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Applications · Language, Speech and Dialog

Pingchuan Ma, Johnson Tsun-Hsuan Wang, Minghao Guo, Zhiqing Sun, Josh Tenenbaum, Daniela Rus, Chuang Gan, Wojciech Matusik

Large Language Models have recently gained significant attention in scientific discovery for their extensive knowledge and advanced reasoning capabilities. However, they encounter challenges in effectively simulating observational feedback and grounding it with language to propel advancements in physical scientific discovery. Conversely, human scientists undertake scientific discovery by formulating hypotheses, conducting experiments, and revising theories through observational analysis. Inspired by this, we propose to enhance the knowledge-driven, abstract reasoning abilities of LLMs with the computational strength of simulations. We introduce Scientific Generative Agent (SGA), a bilevel optimization framework: LLMs act as knowledgeable and versatile thinkers, proposing scientific hypotheses and reason about discrete components, such as physics equations or molecule structures; meanwhile, simulations function as experimental platforms, providing observational feedback and optimizing via differentiability for continuous parts, such as physical parameters. We conduct extensive experiments to demonstrate our framework's efficacy in constitutive law discovery and molecular design, unveiling novel solutions that differ from conventional human expectations yet remain coherent upon analysis.

Optimization · Discrete and Combinatorial Optimization

PAUL DUETTING, Federico Fusco, Silvio Lattanzi, Ashkan Norouzi-Fard, Morteza Zadimoghaddam

Maximizing monotone submodular functions under cardinality constraints is a classic optimization task with several applications in data mining and machine learning. In this paper, we study this problem in a dynamic environment with consistency constraints: elements arrive in a streaming fashion, and the goal is maintaining a constant approximation to the optimal solution while having a stable solution (i.e., the number of changes between two consecutive solutions is bounded). In this setting, we provide algorithms with different trade-offs between consistency and approximation quality. We also complement our theoretical results with an experimental analysis showing the effectiveness of our algorithms in real-world instances.

Optimization · Optimization and Learning under Uncertainty

Yucen Li, Tim G. J. Rudner, Andrew Gordon Wilson

Bayesian optimization is a highly efficient approach to optimizing objective functions which are expensive to query. These objectives are typically represented by Gaussian process (GP) surrogate models which are easy to optimize and support exact inference. While standard GP surrogates have been well-established in Bayesian optimization, Bayesian neural networks (BNNs) have recently become practical function approximators, with many benefits over standard GPs such as the ability to naturally handle non-stationarity and learn representations for high-dimensional data. In this paper, we study BNNs as alternatives to standard GP surrogates for optimization. We consider a variety of approximate inference procedures for finite-width BNNs, including high-quality Hamiltonian Monte Carlo, low-cost stochastic MCMC, and heuristics such as deep ensembles. We also consider infinite-width BNNs, linearized Laplace approximations, and partially stochastic models such as deep kernel learning. We evaluate this collection of surrogate models on diverse problems with varying dimensionality, number of objectives, non-stationarity, and discrete and continuous inputs. We find: (i) the ranking of methods is highly problem dependent, suggesting the need for tailored inductive biases; (ii) HMC is the most successful approximate inference procedure for fully stochastic BNNs; (iii) full stochasticity may be unnecessary as deep kernel learning is relatively competitive; (iv) deep ensembles perform relatively poorly; (v) infinite-width BNNs are particularly promising, especially in high dimensions.

Applications · Computer Vision

Yang Jin, Kun Xu, Kun Xu, Liwei Chen, Chao Liao, Jianchao Tan, Quzhe Huang, Bin CHEN, Chengru Song, dai meng 等

Recently, the remarkable advance of the Large Language Model (LLM) has inspired researchers to transfer its extraordinary reasoning capability to both vision and language data. However, the prevailing approaches primarily regard the visual input as a prompt and focus exclusively on optimizing the text generation process conditioned upon vision content by a frozen LLM. Such an inequitable treatment of vision and language heavily constrains the model's potential. In this paper, we break through this limitation by representing both vision and language in a unified form. Specifically, we introduce a well-designed visual tokenizer to translate the non-linguistic image into a sequence of discrete tokens like a foreign language that LLM can read. The resulting visual tokens encompass high-level semantics worthy of a word and also support dynamic sequence length varying from the image. Coped with this tokenizer, the presented foundation model called LaVIT can handle both image and text indiscriminately under the same generative learning paradigm. This unification empowers LaVIT to serve as an impressive generalist interface to understand and generate multi-modal content simultaneously. Extensive experiments further showcase that it outperforms the existing models by a large margin on massive vision-language tasks. Our code and models are available at https://github.com/jy0205/LaVIT.

Deep Learning

Renbo Tu, Colin White, Jean Kossaifi, Boris Bonev, Gennady Pekhimenko, Kamyar Azizzadenesheli, anima anandkumar

Neural operators, such as Fourier Neural Operators (FNO), form a principled approach for learning solution operators for partial differential equations (PDE) and other mappings between function spaces. However, many real-world problems require high-resolution training data, and the training time and limited GPU memory pose big barriers. One solution is to train neural operators in mixed precision to reduce the memory requirement and increase training speed. However, existing mixed-precision training techniques are designed for standard neural networks, and we find that their direct application to FNO leads to numerical overflow and poor memory efficiency. Further, at first glance, it may appear that mixed precision in FNO will lead to drastic accuracy degradation since reducing the precision of the Fourier transform yields poor results in classical numerical solvers. We show that this is not the case; in fact, we prove that reducing the precision in FNO still guarantees a good approximation bound, when done in a targeted manner. Specifically, we build on the intuition that neural operator learning inherently induces an approximation error, arising from discretizing the infinite-dimensional ground-truth input function, implying that training in full precision is not needed. We formalize this intuition by rigorously characterizing the approximation and precision errors of FNO and bounding these errors for general input functions. We prove that the precision error is asymptotically comparable to the approximation error. Based on this, we design a simple method to optimize the memory-intensive half-precision tensor contractions by greedily finding the optimal contraction order. Through extensive experiments on different state-of-the-art neural operators, datasets, and GPUs, we demonstrate that our approach reduces GPU memory usage by up to 50% and improves throughput by 58% with little or no reduction in accuracy.

Yang Song, Prafulla Dhariwal

Consistency models are a nascent family of generative models that can sample high quality data in one step without the need for adversarial training. Current consistency models achieve optimal sample quality by distilling from pre-trained diffusion models and employing learned metrics such as LPIPS. However, distillation limits the quality of consistency models to that of the pre-trained diffusion model, and LPIPS causes undesirable bias in evaluation. To tackle these challenges, we present improved techniques for consistency training, where consistency models learn directly from data without distillation. We delve into the theory behind consistency training and identify a previously overlooked flaw, which we address by eliminating Exponential Moving Average from the teacher consistency model. To replace learned metrics like LPIPS, we adopt Pseudo-Huber losses from robust statistics. Additionally, we introduce a lognormal noise schedule for the consistency training objective, and propose to double total discretization steps every set number of training iterations. Combined with better hyperparameter tuning, these modifications enable consistency models to achieve FID scores of 2.51 and 3.25 on CIFAR-10 and ImageNet $64\times 64$ respectively in a single sampling step. These scores mark a 3.5$\times$ and 4$\times$ improvement compared to prior consistency training approaches. Through two-step sampling, we further reduce FID scores to 2.24 and 2.77 on these two datasets, surpassing those obtained via distillation in both one-step and two-step settings, while narrowing the gap between consistency models and other state-of-the-art generative models.

Satwik Bhattamishra, Arkil Patel, Phil Blunsom, Varun Kanade

In order to understand the in-context learning phenomenon, recent works have adopted a stylized experimental framework and demonstrated that Transformers can match the performance of gradient-based learning algorithms for various classes of real-valued functions. However, the limitations of Transformers in implementing learning algorithms, and their ability to learn other forms of algorithms are not well understood. Additionally, the degree to which these capabilities are confined to attention-based models is unclear. Furthermore, it remains to be seen whether the insights derived from these stylized settings can be extrapolated to pretrained Large Language Models (LLMs). In this work, we take a step towards answering these questions by demonstrating the following: (a) On a test-bed with a variety of Boolean function classes, we find that Transformers can nearly match the optimal learning algorithm for 'simpler' tasks, while their performance deteriorates on more 'complex' tasks. Additionally, we find that certain attention-free models perform (almost) identically to Transformers on a range of tasks. (b) When provided a *teaching sequence*, i.e. a set of examples that uniquely identifies a function in a class, we show that Transformers learn more sample-efficiently. Interestingly, our results show that Transformers can learn to implement *two distinct* algorithms to solve a *single* task, and can adaptively select the more sample-efficient algorithm depending on the sequence of in-context examples. (c) Lastly, we show that extant LLMs, e.g. LLaMA-2, GPT-4, can compete with nearest-neighbor baselines on prediction tasks that are guaranteed to not be in their training set.

Nathan Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho 等

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our $\textit{Discrete Walk-Jump Sampling}$ formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the $\textit{distributional conformity score}$ to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100\% of generated samples are successfully expressed and purified and 70\% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Yang Song, Prafulla Dhariwal

Consistency models are a nascent family of generative models that can sample high quality data in one step without the need for adversarial training. Current consistency models achieve optimal sample quality by distilling from pre-trained diffusion models and employing learned metrics such as LPIPS. However, distillation limits the quality of consistency models to that of the pre-trained diffusion model, and LPIPS causes undesirable bias in evaluation. To tackle these challenges, we present improved techniques for consistency training, where consistency models learn directly from data without distillation. We delve into the theory behind consistency training and identify a previously overlooked flaw, which we address by eliminating Exponential Moving Average from the teacher consistency model. To replace learned metrics like LPIPS, we adopt Pseudo-Huber losses from robust statistics. Additionally, we introduce a lognormal noise schedule for the consistency training objective, and propose to double total discretization steps every set number of training iterations. Combined with better hyperparameter tuning, these modifications enable consistency models to achieve FID scores of 2.51 and 3.25 on CIFAR-10 and ImageNet $64\times 64$ respectively in a single sampling step. These scores mark a 3.5$\times$ and 4$\times$ improvement compared to prior consistency training approaches. Through two-step sampling, we further reduce FID scores to 2.24 and 2.77 on these two datasets, surpassing those obtained via distillation in both one-step and two-step settings, while narrowing the gap between consistency models and other state-of-the-art generative models.

Applications · Chemistry and Drug Discovery

Nathan Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho 等

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our $\textit{Discrete Walk-Jump Sampling}$ formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the $\textit{distributional conformity score}$ to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100\% of generated samples are successfully expressed and purified and 70\% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

Optimization · Optimization and Learning under Uncertainty

Rares Cristian, Georgia Perakis

We study contextual stochastic optimization problems. Optimization problems have uncertain parameters stemming from unknown, context-dependent, distributions. Due to the inherent uncertainty in these problems, one is often interested not only in minimizing expected cost, but also to be robust and protect against worst case scenarios. We propose a novel method that combines the learning stage with knowledge of the downstream optimization task. The method prescribes decisions which aim to maximize the likelihood that the cost is below a (user-controlled) threshold. The key idea is (1) to discretize the feasible region into subsets so that the uncertain objective function can be well approximated deterministically within each subset, and (2) devise a secondary optimization problem to prescribe decisions by integrating the individual approximations determined in step (1). We provide theoretical guarantees bounding the underlying regret of decisions proposed by our method. In addition, experimental results demonstrate that our approach is competitive in terms of average regret and yields more robust solutions than other methods proposed in the literature, including up to 20 times lower worst-case cost on a real-world electricity generation problem.

Nithin Chalapathi, Yiheng Du, Aditi Krishnapriyan

Imposing known physical constraints, such as conservation laws, during neural network training introduces an inductive bias that can improve accuracy, reliability, convergence, and data efficiency for modeling physical dynamics. While such constraints can be softly imposed via loss function penalties, recent advancements in differentiable physics and optimization improve performance by incorporating PDE-constrained optimization as individual layers in neural networks. This enables a stricter adherence to physical constraints. However, imposing hard constraints significantly increases computational and memory costs, especially for complex dynamical systems. This is because it requires solving an optimization problem over a large number of points in a mesh, representing spatial and temporal discretizations, which greatly increases the complexity of the constraint. To address this challenge, we develop a scalable approach to enforce hard physical constraints using Mixture-of-Experts (MoE), which can be used with any neural network architecture. Our approach imposes the constraint over smaller decomposed domains, each of which is solved by an ``expert'' through differentiable optimization. During training, each expert independently performs a localized backpropagation step by leveraging the implicit function theorem; the independence of each expert allows for parallelization across multiple GPUs. Compared to standard differentiable optimization, our scalable approach achieves greater accuracy in the neural PDE solver setting for predicting the dynamics of challenging non-linear systems. We also improve training stability and require significantly less computation time during both training and inference stages.

Applications · Chemistry and Drug Discovery

Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi Jaakkola, Regina Barzilay, Ila Fiete

The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain optimization to a small mutational radius, but this drastically limits the design space. Instead of heuristics, we propose smoothing the fitness landscape to facilitate protein optimization. First, we formulate protein fitness as a graph signal then use Tikunov regularization to smooth the fitness landscape. We find optimizing in this smoothed landscape leads to improved performance across multiple methods in the GFP and AAV benchmarks. Second, we achieve state-of-the-art results utilizing discrete energy-based models and MCMC in the smoothed landscape. Our method, called Gibbs sampling with Graph-based Smoothing (GGS), demonstrates a unique ability to achieve 2.5 fold fitness improvement (with in-silico evaluation) over its training set. GGS demonstrates potential to optimize proteins in the limited data regime. Code: https://github.com/kirjner/GGS

Yufeng Zhang, Hang Yu, Jianguo Li, Weiyao Lin

Learned lossless data compression has garnered significant attention recently due to its superior compression ratios compared to traditional compressors. However, the computational efficiency of these models jeopardizes their practicality. This paper proposes a novel system for improving the compression ratio while maintaining computational efficiency for learned lossless data compression. Our approach incorporates two essential innovations. First, we propose the Finite-State AutoRegressive (FSAR) entropy coder, an efficient autoregressive Markov model based entropy coder that utilizes a lookup table to expedite autoregressive entropy coding. Next, we present a Straight-Through Hardmax Quantization (STHQ) scheme to enhance the optimization of discrete latent space. Our experiments show that the proposed lossless compression method could improve the compression ratio by up to 6\% compared to the baseline, with negligible extra computational time. Our work provides valuable insights into enhancing the computational efficiency of learned lossless data compression, which can have practical applications in various fields. Code is available at https://github.com/alipay/Finite_State_Autoregressive_Entropy_Coding.

Guoqiang Zhang, Kenta Niwa, W. Bastiaan Kleijn

A popular approach to sample a diffusion-based generative model is to solve an ordinary differential equation (ODE). In existing samplers, the coefficients of the ODE solvers are pre-determined by the ODE formulation, the reverse discrete timesteps, and the employed ODE methods. In this paper, we consider accelerating several popular ODE-based sampling processes (including EDM, DDIM, and DPM-Solver) by optimizing certain coefficients via improved integration approximation (IIA). We propose to minimize, for each time step, a mean squared error (MSE) function with respect to the selected coefficients. The MSE is constructed by applying the original ODE solver for a set of fine-grained timesteps, which in principle provides a more accurate integration approximation in predicting the next diffusion state. The proposed IIA technique does not require any change of a pre-trained model, and only introduces a very small computational overhead for solving a number of quadratic optimization problems. Extensive experiments show that considerably better FID scores can be achieved by using IIA-EDM, IIA-DDIM, and IIA-DPM-Solver than the original counterparts when the neural function evaluation (NFE) is small (i.e., less than 25).

Optimization · Bilevel optimization

Bo Zhou, Ruiwei Jiang, Siqian Shen

Bilevel programs (BPs) find a wide range of applications in fields such as energy, transportation, and machine learning. As compared to BPs with continuous (linear/convex) optimization problems in both levels, the BPs with discrete decision variables have received much less attention, largely due to the ensuing computational intractability and the incapability of gradient-based algorithms for handling discrete optimization formulations. In this paper, we develop deep learning techniques to address this challenge. Specifically, we consider a BP with binary tender, wherein the upper and lower levels are linked via binary variables. We train a neural network to approximate the optimal value of the lower-level problem, as a function of the binary tender. Then, we obtain a single-level reformulation of the BP through a mixed-integer representation of the value function. Furthermore, we conduct a comparative analysis between two types of neural networks: general neural networks and the novel input supermodular neural networks, studying their representational capacities. To solve high-dimensional BPs, we introduce an enhanced sampling method to generate higher-quality samples and implement an iterative process to refine solutions. We demonstrate the performance of these approaches through extensive numerical experiments, whose lower-level problems are linear and mixed-integer programs, respectively.

Deep Learning · Other Representation Learning

Vladimir Kostic, Pietro Novelli, Riccardo Grazzi, Karim Lounici, massimiliano pontil

We consider the general class of time-homogeneous stochastic dynamical systems, both discrete and continuous, and study the problem of learning a representation of the state that faithfully captures its dynamics. This is instrumental to learning the transfer operator or the generator of the system, which in turn can be used for numerous tasks, such as forecasting and interpreting the system dynamics. We show that the search for a good representation can be cast as an optimization problem over neural networks. Our approach is supported by recent results in statistical learning theory, highlighting the role of approximation error and metric distortion in the learning problem. The objective function we propose is associated with projection operators from the representation space to the data space, overcomes metric distortion, and can be empirically estimated from data. In the discrete-time setting, we further derive a relaxed objective function that is differentiable and numerically well-conditioned. We compare our method against state-of-the-art approaches on different datasets, showing better performance across the board.

Optimization · Optimization and Learning under Uncertainty

Justin Dumouchelle, Esther Julien, Jannis Kurtz, Elias Khalil

Robust optimization provides a mathematical framework for modeling and solving decision-making problems under worst-case uncertainty. This work addresses two-stage robust optimization (2RO) problems (also called *adjustable robust optimization*), wherein first-stage and second-stage decisions are made before and after uncertainty is realized, respectively. This results in a nested min-max-min optimization problem which is extremely challenging computationally, especially when the decisions are discrete. We propose Neur2RO, an efficient machine learning-driven instantiation of column-and-constraint generation (CCG), a classical iterative algorithm for 2RO. Specifically, we learn to estimate the value function of the second-stage problem via a novel neural network architecture that is easy to optimize over by design. Embedding our neural network into CCG yields high-quality solutions quickly as evidenced by experiments on two 2RO benchmarks, knapsack and capital budgeting. For knapsack, Neur2RO finds solutions that are within roughly $2$% of the best-known values in a few seconds compared to the three hours of the state-of-the-art exact branch-and-price algorithm; for larger and more complex instances, Neur2RO finds even better solutions. For capital budgeting, Neur2RO outperforms three variants of the $k$-adaptability algorithm, particularly on the largest instances, with a $10$ to $100$-fold reduction in solution time. Our code and data are available at https://github.com/khalil-research/Neur2RO.

Applications · Computer Vision

Thanh-Tung Le, Khai Nguyen, shanlin sun, Kun Han, Nhat Ho, Xiaohui Xie

Mesh deformation plays a pivotal role in many 3D vision tasks including dynamic simulations, rendering, and reconstruction. However, defining an efficient discrepancy between predicted and target meshes remains an open problem. A prevalent approach in current deep learning is the set-based approach which measures the discrepancy between two surfaces by comparing two randomly sampled point-clouds from the two meshes with Chamfer pseudo-distance. Nevertheless, the set-based approach still has limitations such as lacking a theoretical guarantee for choosing the number of points in sampled point-clouds, and the pseudo-metricity and the quadratic complexity of the Chamfer divergence. To address these issues, we propose a novel metric for learning mesh deformation. The metric is defined by sliced Wasserstein distance on meshes represented as probability measures that generalize the set-based approach. By leveraging probability measure space, we gain flexibility in encoding meshes using diverse forms of probability measures, such as continuous, empirical, and discrete measures via \textit{varifold} representation. After having encoded probability measures, we can compare meshes by using the sliced Wasserstein distance which is an effective optimal transport distance with linear computational complexity and can provide a fast statistical rate for approximating the surface of meshes. To the end, we employ a neural ordinary differential equation (ODE) to deform the input surface into the target shape by modeling the trajectories of the points on the surface. Our experiments on cortical surface reconstruction demonstrate that our approach surpasses other competing methods in multiple datasets and metrics.

Applications

Zitao Song, Wendi Ren, Shuang Li

Excitatory point processes (i.e., event flows) occurring over dynamic graphs (i.e., evolving topologies) provide a fine-grained model to capture how discrete events may spread over time and space. How to effectively steer the event flows by modifying the dynamic graph structures presents an interesting problem, motivated by curbing the spread of infectious diseases through strategically locking down cities to mitigating traffic congestion via traffic light optimization. To address the intricacies of planning and overcome the high dimensionality inherent to such decision-making problems, we design an Amortized Network Interventions (ANI) framework, allowing for the pooling of optimal policies from history and other contexts while ensuring a permutation equivalent property. This property enables efficient knowledge transfer and sharing across diverse contexts. Each task is solved by an H-step lookahead model-based reinforcement learning, where neural ODEs are introduced to model the dynamics of the excitatory point processes. Instead of simulating rollouts from the dynamics model, we derive an analytical mean-field approximation for the event flows given the dynamics, making the online planning more efficiently solvable. We empirically illustrate that this ANI approach substantially enhances policy learning for unseen dynamics and exhibits promising outcomes in steering event flows through network intervention using synthetic and real COVID datasets.