estimating Inverse-Hessian Vector Products (IHVPs) for the case when the Hessian can be approximated as a sum of rank-one matrices, as in the classic approximation of the Hessian by the empirical Fisher matrix. We propose two new algorithms as part of a framework called M-FAC: the first algorithm is tailored towards network compression and can compute the IHVP for dimension d, if the Hessian is given as a sum of m rank-one matrices, using O(dm^2) precomputation, O(dm) cost for computing the IHVP, and query cost O(m) for any single element of the inverse Hessian. The second algorithm targets an optimization setting, where we wish to compute the product between the inverse Hessian, estimated over a sliding window of optimization steps, and a given gradient direction, as required for preconditioned SGD. We give an algorithm with cost O(dm + m^2) for computing the IHVP and O(dm + m^3) for adding or removing any gradient from the sliding window. These two algorithms yield state-of-the-art results for network pruning and optimization with lower computational overhead relative to existing second-order methods. Implementations are available at [9] and [17].

  • 3 authors
·
Jul 7, 2021

MAP: Low-compute Model Merging with Amortized Pareto Fronts via Quadratic Approximation

Model merging has emerged as an effective approach to combine multiple single-task models into a multitask model. This process typically involves computing a weighted average of the model parameters without any additional training. Existing model-merging methods focus on enhancing average task accuracy. However, interference and conflicts between the objectives of different tasks can lead to trade-offs during the merging process. In real-world applications, a set of solutions with various trade-offs can be more informative, helping practitioners make decisions based on diverse preferences. In this paper, we introduce a novel and low-compute algorithm, Model Merging with Amortized Pareto Front (MAP). MAP efficiently identifies a Pareto set of scaling coefficients for merging multiple models, reflecting the trade-offs involved. It amortizes the substantial computational cost of evaluations needed to estimate the Pareto front by using quadratic approximation surrogate models derived from a pre-selected set of scaling coefficients. Experimental results on vision and natural language processing tasks demonstrate that MAP can accurately identify the Pareto front, providing practitioners with flexible solutions to balance competing task objectives. We also introduce Bayesian MAP for scenarios with a relatively low number of tasks and Nested MAP for situations with a high number of tasks, further reducing the computational cost of evaluation.

  • 10 authors
·
Jun 11, 2024

Divide-and-Conquer Meets Consensus: Unleashing the Power of Functions in Code Generation

Despite recent progress made by large language models in code generation, they still struggle with programs that meet complex requirements. Recent work utilizes plan-and-solve decomposition to decrease the complexity and leverage self-tests to refine the generated program. Yet, planning deep-inside requirements in advance can be challenging, and the tests need to be accurate to accomplish self-improvement. To this end, we propose FunCoder, a code generation framework incorporating the divide-and-conquer strategy with functional consensus. Specifically, FunCoder recursively branches off sub-functions as smaller goals during code generation, represented by a tree hierarchy. These sub-functions are then composited to attain more complex objectives. Additionally, we designate functions via a consensus formed by identifying similarities in program behavior, mitigating error propagation. FunCoder outperforms state-of-the-art methods by +9.8% on average in HumanEval, MBPP, xCodeEval and MATH with GPT-3.5 and GPT-4. Moreover, our method demonstrates superiority on smaller models: With FunCoder, StableCode-3b surpasses GPT-3.5 by +18.6% and achieves 97.7% of GPT-4's performance on HumanEval. Further analysis reveals that our proposed dynamic function decomposition is capable of handling complex requirements, and the functional consensus prevails over self-testing in correctness evaluation.

  • 7 authors
·
May 30, 2024

Cheaply Evaluating Inference Efficiency Metrics for Autoregressive Transformer APIs

Large language models (LLMs) power many state-of-the-art systems in natural language processing. However, these models are extremely computationally expensive, even at inference time, raising the natural question: when is the extra cost of deploying a larger model worth the anticipated boost in capabilities? Better understanding this tradeoff fundamentally could benefit from an inference efficiency metric that is both (i) easily comparable across models from different providers, and (ii) representative of the true cost of running queries in an isolated performance environment. Unfortunately, access to LLMs today is largely restricted to black-box text generation APIs and raw runtimes measured through this interface do not satisfy these desiderata: model providers can apply various software and hardware optimizations orthogonal to the model, and models served on shared infrastructure are susceptible to performance contention. To circumvent these problems, we propose a new metric for comparing inference efficiency across models. This metric puts models on equal footing as though they were served (i) on uniform hardware and software, and (ii) without performance contention. We call this metric the idealized runtime, and we propose a methodology to efficiently estimate this metric for autoregressive Transformer models. We also propose cost-aware variants that incorporate the number of accelerators needed to serve the model. Using these metrics, we compare ten state-of-the-art LLMs to provide the first analysis of inference efficiency-capability tradeoffs; we make several observations from this analysis, including the fact that the superior inference runtime performance of certain APIs is often a byproduct of optimizations within the API rather than the underlying model. Our methodology also facilitates the efficient comparison of different software and hardware stacks.

  • 6 authors
·
May 3, 2023

Doing More with Less -- Implementing Routing Strategies in Large Language Model-Based Systems: An Extended Survey

Large Language Models (LLM)-based systems, i.e. interconnected elements that include an LLM as a central component (e.g., conversational agents), are typically monolithic static architectures that rely on a single LLM for all user queries. However, they often require different preprocessing strategies, levels of reasoning, or knowledge. Generalist LLMs (i.e. GPT-4), trained on very large multi-topic corpora, can perform well in a variety of tasks. However, they require significant financial, energy, and hardware resources that may not be justified for basic tasks. This implies potentially investing in unnecessary costs for a given query. To overcome this problem, a routing mechanism routes user queries to the most suitable components, such as smaller LLMs or experts in specific topics. This approach may improve response quality while minimising costs. Routing can be expanded to other components of the conversational agent architecture, such as the selection of optimal embedding strategies. This paper explores key considerations for integrating routing into LLM-based systems, focusing on resource management, cost definition, and strategy selection. Our main contributions include a formalisation of the problem, a novel taxonomy of existing approaches emphasising relevance and resource efficiency, and a comparative analysis of these strategies in relation to industry practices. Finally, we identify critical challenges and directions for future research.

  • 6 authors
·
Feb 1, 2025