Barnabás Póczos

Hai Pham, Young Jin Kim, Subhabrata Mukherjee et al. · cmu, microsoft-research

Mixture-of-experts (MoE) architecture has been proven a powerful method for diverse tasks in training deep models in many applications. However, current MoE implementations are task agnostic, treating all tokens from different tasks in the same manner. In this work, we instead design a novel method that incorporates task information into MoE models at different granular levels with shared dynamic task-based adapters. Our experiments and analysis show the advantages of our approaches over the dense and canonical MoE models on multi-task multilingual machine translations. With task-specific adapters, our models can additionally generalize to new tasks efficiently.

Chenghui Zhou, Barnabas Poczos

Variational autoencoder (VAE) is a popular method for drug discovery and various architectures and pipelines have been proposed to improve its performance. However, VAE approaches are known to suffer from poor manifold recovery when the data lie on a low-dimensional manifold embedded in a higher dimensional ambient space [Dai and Wipf, 2019]. The consequences of it in drug discovery are somewhat under-explored. In this paper, we explore applying a multi-stage VAE approach, that can improve manifold recovery on a synthetic dataset, to the field of drug discovery. We experimentally evaluate our multi-stage VAE approach using the ChEMBL dataset and demonstrate its ability to improve the property statistics of generated molecules substantially from pre-existing methods without incorporating property predictors into the training pipeline. We further fine-tune our models on two curated and much smaller molecule datasets that target different proteins. Our experiments show an increase in the number of active molecules generated by the multi-stage VAE in comparison to their one-stage equivalent. For each of the two tasks, our baselines include methods that use learned property predictors to incorporate target metrics directly into the training objective and we discuss complications that arise with this methodology.

Chenghui Zhou, Barnabas Poczos

Variational autoencoder (VAE) is a popular method for drug discovery and there had been a great deal of architectures and pipelines proposed to improve its performance. But the VAE model itself suffers from deficiencies such as poor manifold recovery when data lie on low-dimensional manifold embedded in higher dimensional ambient space and they manifest themselves in each applications differently. The consequences of it in drug discovery is somewhat under-explored. In this paper, we study how to improve the similarity of the data generated via VAE and the training dataset by improving manifold recovery via a 2-stage VAE where the second stage VAE is trained on the latent space of the first one. We experimentally evaluated our approach using the ChEMBL dataset as well as a polymer datasets. In both dataset, the 2-stage VAE method is able to improve the property statistics significantly from a pre-existing method.

Han Nguyen, Hai Pham, Sashank J. Reddi et al.

Despite their popularity in deep learning and machine learning in general, the theoretical properties of adaptive optimizers such as Adagrad, RMSProp, Adam or AdamW are not yet fully understood. In this paper, we develop a novel framework to study the stability and generalization of these optimization methods. Based on this framework, we show provable guarantees about such properties that depend heavily on a single parameter $β_2$. Our empirical experiments support our claims and provide practical insights into the stability and generalization properties of adaptive optimization methods.

Saumya Goyal, Rohith Rongali, Ritabrata Ray et al.

We study learning to learn for regression problems through the lens of hyperparameter tuning. We propose the Langevin Gradient Descent Algorithm (LGD), which approximates the mean of the posterior distribution defined by the loss function and regularizer of a convex regression task. We prove the existence of an optimal hyperparameter configuration for which the LGD algorithm achieves the Bayes' optimal solution for squared loss. Subsequently, we study generalization guarantees on meta-learning optimal hyperparameters for the LGD algorithm from a given set of tasks in the data-driven setting. For a number of parameters $d$ and hyperparameter dimension $h$, we show a pseudo-dimension bound of $O(dh)$, upto logarithmic terms under mild assumptions on LGD. This matches the dimensional dependence of the bounds obtained in prior work for the elastic net, which only allows for $h=2$ hyperparameters, and extends their bounds to regression on convex loss. Finally, we show empirical evidence of the success of LGD and the meta-learning procedure for few-shot learning on linear regression using a few synthetically created datasets.

Yuchen Shen, Barnabás Póczos

With the increasing attention to molecular machine learning, various innovations have been made in designing better models or proposing more comprehensive benchmarks. However, less is studied on the data preprocessing schedule for molecular graphs, where a different view of the molecular graph could potentially boost the model's performance. Inspired by the Byte-Pair Encoding (BPE) algorithm, a subword tokenization method popularly adopted in Natural Language Processing, we propose GraphBPE, which tokenizes a molecular graph into different substructures and acts as a preprocessing schedule independent of the model architectures. Our experiments on 3 graph-level classification and 3 graph-level regression datasets show that data preprocessing could boost the performance of models for molecular graphs, and GraphBPE is effective for small classification datasets and it performs on par with other tokenization methods across different model architectures.

Kai Hu, Barnabas Poczos

In this paper, we propose a novel regularization method, RotationOut, for neural networks. Different from Dropout that handles each neuron/channel independently, RotationOut regards its input layer as an entire vector and introduces regularization by randomly rotating the vector. RotationOut can also be used in convolutional layers and recurrent layers with small modifications. We further use a noise analysis method to interpret the difference between RotationOut and Dropout in co-adaptation reduction. Using this method, we also show how to use RotationOut/Dropout together with Batch Normalization. Extensive experiments in vision and language tasks are conducted to show the effectiveness of the proposed method. Codes are available at \url{https://github.com/RotationOut/RotationOut}.

Kirthevasan Kandasamy, Karun Raju Vysyaraju, Willie Neiswanger et al.

Bayesian Optimisation (BO) refers to a suite of techniques for global optimisation of expensive black box functions, which use introspective Bayesian models of the function to efficiently search for the optimum. While BO has been applied successfully in many applications, modern optimisation tasks usher in new challenges where conventional methods fail spectacularly. In this work, we present Dragonfly, an open source Python library for scalable and robust BO. Dragonfly incorporates multiple recently developed methods that allow BO to be applied in challenging real world settings; these include better methods for handling higher dimensional domains, methods for handling multi-fidelity evaluations when cheap approximations of an expensive function are available, methods for optimising over structured combinatorial spaces, such as the space of neural network architectures, and methods for handling parallel evaluations. Additionally, we develop new methodological improvements in BO for selecting the Bayesian model, selecting the acquisition function, and optimising over complex domains with different variable types and additional constraints. We compare Dragonfly to a suite of other packages and algorithms for global optimisation and demonstrate that when the above methods are integrated, they enable significant improvements in the performance of BO. The Dragonfly library is available at dragonfly.github.io.

Tongzhou Liao, Barnabás Póczos

Graph Neural Networks (GNNs) have become important tools for machine learning on graph-structured data. In this paper, we explore the synergistic combination of graph encoding, graph rewiring, and graph attention, by introducing Graph Attention with Stochastic Structures (GRASS), a novel GNN architecture. GRASS utilizes relative random walk probabilities (RRWP) encoding and a novel decomposed variant (D-RRWP) to efficiently capture structural information. It rewires the input graph by superimposing a random regular graph to enhance long-range information propagation. It also employs a novel additive attention mechanism tailored for graph-structured data. Our empirical evaluations demonstrate that GRASS achieves state-of-the-art performance on multiple benchmark datasets, including a 20.3% reduction in mean absolute error on the ZINC dataset.

Dhananjay Ashok, Barnabas Poczos

While most research on controllable text generation has focused on steering base Language Models, the emerging instruction-tuning and prompting paradigm offers an alternate approach to controllability. We compile and release ConGenBench, a testbed of 17 different controllable generation tasks, using a subset of it to benchmark the performance of 9 different baselines and methods on Instruction-tuned Language Models. To our surprise, we find that prompting-based approaches outperform controllable text generation methods on most datasets and tasks, highlighting a need for research on controllable text generation with Instruction-tuned Language Models in specific. Prompt-based approaches match human performance on most stylistic tasks while lagging on structural tasks, foregrounding a need to study more varied constraints and more challenging stylistic tasks. To facilitate such research, we provide an algorithm that uses only a task dataset and a Large Language Model with in-context capabilities to automatically generate a constraint dataset. This method eliminates the fields dependence on pre-curated constraint datasets, hence vastly expanding the range of constraints that can be studied in the future.

Peng Qiu, Hanqi Feng, Meng-Chun Zhang et al.

Red-blood-cell lysis (HC50) is the principal safety barrier for antimicrobial-peptide (AMP) therapeutics, yet existing models only say "toxic" or "non-toxic." AmpLyze closes this gap by predicting the actual HC50 value from sequence alone and explaining the residues that drive toxicity. The model couples residue-level ProtT5/ESM2 embeddings with sequence-level descriptors in dual local and global branches, aligned by a cross-attention module and trained with log-cosh loss for robustness to assay noise. The optimal AmpLyze model reaches a PCC of 0.756 and an MSE of 0.987, outperforming classical regressors and the state-of-the-art. Ablations confirm that both branches are essential, and cross-attention adds a further 1% PCC and 3% MSE improvement. Expected-Gradients attributions reveal known toxicity hotspots and suggest safer substitutions. By turning hemolysis assessment into a quantitative, sequence-based, and interpretable prediction, AmpLyze facilitates AMP design and offers a practical tool for early-stage toxicity screening.

Amira Alakhdar, Barnabas Poczos, Newell Washburn

Developing bioactive molecules remains a central, time- and cost-heavy challenge in drug discovery, particularly for novel targets lacking structural or functional data. Pharmacophore modeling presents an alternative for capturing the key features required for molecular bioactivity against a biological target. In this work, we present PharmaDiff, a pharmacophore-conditioned diffusion model for 3D molecular generation. PharmaDiff employs a transformer-based architecture to integrate an atom-based representation of the 3D pharmacophore into the generative process, enabling the precise generation of 3D molecular graphs that align with predefined pharmacophore hypotheses. Through comprehensive testing, PharmaDiff demonstrates superior performance in matching 3D pharmacophore constraints compared to ligand-based drug design methods. Additionally, it achieves higher docking scores across a range of proteins in structure-based drug design, without the need for target protein structures. By integrating pharmacophore modeling with 3D generative techniques, PharmaDiff offers a powerful and flexible framework for rational drug design.

Amira Alakhdar, Barnabas Poczos, Newell Washburn

Diffusion models have emerged as powerful tools for molecular generation, particularly in the context of 3D molecular structures. Inspired by non-equilibrium statistical physics, these models can generate 3D molecular structures with specific properties or requirements crucial to drug discovery. Diffusion models were particularly successful at learning 3D molecular geometries' complex probability distributions and their corresponding chemical and physical properties through forward and reverse diffusion processes. This review focuses on the technical implementation of diffusion models tailored for 3D molecular generation. It compares the performance, evaluation methods, and implementation details of various diffusion models used for molecular generation tasks. We cover strategies for atom and bond representation, architectures of reverse diffusion denoising networks, and challenges associated with generating stable 3D molecular structures. This review also explores the applications of diffusion models in $\textit{de novo}$ drug design and related areas of computational chemistry, such as structure-based drug design, including target-specific molecular generation, molecular docking, and molecular dynamics of protein-ligand complexes. We also cover conditional generation on physical properties, conformation generation, and fragment-based drug design. By summarizing the state-of-the-art diffusion models for 3D molecular generation, this review sheds light on their role in advancing drug discovery as well as their current limitations.

Dhananjay Ashok, Atharva Kulkarni, Hai Pham et al.

Due to the prohibitively high cost of creating error correction datasets, most Factual Claim Correction methods rely on a powerful verification model to guide the correction process. This leads to a significant drop in performance in domains like scientific claims, where good verification models do not always exist. In this work, we introduce SciFix, a scientific claim correction system that does not require a verifier but can outperform existing methods by a considerable margin -- achieving correction accuracy of 84% on the SciFact dataset, 77% on SciFact-Open and 72% on the CovidFact dataset, compared to next best accuracies of 7%, 5%, and 15% on the same datasets respectively. Our method leverages the power of prompting with LLMs during training to create a richly annotated dataset that can be used for fully supervised training and regularization. We additionally use a claim-aware decoding procedure to improve the quality of corrected claims. Our method outperforms the very LLM that was used to generate the annotated dataset -- with Few-Shot Prompting on GPT3.5 achieving 58%, 61%, and 64% on the respective datasets, a consistently lower correction accuracy, despite using nearly 800 times as many parameters as our model.

Otilia Stretcu, Emmanouil Antonios Platanios, Tom M. Mitchell et al.

When faced with learning challenging new tasks, humans often follow sequences of steps that allow them to incrementally build up the necessary skills for performing these new tasks. However, in machine learning, models are most often trained to solve the target tasks directly.Inspired by human learning, we propose a novel curriculum learning approach which decomposes challenging tasks into sequences of easier intermediate goals that are used to pre-train a model before tackling the target task. We focus on classification tasks, and design the intermediate tasks using an automatically constructed label hierarchy. We train the model at each level of the hierarchy, from coarse labels to fine labels, transferring acquired knowledge across these levels. For instance, the model will first learn to distinguish animals from objects, and then use this acquired knowledge when learning to classify among more fine-grained classes such as cat, dog, car, and truck. Most existing curriculum learning algorithms for supervised learning consist of scheduling the order in which the training examples are presented to the model. In contrast, our approach focuses on the output space of the model. We evaluate our method on several established datasets and show significant performance gains especially on classification problems with many labels. We also evaluate on a new synthetic dataset which allows us to study multiple aspects of our method.

George Stoica, Emmanouil Antonios Platanios, Barnabás Póczos

TACRED is one of the largest and most widely used sentence-level relation extraction datasets. Proposed models that are evaluated using this dataset consistently set new state-of-the-art performance. However, they still exhibit large error rates despite leveraging external knowledge and unsupervised pretraining on large text corpora. A recent study suggested that this may be due to poor dataset quality. The study observed that over 50% of the most challenging sentences from the development and test sets are incorrectly labeled and account for an average drop of 8% f1-score in model performance. However, this study was limited to a small biased sample of 5k (out of a total of 106k) sentences, substantially restricting the generalizability and broader implications of its findings. In this paper, we address these shortcomings by: (i) performing a comprehensive study over the whole TACRED dataset, (ii) proposing an improved crowdsourcing strategy and deploying it to re-annotate the whole dataset, and (iii) performing a thorough analysis to understand how correcting the TACRED annotations affects previously published results. After verification, we observed that 23.9% of TACRED labels are incorrect. Moreover, evaluating several models on our revised dataset yields an average f1-score improvement of 14.3% and helps uncover significant relationships between the different models (rather than simply offsetting or scaling their scores by a constant factor). Finally, aside from our analysis we also release Re-TACRED, a new completely re-annotated version of the TACRED dataset that can be used to perform reliable evaluation of relation extraction models.

Yiwei Lyu, Paul Pu Liang, Hai Pham et al.

Text style transfer aims to controllably generate text with targeted stylistic changes while maintaining core meaning from the source sentence constant. Many of the existing style transfer benchmarks primarily focus on individual high-level semantic changes (e.g. positive to negative), which enable controllability at a high level but do not offer fine-grained control involving sentence structure, emphasis, and content of the sentence. In this paper, we introduce a large-scale benchmark, StylePTB, with (1) paired sentences undergoing 21 fine-grained stylistic changes spanning atomic lexical, syntactic, semantic, and thematic transfers of text, as well as (2) compositions of multiple transfers which allow modeling of fine-grained stylistic changes as building blocks for more complex, high-level transfers. By benchmarking existing methods on StylePTB, we find that they struggle to model fine-grained changes and have an even more difficult time composing multiple styles. As a result, StylePTB brings novel challenges that we hope will encourage future research in controllable text style transfer, compositional models, and learning disentangled representations. Solving these challenges would present important steps towards controllable text generation.

George Stoica, Emmanouil Antonios Platanios, Barnabás Póczos

Relation extraction (RE) aims to predict a relation between a subject and an object in a sentence, while knowledge graph link prediction (KGLP) aims to predict a set of objects, O, given a subject and a relation from a knowledge graph. These two problems are closely related as their respective objectives are intertwined: given a sentence containing a subject and an object o, a RE model predicts a relation that can then be used by a KGLP model together with the subject, to predict a set of objects O. Thus, we expect object o to be in set O. In this paper, we leverage this insight by proposing a multi-task learning approach that improves the performance of RE models by jointly training on RE and KGLP tasks. We illustrate the generality of our approach by applying it on several existing RE models and empirically demonstrate how it helps them achieve consistent performance gains.

Zirui Wang, Sanket Vaibhav Mehta, Barnabás Póczos et al.

Current natural language processing models work well on a single task, yet they often fail to continuously learn new tasks without forgetting previous ones as they are re-trained throughout their lifetime, a challenge known as lifelong learning. State-of-the-art lifelong language learning methods store past examples in episodic memory and replay them at both training and inference time. However, as we show later in our experiments, there are three significant impediments: (1) needing unrealistically large memory module to achieve good performance, (2) suffering from negative transfer, (3) requiring multiple local adaptation steps for each test example that significantly slows down the inference speed. In this paper, we identify three common principles of lifelong learning methods and propose an efficient meta-lifelong framework that combines them in a synergistic fashion. To achieve sample efficiency, our method trains the model in a manner that it learns a better initialization for local adaptation. Extensive experiments on text classification and question answering benchmarks demonstrate the effectiveness of our framework by achieving state-of-the-art performance using merely 1% memory size and narrowing the gap with multi-task learning. We further show that our method alleviates both catastrophic forgetting and negative transfer at the same time.

Mariya Toneva, Otilia Stretcu, Barnabas Poczos et al.

How meaning is represented in the brain is still one of the big open questions in neuroscience. Does a word (e.g., bird) always have the same representation, or does the task under which the word is processed alter its representation (answering "can you eat it?" versus "can it fly?")? The brain activity of subjects who read the same word while performing different semantic tasks has been shown to differ across tasks. However, it is still not understood how the task itself contributes to this difference. In the current work, we study Magnetoencephalography (MEG) brain recordings of participants tasked with answering questions about concrete nouns. We investigate the effect of the task (i.e. the question being asked) on the processing of the concrete noun by predicting the millisecond-resolution MEG recordings as a function of both the semantics of the noun and the task. Using this approach, we test several hypotheses about the task-stimulus interactions by comparing the zero-shot predictions made by these hypotheses for novel tasks and nouns not seen during training. We find that incorporating the task semantics significantly improves the prediction of MEG recordings, across participants. The improvement occurs 475-550ms after the participants first see the word, which corresponds to what is considered to be the ending time of semantic processing for a word. These results suggest that only the end of semantic processing of a word is task-dependent, and pose a challenge for future research to formulate new hypotheses for earlier task effects as a function of the task and stimuli.

Hai Pham, Amrith Setlur, Saket Dingliwal et al.

Despite the advent of deep learning in computer vision, the general handwriting recognition problem is far from solved. Most existing approaches focus on handwriting datasets that have clearly written text and carefully segmented labels. In this paper, we instead focus on learning handwritten characters from maintenance logs, a constrained setting where data is very limited and noisy. We break the problem into two consecutive stages of word segmentation and word recognition respectively and utilize data augmentation techniques to train both stages. Extensive comparisons with popular baselines for scene-text detection and word recognition show that our system achieves a lower error rate and is more suited to handle noisy and difficult documents

Amrith Setlur, Barnabas Poczos, Alan W Black

This paper extends recent work on nonlinear Independent Component Analysis (ICA) by introducing a theoretical framework for nonlinear Independent Subspace Analysis (ISA) in the presence of auxiliary variables. Observed high dimensional acoustic features like log Mel spectrograms can be considered as surface level manifestations of nonlinear transformations over individual multivariate sources of information like speaker characteristics, phonological content etc. Under assumptions of energy based models we use the theory of nonlinear ISA to propose an algorithm that learns unsupervised speech representations whose subspaces are independent and potentially highly correlated with the original non-stationary multivariate sources. We show how nonlinear ICA with auxiliary variables can be extended to a generic identifiable model for subspaces as well while also providing sufficient conditions for the identifiability of these high dimensional subspaces. Our proposed methodology is generic and can be integrated with standard unsupervised approaches to learn speech representations with subspaces that can theoretically capture independent higher order speech signals. We evaluate the gains of our algorithm when integrated with the Autoregressive Predictive Decoding (APC) model by showing empirical results on the speaker verification and phoneme recognition tasks.

Amrith Setlur, Saket Dingliwal, Barnabas Poczos

Meta-learning has proven to be successful for few-shot learning across the regression, classification, and reinforcement learning paradigms. Recent approaches have adopted Bayesian interpretations to improve gradient-based meta-learners by quantifying the uncertainty of the post-adaptation estimates. Most of these works almost completely ignore the latent relationship between the covariate distribution $(p(x))$ of a task and the corresponding conditional distribution $p(y|x)$. In this paper, we identify the need to explicitly model the meta-distribution over the task covariates in a hierarchical Bayesian framework. We begin by introducing a graphical model that leverages the samples from the marginal $p(x)$ to better infer the posterior over the optimal parameters of the conditional distribution $(p(y|x))$ for each task. Based on this model we propose a computationally feasible meta-learning algorithm by introducing meaningful relaxations in our final objective. We demonstrate the gains of our algorithm over initialization based meta-learning baselines on popular classification benchmarks. Finally, to understand the potential benefit of modeling task covariates we further evaluate our method on a synthetic regression dataset.

Aman Madaan, Amrith Setlur, Tanmay Parekh et al.

This paper introduces a new task of politeness transfer which involves converting non-polite sentences to polite sentences while preserving the meaning. We also provide a dataset of more than 1.39 instances automatically labeled for politeness to encourage benchmark evaluations on this new task. We design a tag and generate pipeline that identifies stylistic attributes and subsequently generates a sentence in the target style while preserving most of the source content. For politeness as well as five other transfer tasks, our model outperforms the state-of-the-art methods on automatic metrics for content preservation, with a comparable or better performance on style transfer accuracy. Additionally, our model surpasses existing methods on human evaluations for grammaticality, meaning preservation and transfer accuracy across all the six style transfer tasks. The data and code is located at https://github.com/tag-and-generate.

Ananya Uppal, Shashank Singh, Barnabas Poczos

We study minimax convergence rates of nonparametric density estimation in the Huber contamination model, in which a proportion of the data comes from an unknown outlier distribution. We provide the first results for this problem under a large family of losses, called Besov integral probability metrics (IPMs), that includes $\mathcal{L}^p$, Wasserstein, Kolmogorov-Smirnov, and other common distances between probability distributions. Specifically, under a range of smoothness assumptions on the population and outlier distributions, we show that a re-scaled thresholding wavelet series estimator achieves minimax optimal convergence rates under a wide variety of losses. Finally, based on connections that have recently been shown between nonparametric density estimation under IPM losses and generative adversarial networks (GANs), we show that certain GAN architectures also achieve these minimax rates.

Biswajit Paria, Chih-Kuan Yeh, Ian E. H. Yen et al.

Deep representation learning has become one of the most widely adopted approaches for visual search, recommendation, and identification. Retrieval of such representations from a large database is however computationally challenging. Approximate methods based on learning compact representations, have been widely explored for this problem, such as locality sensitive hashing, product quantization, and PCA. In this work, in contrast to learning compact representations, we propose to learn high dimensional and sparse representations that have similar representational capacity as dense embeddings while being more efficient due to sparse matrix multiplication operations which can be much faster than dense multiplication. Following the key insight that the number of operations decreases quadratically with the sparsity of embeddings provided the non-zero entries are distributed uniformly across dimensions, we propose a novel approach to learn such distributed sparse embeddings via the use of a carefully constructed regularization function that directly minimizes a continuous relaxation of the number of floating-point operations (FLOPs) incurred during retrieval. Our experiments show that our approach is competitive to the other baselines and yields a similar or better speed-vs-accuracy tradeoff on practical datasets.

Ilqar Ramazanli, Han Nguyen, Hai Pham et al.

We study distributed optimization algorithms for minimizing the average of \emph{heterogeneous} functions distributed across several machines with a focus on communication efficiency. In such settings, naively using the classical stochastic gradient descent (SGD) or its variants (e.g., SVRG) with a uniform sampling of machines typically yields poor performance. It often leads to the dependence of convergence rate on maximum Lipschitz constant of gradients across the devices. In this paper, we propose a novel \emph{adaptive} sampling of machines specially catered to these settings. Our method relies on an adaptive estimate of local Lipschitz constants base on the information of past gradients. We show that the new way improves the dependence of convergence rate from maximum Lipschitz constant to \emph{average} Lipschitz constant across machines, thereby, significantly accelerating the convergence. Our experiments demonstrate that our method indeed speeds up the convergence of the standard SVRG algorithm in heterogeneous environments.

Ilqar Ramazanli, Barnabas Poczos

We study the problem of exact completion for $m \times n$ sized matrix of rank $r$ with the adaptive sampling method. We introduce a relation of the exact completion problem with the sparsest vector of column and row spaces (which we call \textit{sparsity-number} here). Using this relation, we propose matrix completion algorithms that exactly recovers the target matrix. These algorithms are superior to previous works in two important ways. First, our algorithms exactly recovers $μ_0$-coherent column space matrices by probability at least $1 - ε$ using much smaller observations complexity than $\mathcal{O}(μ_0 rn \mathrm{log}\frac{r}ε)$ the state of art. Specifically, many of the previous adaptive sampling methods require to observe the entire matrix when the column space is highly coherent. However, we show that our method is still able to recover this type of matrices by observing a small fraction of entries under many scenarios. Second, we propose an exact completion algorithm, which requires minimal pre-information as either row or column space is not being highly coherent. At the end of the paper, we provide experimental results that illustrate the strength of the algorithms proposed here.

Chenghui Zhou, Chun-Liang Li, Barnabas Poczos

Program synthesis has emerged as a successful approach to the image parsing task. Most prior works rely on a two-step scheme involving supervised pretraining of a Seq2Seq model with synthetic programs followed by reinforcement learning (RL) for fine-tuning with real reference images. Fully unsupervised approaches promise to train the model directly on the target images without requiring curated pretraining datasets. However, they struggle with the inherent sparsity of meaningful programs in the search space. In this paper, we present the first unsupervised algorithm capable of parsing constructive solid geometry (CSG) images into context-free grammar (CFG) without pretraining via non-differentiable renderer. To tackle the \emph{non-Markovian} sparse reward problem, we combine three key ingredients -- (i) a grammar-encoded tree LSTM ensuring program validity (ii) entropy regularization and (iii) sampling without replacement from the CFG syntax tree. Empirically, our algorithm recovers meaningful programs in large search spaces (up to $3.8 \times 10^{28}$). Further, even though our approach is fully unsupervised, it generalizes better than supervised methods on the synthetic 2D CSG dataset. On the 2D computer aided design (CAD) dataset, our approach significantly outperforms the supervised pretrained model and is competitive to the refined model.

Austin Dill, Songwei Ge, Eunsu Kang et al.

In order to generate novel 3D shapes with machine learning, one must allow for interpolation. The typical approach for incorporating this creative process is to interpolate in a learned latent space so as to avoid the problem of generating unrealistic instances by exploiting the model's learned structure. The process of the interpolation is supposed to form a semantically smooth morphing. While this approach is sound for synthesizing realistic media such as lifelike portraits or new designs for everyday objects, it subjectively fails to directly model the unexpected, unrealistic, or creative. In this work, we present a method for learning how to interpolate point clouds. By encoding prior knowledge about real-world objects, the intermediate forms are both realistic and unlike any existing forms. We show not only how this method can be used to generate "creative" point clouds, but how the method can also be leveraged to generate 3D models suitable for sculpture.

Joel Ruben Antony Moniz, Eunsu Kang, Barnabás Póczos

In this work, we aim to propose a set of techniques to improve the controllability and aesthetic appeal when DeepDream, which uses a pre-trained neural network to modify images by hallucinating objects into them, is applied to videos. In particular, we demonstrate a simple modification that improves control over the class of object that DeepDream is induced to hallucinate. We also show that the flickering artifacts which frequently appear when DeepDream is applied on videos can be mitigated by the use of an additional temporal consistency loss term.

Amrith Setlur, Barnabás Póczós

Temporal Point Processes (TPP) with partial likelihoods involving a latent structure often entail an intractable marginalization, thus making inference hard. We propose a novel approach to Maximum Likelihood Estimation (MLE) involving approximate inference over the latent variables by minimizing a tight upper bound on the approximation gap. Given a discrete latent variable $Z$, the proposed approximation reduces inference complexity from $O(|Z|^c)$ to $O(|Z|)$. We use convex conjugates to determine this upper bound in a closed form and show that its addition to the optimization objective results in improved results for models assuming proportional hazards as in Survival Analysis.

Adarsh Dave, Jared Mitchell, Kirthevasan Kandasamy et al.

Innovations in batteries take years to formulate and commercialize, requiring extensive experimentation during the design and optimization phases. We approached the design and selection of a battery electrolyte through a black-box optimization algorithm directly integrated into a robotic test-stand. We report here the discovery of a novel battery electrolyte by this experiment completely guided by the machine-learning software without human intervention. Motivated by the recent trend toward super-concentrated aqueous electrolytes for high-performance batteries, we utilize Dragonfly - a Bayesian machine-learning software package - to search mixtures of commonly used lithium and sodium salts for super-concentrated aqueous electrolytes with wide electrochemical stability windows. Dragonfly autonomously managed the robotic test-stand, recommending electrolyte designs to test and receiving experimental feedback in real time. In 40 hours of continuous experimentation over a four-dimensional design space with millions of potential candidates, Dragonfly discovered a novel, mixed-anion aqueous sodium electrolyte with a wider electrochemical stability window than state-of-the-art sodium electrolyte. A human-guided design process may have missed this optimal electrolyte. This result demonstrates the possibility of integrating robotics with machine-learning to rapidly and autonomously discover novel battery materials.

Songwei Ge, Austin Dill, Eunsu Kang et al.

We explore the intersection of human and machine creativity by generating sculptural objects through machine learning. This research raises questions about both the technical details of automatic art generation and the interaction between AI and people, as both artists and the audience of art. We introduce two algorithms for generating 3D point clouds and then discuss their actualization as sculpture and incorporation into a holistic art installation. Specifically, the Amalgamated DeepDream (ADD) algorithm solves the sparsity problem caused by the naive DeepDream-inspired approach and generates creative and printable point clouds. The Partitioned DeepDream (PDD) algorithm further allows us to explore more diverse 3D object creation by combining point cloud clustering algorithms and ADD.

Ksenia Korovina, Sailun Xu, Kirthevasan Kandasamy et al.

In applications such as molecule design or drug discovery, it is desirable to have an algorithm which recommends new candidate molecules based on the results of past tests. These molecules first need to be synthesized and then tested for objective properties. We describe ChemBO, a Bayesian optimization framework for generating and optimizing organic molecules for desired molecular properties. While most existing data-driven methods for this problem do not account for sample efficiency or fail to enforce realistic constraints on synthesizability, our approach explores the synthesis graph in a sample-efficient way and produces synthesizable candidates. We implement ChemBO as a Gaussian process model and explore existing molecular kernels for it. Moreover, we propose a novel optimal-transport based distance and kernel that accounts for graphical information explicitly. In our experiments, we demonstrate the efficacy of the proposed approach on several molecular optimization problems.

Haiguang Liao, Wentai Zhang, Xuliang Dong et al.

Global routing has been a historically challenging problem in electronic circuit design, where the challenge is to connect a large and arbitrary number of circuit components with wires without violating the design rules for the printed circuit boards or integrated circuits. Similar routing problems also exist in the design of complex hydraulic systems, pipe systems and logistic networks. Existing solutions typically consist of greedy algorithms and hard-coded heuristics. As such, existing approaches suffer from a lack of model flexibility and non-optimum solutions. As an alternative approach, this work presents a deep reinforcement learning method for solving the global routing problem in a simulated environment. At the heart of the proposed method is deep reinforcement learning that enables an agent to produce an optimal policy for routing based on the variety of problems it is presented with leveraging the conjoint optimization mechanism of deep reinforcement learning. Conjoint optimization mechanism is explained and demonstrated in details; the best network structure and the parameters of the learned model are explored. Based on the fine-tuned model, routing solutions and rewards are presented and analyzed. The results indicate that the approach can outperform the benchmark method of a sequential A* method, suggesting a promising potential for deep reinforcement learning for global routing and other routing or path planning problems in general. Another major contribution of this work is the development of a global routing problem sets generator with the ability to generate parameterized global routing problem sets with different size and constraints, enabling evaluation of different routing algorithms and the generation of training datasets for future data-driven routing approaches.

Simon S. Du, Kangcheng Hou, Barnabás Póczos et al.

While graph kernels (GKs) are easy to train and enjoy provable theoretical guarantees, their practical performances are limited by their expressive power, as the kernel function often depends on hand-crafted combinatorial features of graphs. Compared to graph kernels, graph neural networks (GNNs) usually achieve better practical performance, as GNNs use multi-layer architectures and non-linear activation functions to extract high-order information of graphs as features. However, due to the large number of hyper-parameters and the non-convex nature of the training procedure, GNNs are harder to train. Theoretical guarantees of GNNs are also not well-understood. Furthermore, the expressive power of GNNs scales with the number of parameters, and thus it is hard to exploit the full power of GNNs when computing resources are limited. The current paper presents a new class of graph kernels, Graph Neural Tangent Kernels (GNTKs), which correspond to infinitely wide multi-layer GNNs trained by gradient descent. GNTKs enjoy the full expressive power of GNNs and inherit advantages of GKs. Theoretically, we show GNTKs provably learn a class of smooth functions on graphs. Empirically, we test GNTKs on graph classification datasets and show they achieve strong performance.

Chun-Liang Li, Tomas Simon, Jason Saragih et al.

We present LBS-AE; a self-supervised autoencoding algorithm for fitting articulated mesh models to point clouds. As input, we take a sequence of point clouds to be registered as well as an artist-rigged mesh, i.e. a template mesh equipped with a linear-blend skinning (LBS) deformation space parameterized by a skeleton hierarchy. As output, we learn an LBS-based autoencoder that produces registered meshes from the input point clouds. To bridge the gap between the artist-defined geometry and the captured point clouds, our autoencoder models pose-dependent deviations from the template geometry. During training, instead of using explicit correspondences, such as key points or pose supervision, our method leverages LBS deformations to bootstrap the learning process. To avoid poor local minima from erroneous point-to-point correspondences, we utilize a structured Chamfer distance based on part-segmentations, which are learned concurrently using self-supervision. We demonstrate qualitative results on real captured hands, and report quantitative evaluations on the FAUST benchmark for body registration. Our method achieves performance that is superior to other unsupervised approaches and comparable to methods using supervised examples.

Emmanouil Antonios Platanios, Otilia Stretcu, Graham Neubig et al.

Current state-of-the-art NMT systems use large neural networks that are not only slow to train, but also often require many heuristics and optimization tricks, such as specialized learning rate schedules and large batch sizes. This is undesirable as it requires extensive hyperparameter tuning. In this paper, we propose a curriculum learning framework for NMT that reduces training time, reduces the need for specialized heuristics or large batch sizes, and results in overall better performance. Our framework consists of a principled way of deciding which training samples are shown to the model at different times during training, based on the estimated difficulty of a sample and the current competence of the model. Filtering training samples in this manner prevents the model from getting stuck in bad local optima, making it converge faster and reach a better solution than the common approach of uniformly sampling training examples. Furthermore, the proposed method can be easily applied to existing NMT models by simply modifying their input data pipelines. We show that our framework can help improve the training time and the performance of both recurrent neural network models and Transformers, achieving up to a 70% decrease in training time, while at the same time obtaining accuracy improvements of up to 2.2 BLEU.

Chun-Liang Li, Wei-Cheng Chang, Youssef Mroueh et al.

Kernels are powerful and versatile tools in machine learning and statistics. Although the notion of universal kernels and characteristic kernels has been studied, kernel selection still greatly influences the empirical performance. While learning the kernel in a data driven way has been investigated, in this paper we explore learning the spectral distribution of kernel via implicit generative models parametrized by deep neural networks. We called our method Implicit Kernel Learning (IKL). The proposed framework is simple to train and inference is performed via sampling random Fourier features. We investigate two applications of the proposed IKL as examples, including generative adversarial networks with MMD (MMD GAN) and standard supervised learning. Empirically, MMD GAN with IKL outperforms vanilla predefined kernels on both image and text generation benchmarks; using IKL with Random Kitchen Sinks also leads to substantial improvement over existing state-of-the-art kernel learning algorithms on popular supervised learning benchmarks. Theory and conditions for using IKL in both applications are also studied as well as connections to previous state-of-the-art methods.

Michael Andrews, John Alison, Sitong An et al.

We describe the construction of end-to-end jet image classifiers based on simulated low-level detector data to discriminate quark- vs. gluon-initiated jets with high-fidelity simulated CMS Open Data. We highlight the importance of precise spatial information and demonstrate competitive performance to existing state-of-the-art jet classifiers. We further generalize the end-to-end approach to event-level classification of quark vs. gluon di-jet QCD events. We compare the fully end-to-end approach to using hand-engineered features and demonstrate that the end-to-end algorithm is robust against the effects of underlying event and pile-up.

Ananya Uppal, Shashank Singh, Barnabás Póczos

We study the problem of estimating a nonparametric probability density under a large family of losses called Besov IPMs, which include, for example, $\mathcal{L}^p$ distances, total variation distance, and generalizations of both Wasserstein and Kolmogorov-Smirnov distances. For a wide variety of settings, we provide both lower and upper bounds, identifying precisely how the choice of loss function and assumptions on the data interact to determine the minimax optimal convergence rate. We also show that linear distribution estimates, such as the empirical distribution or kernel density estimator, often fail to converge at the optimal rate. Our bounds generalize, unify, or improve several recent and classical results. Moreover, IPMs can be used to formalize a statistical model of generative adversarial networks (GANs). Thus, we show how our results imply bounds on the statistical error of a GAN, showing, for example, that GANs can strictly outperform the best linear estimator.

Willie Neiswanger, Kirthevasan Kandasamy, Barnabas Poczos et al.

Optimizing an expensive-to-query function is a common task in science and engineering, where it is beneficial to keep the number of queries to a minimum. A popular strategy is Bayesian optimization (BO), which leverages probabilistic models for this task. Most BO today uses Gaussian processes (GPs), or a few other surrogate models. However, there is a broad set of Bayesian modeling techniques that could be used to capture complex systems and reduce the number of queries in BO. Probabilistic programming languages (PPLs) are modern tools that allow for flexible model definition, prior specification, model composition, and automatic inference. In this paper, we develop ProBO, a BO procedure that uses only standard operations common to most PPLs. This allows a user to drop in a model built with an arbitrary PPL and use it directly in BO. We describe acquisition functions for ProBO, and strategies for efficiently optimizing these functions given complex models or costly inference procedures. Using existing PPLs, we implement new models to aid in a few challenging optimization settings, and demonstrate these on model hyperparameter and architecture search tasks.

Wei-Cheng Chang, Chun-Liang Li, Yiming Yang et al.

Detecting the emergence of abrupt property changes in time series is a challenging problem. Kernel two-sample test has been studied for this task which makes fewer assumptions on the distributions than traditional parametric approaches. However, selecting kernels is non-trivial in practice. Although kernel selection for two-sample test has been studied, the insufficient samples in change point detection problem hinder the success of those developed kernel selection algorithms. In this paper, we propose KL-CPD, a novel kernel learning framework for time series CPD that optimizes a lower bound of test power via an auxiliary generative model. With deep kernel parameterization, KL-CPD endows kernel two-sample test with the data-driven kernel to detect different types of change-points in real-world applications. The proposed approach significantly outperformed other state-of-the-art methods in our comparative evaluation of benchmark datasets and simulation studies.

Hai Pham, Paul Pu Liang, Thomas Manzini et al.

Multimodal sentiment analysis is a core research area that studies speaker sentiment expressed from the language, visual, and acoustic modalities. The central challenge in multimodal learning involves inferring joint representations that can process and relate information from these modalities. However, existing work learns joint representations by requiring all modalities as input and as a result, the learned representations may be sensitive to noisy or missing modalities at test time. With the recent success of sequence to sequence (Seq2Seq) models in machine translation, there is an opportunity to explore new ways of learning joint representations that may not require all input modalities at test time. In this paper, we propose a method to learn robust joint representations by translating between modalities. Our method is based on the key insight that translation from a source to a target modality provides a method of learning joint representations using only the source modality as input. We augment modality translations with a cycle consistency loss to ensure that our joint representations retain maximal information from all modalities. Once our translation model is trained with paired multimodal data, we only need data from the source modality at test time for final sentiment prediction. This ensures that our model remains robust from perturbations or missing information in the other modalities. We train our model with a coupled translation-prediction objective and it achieves new state-of-the-art results on multimodal sentiment analysis datasets: CMU-MOSI, ICT-MMMO, and YouTube. Additional experiments show that our model learns increasingly discriminative joint representations with more input modalities while maintaining robustness to missing or perturbed modalities.

Zirui Wang, Zihang Dai, Barnabás Póczos et al.

When labeled data is scarce for a specific target task, transfer learning often offers an effective solution by utilizing data from a related source task. However, when transferring knowledge from a less related source, it may inversely hurt the target performance, a phenomenon known as negative transfer. Despite its pervasiveness, negative transfer is usually described in an informal manner, lacking rigorous definition, careful analysis, or systematic treatment. This paper proposes a formal definition of negative transfer and analyzes three important aspects thereof. Stemming from this analysis, a novel technique is proposed to circumvent negative transfer by filtering out unrelated source data. Based on adversarial networks, the technique is highly generic and can be applied to a wide range of transfer learning algorithms. The proposed approach is evaluated on six state-of-the-art deep transfer methods via experiments on four benchmark datasets with varying levels of difficulty. Empirically, the proposed method consistently improves the performance of all baseline methods and largely avoids negative transfer, even when the source data is degenerate.

Siyu He, Yin Li, Yu Feng et al.

Matter evolved under influence of gravity from minuscule density fluctuations. Non-perturbative structure formed hierarchically over all scales, and developed non-Gaussian features in the Universe, known as the Cosmic Web. To fully understand the structure formation of the Universe is one of the holy grails of modern astrophysics. Astrophysicists survey large volumes of the Universe and employ a large ensemble of computer simulations to compare with the observed data in order to extract the full information of our own Universe. However, to evolve trillions of galaxies over billions of years even with the simplest physics is a daunting task. We build a deep neural network, the Deep Density Displacement Model (hereafter D$^3$M), to predict the non-linear structure formation of the Universe from simple linear perturbation theory. Our extensive analysis, demonstrates that D$^3$M outperforms the second order perturbation theory (hereafter 2LPT), the commonly used fast approximate simulation method, in point-wise comparison, 2-point correlation, and 3-point correlation. We also show that D$^3$M is able to accurately extrapolate far beyond its training data, and predict structure formation for significantly different cosmological parameters. Our study proves, for the first time, that deep learning is a practical and accurate alternative to approximate simulations of the gravitational structure formation of the Universe.

Chun-Liang Li, Eunsu Kang, Songwei Ge et al.

Our team of artists and machine learning researchers designed a creative algorithm that can generate authentic sculptural artworks. These artworks do not mimic any given forms and cannot be easily categorized into the dataset categories. Our approach extends DeepDream from images to 3D point clouds. The proposed algorithm, Amalgamated DeepDream (ADD), leverages the properties of point clouds to create objects with better quality than the naive extension. ADD presents promise for the creativity of machines, the kind of creativity that pushes artists to explore novel methods or materials and to create new genres instead of creating variations of existing forms or styles within one genre. For example, from Realism to Abstract Expressionism, or to Minimalism. Lastly, we present the sculptures that are 3D printed based on the point clouds created by ADD.

Chun-Liang Li, Manzil Zaheer, Yang Zhang et al.

Generative Adversarial Networks (GAN) can achieve promising performance on learning complex data distributions on different types of data. In this paper, we first show a straightforward extension of existing GAN algorithm is not applicable to point clouds, because the constraint required for discriminators is undefined for set data. We propose a two fold modification to GAN algorithm for learning to generate point clouds (PC-GAN). First, we combine ideas from hierarchical Bayesian modeling and implicit generative models by learning a hierarchical and interpretable sampling process. A key component of our method is that we train a posterior inference network for the hidden variables. Second, instead of using only state-of-the-art Wasserstein GAN objective, we propose a sandwiching objective, which results in a tighter Wasserstein distance estimate than the commonly used dual form. Thereby, PC-GAN defines a generic framework that can incorporate many existing GAN algorithms. We validate our claims on ModelNet40 benchmark dataset. Using the distance between generated point clouds and true meshes as metric, we find that PC-GAN trained by the sandwiching objective achieves better results on test data than the existing methods. Moreover, as a byproduct, PC- GAN learns versatile latent representations of point clouds, which can achieve competitive performance with other unsupervised learning algorithms on object recognition task. Lastly, we also provide studies on generating unseen classes of objects and transforming image to point cloud, which demonstrates the compelling generalization capability and potentials of PC-GAN.

Simon S. Du, Xiyu Zhai, Barnabas Poczos et al.

One of the mysteries in the success of neural networks is randomly initialized first order methods like gradient descent can achieve zero training loss even though the objective function is non-convex and non-smooth. This paper demystifies this surprising phenomenon for two-layer fully connected ReLU activated neural networks. For an $m$ hidden node shallow neural network with ReLU activation and $n$ training data, we show as long as $m$ is large enough and no two inputs are parallel, randomly initialized gradient descent converges to a globally optimal solution at a linear convergence rate for the quadratic loss function. Our analysis relies on the following observation: over-parameterization and random initialization jointly restrict every weight vector to be close to its initialization for all iterations, which allows us to exploit a strong convexity-like property to show that gradient descent converges at a global linear rate to the global optimum. We believe these insights are also useful in analyzing deep models and other first order methods.