Teddy Koker

Teddy Koker, Mit Kotak, Tess Smidt · mit

Foundation models for materials modeling are advancing quickly, but their training remains expensive, often placing state-of-the-art methods out of reach for many research groups. We introduce Nequix, a compact E(3)-equivariant potential that pairs a simplified NequIP design with modern training practices, including equivariant root-mean-square layer normalization and the Muon optimizer, to retain accuracy while substantially reducing compute requirements. Nequix has 700K parameters and was trained in 100 A100 GPU-hours. On the Matbench-Discovery and MDR Phonon benchmarks, Nequix ranks third overall while requiring a 20 times lower training cost than most other methods, and it delivers two orders of magnitude faster inference speed than the current top-ranked model. We release model weights and fully reproducible codebase at https://github.com/atomicarchitects/nequix.

Huan He, Owen Queen, Teddy Koker et al. · mit

Unsupervised domain adaptation (UDA) enables the transfer of models trained on source domains to unlabeled target domains. However, transferring complex time series models presents challenges due to the dynamic temporal structure variations across domains. This leads to feature shifts in the time and frequency representations. Additionally, the label distributions of tasks in the source and target domains can differ significantly, posing difficulties in addressing label shifts and recognizing labels unique to the target domain. Effectively transferring complex time series models remains a formidable problem. We present Raincoat, the first model for both closed-set and universal domain adaptation on complex time series. Raincoat addresses feature and label shifts by considering both temporal and frequency features, aligning them across domains, and correcting for misalignments to facilitate the detection of private labels. Additionally, Raincoat improves transferability by identifying label shifts in target domains. Our experiments with 5 datasets and 13 state-of-the-art UDA methods demonstrate that Raincoat can improve transfer learning performance by up to 16.33% and can handle both closed-set and universal domain adaptation.

Owen Queen, Thomas Hartvigsen, Teddy Koker et al. · mit

Interpreting time series models is uniquely challenging because it requires identifying both the location of time series signals that drive model predictions and their matching to an interpretable temporal pattern. While explainers from other modalities can be applied to time series, their inductive biases do not transfer well to the inherently challenging interpretation of time series. We present TimeX, a time series consistency model for training explainers. TimeX trains an interpretable surrogate to mimic the behavior of a pretrained time series model. It addresses the issue of model faithfulness by introducing model behavior consistency, a novel formulation that preserves relations in the latent space induced by the pretrained model with relations in the latent space induced by TimeX. TimeX provides discrete attribution maps and, unlike existing interpretability methods, it learns a latent space of explanations that can be used in various ways, such as to provide landmarks to visually aggregate similar explanations and easily recognize temporal patterns. We evaluate TimeX on eight synthetic and real-world datasets and compare its performance against state-of-the-art interpretability methods. We also conduct case studies using physiological time series. Quantitative evaluations demonstrate that TimeX achieves the highest or second-highest performance in every metric compared to baselines across all datasets. Through case studies, we show that the novel components of TimeX show potential for training faithful, interpretable models that capture the behavior of pretrained time series models.

Teddy Koker, Keegan Quigley, Will Spaeth et al. · berkeley, mit

Recent work has shown the potential of graph neural networks to efficiently predict material properties, enabling high-throughput screening of materials. Training these models, however, often requires large quantities of labelled data, obtained via costly methods such as ab initio calculations or experimental evaluation. By leveraging a series of material-specific transformations, we introduce CrystalCLR, a framework for constrastive learning of representations with crystal graph neural networks. With the addition of a novel loss function, our framework is able to learn representations competitive with engineered fingerprinting methods. We also demonstrate that via model finetuning, contrastive pretraining can improve the performance of graph neural networks for prediction of material properties and significantly outperform traditional ML models that use engineered fingerprints. Lastly, we observe that CrystalCLR produces material representations that form clusters by compound class.

Shanghua Gao, Teddy Koker, Owen Queen et al.

Although pre-trained transformers and reprogrammed text-based LLMs have shown strong performance on time series tasks, the best-performing architectures vary widely across tasks, with most models narrowly focused on specific areas, such as time series forecasting. Unifying predictive and generative time series tasks within a single model remains challenging. We introduce UniTS, a unified multi-task time series model that utilizes task tokenization to integrate predictive and generative tasks into a single framework. UniTS employs a modified transformer block to capture universal time series representations, enabling transferability from a heterogeneous, multi-domain pre-training dataset-characterized by diverse dynamic patterns, sampling rates, and temporal scales-to a wide range of downstream datasets with varied task specifications and data domains. Tested on 38 datasets across human activity sensors, healthcare, engineering, and finance, UniTS achieves superior performance compared to 12 forecasting models, 20 classification models, 18 anomaly detection models, and 16 imputation models, including adapted text-based LLMs. UniTS also demonstrates strong few-shot and prompt capabilities when applied to new domains and tasks. In single-task settings, UniTS outperforms competitive task-specialized time series models. Code and datasets are available at https://github.com/mims-harvard/UniTS.

Teddy Koker, Abhijeet Gangan, Mit Kotak et al.

Many materials properties depend on higher-order derivatives of the potential energy surface, yet machine learned interatomic potentials (MLIPs) trained with standard a standard loss on energy, force, and stress errors can exhibit error in curvature, degrading the prediction of vibrational properties. We introduce phonon fine-tuning (PFT), which directly supervises second-order force constants of materials by matching MLIP energy Hessians to DFT-computed force constants from finite displacement phonon calculations. To scale to large supercells, PFT stochastically samples Hessian columns and computes the loss with a single Hessian-vector product. We also use a simple co-training scheme to incorporate upstream data to mitigate catastrophic forgetting. On the MDR Phonon benchmark, PFT improves Nequix MP (trained on Materials Project) by 55% on average across phonon thermodynamic properties and achieves state-of-the-art performance among models trained on Materials Project trajectories. PFT also generalizes to improve properties beyond second-derivatives, improving thermal conductivity predictions that rely on third-order derivatives of the potential energy.

Teddy Koker, Keegan Quigley, Eric Taw et al. · mit

The calculation of electron density distribution using density functional theory (DFT) in materials and molecules is central to the study of their quantum and macro-scale properties, yet accurate and efficient calculation remains a long-standing challenge. We introduce ChargE3Net, an E(3)-equivariant graph neural network for predicting electron density in atomic systems. ChargE3Net enables the learning of higher-order equivariant feature to achieve high predictive accuracy and model expressivity. We show that ChargE3Net exceeds the performance of prior work on diverse sets of molecules and materials. When trained on the massive dataset of over 100K materials in the Materials Project database, our model is able to capture the complexity and variability in the data, leading to a significant 26.7% reduction in self-consistent iterations when used to initialize DFT calculations on unseen materials. Furthermore, we show that non-self-consistent DFT calculations using our predicted charge densities yield near-DFT performance on electronic and thermodynamic property prediction at a fraction of the computational cost. Further analysis attributes the greater predictive accuracy to improved modeling of systems with high angular variations. These results illuminate a pathway towards a machine learning-accelerated ab initio calculations for materials discovery.

William Falcon, Ananya Harsh Jha, Teddy Koker et al.

Recent methods for self-supervised learning can be grouped into two paradigms: contrastive and non-contrastive approaches. Their success can largely be attributed to data augmentation pipelines which generate multiple views of a single input that preserve the underlying semantics. In this work, we introduce augmentation-augmented stochastic autoencoders (AASAE), yet another alternative to self-supervised learning, based on autoencoding. We derive AASAE starting from the conventional variational autoencoder (VAE), by replacing the KL divergence regularization, which is agnostic to the input domain, with data augmentations that explicitly encourage the internal representations to encode domain-specific invariances and equivariances. We empirically evaluate the proposed AASAE on image classification, similar to how recent contrastive and non-contrastive learning algorithms have been evaluated. Our experiments confirm the effectiveness of data augmentation as a replacement for KL divergence regularization. The AASAE outperforms the VAE by 30% on CIFAR-10, 40% on STL-10 and 45% on Imagenet. On CIFAR-10 and STL-10, the results for AASAE are largely comparable to the state-of-the-art algorithms for self-supervised learning.

Teddy Koker, Fatemehsadat Mireshghallah, Tom Titcombe et al.

Deep Neural Networks (DNNs) are widely used for decision making in a myriad of critical applications, ranging from medical to societal and even judicial. Given the importance of these decisions, it is crucial for us to be able to interpret these models. We introduce a new method for interpreting image segmentation models by learning regions of images in which noise can be applied without hindering downstream model performance. We apply this method to segmentation of the pancreas in CT scans, and qualitatively compare the quality of the method to existing explainability techniques, such as Grad-CAM and occlusion sensitivity. Additionally we show that, unlike other methods, our interpretability model can be quantitatively evaluated based on the downstream performance over obscured images.