Molecular Modeling

Text generation models are notoriously vulnerable to errors in the training data. With the wide-spread availability of massive amounts of web-crawled data becoming more commonplace, how can we enhance the robustness of models trained on a massive amount of noisy web-crawled text? In our work, we propose Error Norm Truncation (ENT), a robust enhancement method to the standard training objective that truncates noisy data. Compared to methods that only uses the negative log-likelihood loss to estimate data quality, our method provides a more accurate estimation by considering the distribution of non-target tokens, which is often overlooked by previous work. Through comprehensive experiments across language modeling, machine translation, and text summarization, we show that equipping text generation models with ENT improves generation quality over standard training and previous soft and hard truncation methods. Furthermore, we show that our method improves the robustness of models against two of the most detrimental types of noise in machine translation, resulting in an increase of more than 2 BLEU points over the MLE baseline when up to 50\% of noise is added to the data.

Deep implicit functions (DIFs) have emerged as a powerful paradigm for many computer vision tasks such as 3D shape reconstruction, generation, registration, completion, editing, and understanding. However, given a set of 3D shapes with associated covariates there is at present no shape representation method which allows to precisely represent the shapes while capturing the individual dependencies on each covariate. Such a method would be of high utility to researchers to discover knowledge hidden in a population of shapes. For scientific shape discovery purpose, we propose a 3D Neural Additive Model for Interpretable Shape Representation ($\texttt{NAISR}$) which describes individual shapes by deforming a shape atlas in accordance to the effect of disentangled covariates. Our approach captures shape population trends and allows for patient-specific predictions through shape transfer. $\texttt{NAISR}$ is the first approach to combine the benefits of deep implicit shape representations with an atlas deforming according to specified covariates. We evaluate $\texttt{NAISR}$ with respect to shape reconstruction, shape disentanglement, shape evolution, and shape transfer on three datasets, i.e. 1) $\textit{Starman}$, a simulated 2D shape dataset; 2) ADNI hippocampus 3D shape dataset; 3) pediatric airway 3D shape dataset. Our experiments demonstrate that $\texttt{NAISR}$ achieves competitive shape reconstruction performance while retaining interpretability. Our code is available at https://github.com/uncbiag/NAISR.

Diffusion models (DMs) represent state-of-the-art generative models for continuous inputs. DMs work by constructing a Stochastic Differential Equation (SDE) in the input space (ie, position space), and using a neural network to reverse it. In this work, we introduce a novel generative modeling framework grounded in \textbf{phase space dynamics}, where a phase space is defined as {an augmented space encompassing both position and velocity.} Leveraging insights from Stochastic Optimal Control, we construct a path measure in the phase space that enables efficient sampling. {In contrast to DMs, our framework demonstrates the capability to generate realistic data points at an early stage of dynamics propagation.} This early prediction sets the stage for efficient data generation by leveraging additional velocity information along the trajectory. On standard image generation benchmarks, our model yields favorable performance over baselines in the regime of small Number of Function Evaluations (NFEs). Furthermore, our approach rivals the performance of diffusion models equipped with efficient sampling techniques, underscoring its potential as a new tool generative modeling.

Cascaded models are multi-scale generative models with a marked capacity for producing perceptually impressive samples at high resolutions. In this work, we show that they can also be excellent likelihood models, so long as we overcome a fundamental difficulty with probabilistic multi-scale models: the intractability of the likelihood function. Chiefly, in cascaded models each intermediary scale introduces extraneous variables that cannot be tractably marginalized out for likelihood evaluation. This issue vanishes by modeling the diffusion process on latent spaces induced by a class of transformations we call hierarchical volume-preserving maps, which decompose spatially structured data in a hierarchical fashion without introducing local distortions in the latent space. We demonstrate that two such maps are well-known in the literature for multiscale modeling: Laplacian pyramids and wavelet transforms. Not only do such reparameterizations allow the likelihood function to be directly expressed as a joint likelihood over the scales, we show that the Laplacian pyramid and wavelet transform also produces significant improvements to the state-of-the-art on a selection of benchmarks in likelihood modeling, including density estimation, lossless compression, and out-of-distribution detection. Investigating the theoretical basis of our empirical gains we uncover deep connections to score matching under the Earth Mover's Distance (EMD), which is a well-known surrogate for perceptual similarity.

Spatio-temporal (ST) prediction plays a pivotal role in earth sciences, such as meteorological prediction, urban computing. Adequate high-quality data, coupled with deep models capable of inference, are both indispensable and prerequisite for achieving meaningful results. However, the sparsity of data and the high costs associated with deploying sensors lead to significant data imbalances. Models that are overly tailored and lack causal relationships further compromise the generalizabilities of inference methods. Towards this end, we first establish a causal concept for ST predictions, named NuwaDynamics, which targets to identify causal regions in data and endow model with causal reasoning ability in a two-stage process. Concretely, we initially leverage upstream self-supervision to discern causal important patches, imbuing the model with generalized information and conducting informed interventions on complementary trivial patches to extrapolate potential test distributions. This phase is referred to as the discovery step. Advancing beyond discovery step, we transfer the data to downstream tasks for targeted ST objectives, aiding the model in recognizing a broader potential distribution and fostering its causal perceptual capabilities (refer as Update step). Our concept aligns seamlessly with the contemporary backdoor adjustment mechanism in causality theory. Extensive experiments on six real-world ST benchmarks showcase that models can gain outcomes upon the integration of the NuwaDynamics concept. NuwaDynamics also can significantly benefit a wide range of changeable ST tasks like extreme weather and long temporal step super-resolution predictions.

The legality of training language models (LMs) on copyrighted or otherwise restricted data is under intense debate. However, as we show, model performance significantly degrades if trained only on low-risk text (e.g., out-of-copyright books or government documents), due to its limited size and domain coverage. We present SILO, a new language model that manages this risk-performance tradeoff during inference. SILO is built by (1) training a parametric LM on the Open License Corpus (OLC), a new corpus we curate with 228B tokens of public domain and permissively licensed text and (2) augmenting it with a more general and easily modifiable nonparametric datastore (e.g., containing copyrighted books or news) that is only queried during inference. The datastore allows use of high-risk data without training on it, supports sentence-level data attribution, and enables data producers to opt out from the model by removing content from the store. These capabilities can foster compliance with data-use regulations such as the fair use doctrine in the United States and the GDPR in the European Union. Our experiments show that the parametric LM struggles on its own with domains not covered by OLC. However, access to the datastore greatly improves out of domain performance, closing 90% of the performance gap with an LM trained on the Pile, a more diverse corpus with mostly high-risk text. We also analyze which nonparametric approach works best, where the remaining errors lie, and how performance scales with datastore size. Our results suggest that it is possible to build high quality language models while mitigating legal risk.

Generative adversarial networks (GANs) have made great success in image inpainting yet still have difficulties tackling large missing regions. In contrast, iterative probabilistic algorithms, such as autoregressive and denoising diffusion models, have to be deployed with massive computing resources for decent effect. To achieve high-quality results with low computational cost, we present a novel pixel spread model (PSM) that iteratively employs decoupled probabilistic modeling, combining the optimization efficiency of GANs with the prediction tractability of probabilistic models. As a result, our model selectively spreads informative pixels throughout the image in a few iterations, largely enhancing the completion quality and efficiency. On multiple benchmarks, we achieve new state-of-the-art performance. Our code and models will be publicly available.

Diffusion models excel at generating photo-realistic images but come with significant computational costs in both training and sampling. While various techniques address these computational challenges, a less-explored issue is designing an efficient and adaptable network backbone for iterative refinement. Current options like U-Net and Vision Transformer often rely on resource-intensive deep networks and lack the flexibility needed for generating images at variable resolutions or with a smaller network than used in training. This study introduces LEGO bricks, which seamlessly integrate Local-feature Enrichment and Global-content Orchestration. These bricks can be stacked to create a test-time reconfigurable diffusion backbone, allowing selective skipping of bricks to reduce sampling costs and generate higher-resolution images than the training data. LEGO bricks enrich local regions with an MLP and transform them using a Transformer block while maintaining a consistent full-resolution image across all bricks. Experimental results demonstrate that LEGO bricks enhance training efficiency, expedite convergence, and facilitate variable-resolution image generation while maintaining strong generative performance. Moreover, LEGO significantly reduces sampling time compared to other methods, establishing it as a valuable enhancement for diffusion models. Our code and project page are available at https://jegzheng.github.io/LEGODiffusion.

In this paper, we propose a novel approach to conformal prediction for language models (LMs) in which we produce prediction sets with performance guarantees. LM responses are typically sampled from a predicted distribution over the large, combinatorial output space of language. Translating this to conformal prediction, we calibrate a stopping rule for sampling LM outputs that get added to a growing set of candidates until we are confident that the set covers at least one acceptable response. Since some samples may be low-quality, we also simultaneously calibrate a rejection rule for removing candidates from the output set to reduce noise. Similar to conformal prediction, we can prove that the final output set obeys certain desirable distribution-free guarantees. Within these sets of candidate responses, we also show that we can also identify subsets of individual components---such as phrases or sentences---that are each independently correct (e.g., that are not ``hallucinations''), again with guarantees. Our method can be applied to any LM API that supports sampling. Furthermore, we empirically demonstrate that we can achieve many desired coverage levels within a limited number of total samples when applying our method to multiple tasks in open-domain question answering, text summarization, and radiology report generation using different LM variants.

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42\% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.

Sharpness-aware minimization (SAM) reports improving domain generalization by reducing the loss surface curvature in the parameter space. However, generalization during _fine-tuning_ is often more dependent on the transferability of _representations_ in the function space. Trust-region methods (TR) target this goal by regularizing representation curvature to reduce catastrophic forgetting of pre-trained task-agnostic information while adopting task-specific skills. We consider unifying these strategies for low curvature in both parameter space and function space to improve out-of-domain (OOD) generalization. We propose **Trust Region Aware Minimization** (TRAM), a SAM algorithm fine-tuning for low parameter sharpness and smooth, informative representations preserving pre-trained structure. TRAM uses a trust region bound to inform the SAM adversarial neighborhood, introducing an awareness of function curvature within optimization for flatter minima. We empirically validate TRAM in vision (cross-dataset adaptation) and text (OOD language modeling, zero-shot cross-lingual transfer) tasks where robust domain transfer and representation generality are critical. TRAM outperforms SAM- and TR-based optimization across all tasks, notably surpassing competing methods for hard transfer between _anticorrelated_ domains. TRAM establishes a novel standard in fine-tuning for domain-generalizable models with minimal additional computation over previous sharpness-aware methods.

The accurate modeling of dynamics in interactive environments is critical for successful long-range prediction. Such a capability could advance Reinforcement Learning (RL) and Planning algorithms, but achieving it is challenging. Inaccuracies in model estimates can compound, resulting in increased errors over long horizons. We approach this problem from the lens of Koopman theory, where the nonlinear dynamics of the environment can be linearized in a high-dimensional latent space. This allows us to efficiently parallelize the sequential problem of long-range prediction using convolution while accounting for the agent's action at every time step. Our approach also enables stability analysis and better control over gradients through time. Taken together, these advantages result in significant improvement over the existing approaches, both in the efficiency and the accuracy of modeling dynamics over extended horizons. We also show that this model can be easily incorporated into dynamics modeling for model-based planning and model-free RL and report promising experimental results.

Large-scale vision-language pre-trained models have shown promising transferability to various downstream tasks. As the size of these foundation models and the number of downstream tasks grow, the standard full fine-tuning paradigm becomes unsustainable due to heavy computational and storage costs. This paper proposes UniAdapter, which unifies unimodal and multimodal adapters for parameter-efficient cross-modal adaptation on pre-trained vision-language models. Specifically, adapters are distributed to different modalities and their interactions, with the total number of tunable parameters reduced by partial weight sharing. The unified and knowledge-sharing design enables powerful cross-modal representations that can benefit various downstream tasks, requiring only 1.0%-2.0% tunable parameters of the pre-trained model. Extensive experiments on 7 cross-modal downstream benchmarks (including video-text retrieval, image-text retrieval, VideoQA, VQA and Caption) show that in most cases, UniAdapter not only outperforms the state-of-the-arts, but even beats the full fine-tuning strategy. Particularly, on the MSRVTT retrieval task, UniAdapter achieves 49.7% recall@1 with 2.2% model parameters, outperforming the latest competitors by 2.0%. The code and models are available at https://github.com/RERV/UniAdapter.

Generating realistic time series data is important for many engineering and scientific applications. Existing work tackles this problem using generative adversarial networks (GANs). However, GANs are unstable during training, and they can suffer from mode collapse. While variational autoencoders (VAEs) are known to be more robust to the these issues, they are (surprisingly) less considered for time series generation. In this work, we introduce Koopman VAE (KoVAE), a new generative framework that is based on a novel design for the model prior, and that can be optimized for either regular and irregular training data. Inspired by Koopman theory, we represent the latent conditional prior dynamics using a linear map. Our approach enhances generative modeling with two desired features: (i) incorporating domain knowledge can be achieved by leveraging spectral tools that prescribe constraints on the eigenvalues of the linear map; and (ii) studying the qualitative behavior and stability of the system can be performed using tools from dynamical systems theory. Our results show that KoVAE outperforms state-of-the-art GAN and VAE methods across several challenging synthetic and real-world time series generation benchmarks. Whether trained on regular or irregular data, KoVAE generates time series that improve both discriminative and predictive metrics. We also present visual evidence suggesting that KoVAE learns probability density functions that better approximate the empirical ground truth distribution.

In this paper, we introduce FITS, a lightweight yet powerful model for time series analysis. Unlike existing models that directly process raw time-domain data, FITS operates on the principle that time series can be manipulated through interpolation in the complex frequency domain, achieving performance comparable to state-of-the-art models for time series forecasting and anomaly detection tasks. Notably, FITS accomplishes this with a svelte profile of just about $10k$ parameters, making it ideally suited for edge devices and paving the way for a wide range of applications. The code is available for review at: \url{https://anonymous.4open.science/r/FITS}.

Predicting the future is of great interest across many aspects of human activity. Businesses are interested in future trends, traders are interested in future stock prices, and companies are highly interested in future technological breakthroughs. While there are many automated systems for predicting future numerical data, such as weather, stock prices, and demand for products, there is relatively little work in automatically predicting textual data. Humans are interested in textual data predictions because it is a natural format for our consumption, and experts routinely make predictions in a textual format (Christensen et al., 2004; Tetlock & Gardner, 2015; Frick, 2015). However, there has been relatively little formalization of this general problem in the machine learning or natural language processing communities. To address this gap, we introduce the task of future language modeling: probabilistic modeling of texts in the future based on a temporal history of texts. To our knowledge, our work is the first work to formalize the task of predicting the future in this way. We show that it is indeed possible to build future language models that improve upon strong non-temporal language model baselines, opening the door to working on this important, and widely applicable problem.

Masked Language Modeling (MLM) has been one of the most prominent approaches for pretraining bidirectional text encoders due to its simplicity and effectiveness. One notable concern about MLM is that the special $\texttt{[MASK]}$ symbol causes a discrepancy between pretraining data and downstream data as it is present only in pretraining but not in fine-tuning. In this work, we offer a new perspective on the consequence of such a discrepancy: We demonstrate empirically and theoretically that MLM pretraining allocates some model dimensions exclusively for representing $\texttt{[MASK]}$ tokens, resulting in a representation deficiency for real tokens and limiting the pretrained model's expressiveness when it is adapted to downstream data without $\texttt{[MASK]}$ tokens. Motivated by the identified issue, we propose MAE-LM, which pretrains the Masked Autoencoder architecture with MLM where $\texttt{[MASK]}$ tokens are excluded from the encoder. Empirically, we show that MAE-LM improves the utilization of model dimensions for real token representations, and MAE-LM consistently outperforms MLM-pretrained models on the GLUE and SQuAD benchmarks.

The carbon footprint associated with large language models (LLMs) is a significant concern, encompassing emissions from their training, inference, experimentation, and storage processes, including operational and embodied carbon emissions. An essential aspect is accurately estimating the carbon impact of emerging LLMs even before their training, which heavily relies on GPU usage. Existing studies have reported the carbon footprint of LLM training, but only one tool, mlco2, can predict the carbon footprint of new neural networks prior to physical training. However, mlco2 has several serious limitations. It cannot extend its estimation to dense or mixture-of-experts (MoE) LLMs, disregards critical architectural parameters, focuses solely on GPUs, and cannot model embodied carbon footprints. Addressing these gaps, we introduce \textit{\carb}, an end-to-end carbon footprint projection model designed for both dense and MoE LLMs. Compared to mlco2, \carb~significantly enhances the accuracy of carbon footprint estimations for various LLMs. The source code is released at \url{https://github.com/SotaroKaneda/MLCarbon}.

We study the problem of modeling a population of agents pursuing unknown goals subject to unknown computational constraints. In standard models of bounded rationality, sub-optimal decision-making is simulated by adding homoscedastic noise to optimal decisions rather than actually simulating constrained inference. In this work, we introduce a latent inference budget model (L-IBM) that models these constraints explicitly, via a latent variable (inferred jointly with a model of agents’ goals) that controls the runtime of an iterative inference algorithm. L-IBMs make it possible to learn agent models using data from diverse populations of suboptimal actors. In three modeling tasks—inferring navigation goals from routes, inferring communicative intents from human utterances, and predicting next moves in human chess games—we show that L-IBMs match or outperforms Boltzmann models of decision-making under uncertainty. Moreover, the inferred inference budgets are themselves meaningful, efficient to compute, and correlated with measures of player skill, partner skill and task difficulty.