arXiv subjects

Tommi Jaakkola

Publications and source records attributed to Tommi Jaakkola.

At least 127 records · Page 7Linked to original sources

arXiv2019

Analyzing Learned Molecular Representations for Property Prediction

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

cs.LG↗

arXiv2019

Hierarchical Graph-to-Graph Translation for Molecules

The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving the encoding of substructure components with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its attachment to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model significantly outperforms previous state-of-the-art baselines.

physics.chem-ph↗

arXiv2019

Solving graph compression via optimal transport

We propose a new approach to graph compression by appeal to optimal transport. The transport problem is seeded with prior information about node importance, attributes, and edges in the graph. The transport formulation can be setup for either directed or undirected graphs, and its dual characterization is cast in terms of distributions over the nodes. The compression pertains to the support of node distributions and makes the problem challenging to solve directly. To this end, we introduce Boolean relaxations and specify conditions under which these relaxations are exact. The relaxations admit algorithms with provably fast convergence. Moreover, we provide an exact $O(d \log d)$ algorithm for the subproblem of projecting a $d$-dimensional vector to transformed simplex constraints. Our method outperforms state-of-the-art compression methods on graph classification.

cs.LG↗

arXiv2019

Strategic Prediction with Latent Aggregative Games

We introduce a new class of context dependent, incomplete information games to serve as structured prediction models for settings with significant strategic interactions. Our games map the input context to outcomes by first condensing the input into private player types that specify the utilities, weighted interactions, as well as the initial strategies for the players. The game is played over multiple rounds where players respond to weighted aggregates of their neighbors' strategies. The predicted output from the model is a mixed strategy profile (a near-Nash equilibrium) and each observation is thought of as a sample from this strategy profile. We introduce two new aggregator paradigms with provably convergent game dynamics, and characterize the conditions under which our games are identifiable from data. Our games can be parameterized in a transferable manner so that the sets of players can change from one game to another. We demonstrate empirically that our games as models can recover meaningful strategic interactions from real voting data.

cs.LG↗

arXiv2019

Path-Augmented Graph Transformer Network

Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we propose Path-Augmented Graph Transformer Networks (PAGTN) that are explicitly built on longer-range dependencies in graph-structured data. Specifically, we use path features in molecular graphs to create global attention layers. We compare our PAGTN model against the GCN model and show that our model consistently outperforms GCNs on molecular property prediction datasets including quantum chemistry (QM7, QM8, QM9), physical chemistry (ESOL, Lipophilictiy) and biochemistry (BACE, BBBP).

cs.LG↗

arXiv2019

Junction Tree Variational Autoencoder for Molecular Graph Generation

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

cs.LG↗

arXiv2019

Alignment Based Matching Networks for One-Shot Classification and Open-Set Recognition

Deep learning for object classification relies heavily on convolutional models. While effective, CNNs are rarely interpretable after the fact. An attention mechanism can be used to highlight the area of the image that the model focuses on thus offering a narrow view into the mechanism of classification. We expand on this idea by forcing the method to explicitly align images to be classified to reference images representing the classes. The mechanism of alignment is learned and therefore does not require that the reference objects are anything like those being classified. Beyond explanation, our exemplar based cross-alignment method enables classification with only a single example per category (one-shot). Our model cuts the 5-way, 1-shot error rate in Omniglot from 2.1% to 1.4% and in MiniImageNet from 53.5% to 46.5% while simultaneously providing point-wise alignment information providing some understanding on what the network is capturing. This method of alignment also enables the recognition of an unsupported class (open-set) in the one-shot setting while maintaining an F1-score of above 0.5 for Omniglot even with 19 other distracting classes while baselines completely fail to separate the open-set class in the one-shot setting.

cs.CV↗

arXiv2019

Learning Multimodal Graph-to-Graph Translation for Molecular Optimization

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph. A key challenge is therefore to model diverse translation outputs. Our primary contributions include a junction tree encoder-decoder for learning diverse graph translations along with a novel adversarial training method for aligning distributions of molecules. Diverse output distributions in our model are explicitly realized by low-dimensional latent vectors that modulate the translation process. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines.

cs.LG↗

arXiv2018

Grounding Language for Transfer in Deep Reinforcement Learning

In this paper, we explore the utilization of natural language to drive transfer for reinforcement learning (RL). Despite the wide-spread application of deep RL techniques, learning generalized policy representations that work across domains remains a challenging problem. We demonstrate that textual descriptions of environments provide a compact intermediate channel to facilitate effective policy transfer. Specifically, by learning to ground the meaning of text to the dynamics of the environment such as transitions and rewards, an autonomous agent can effectively bootstrap policy learning on a new domain given its description. We employ a model-based RL approach consisting of a differentiable planning module, a model-free component and a factorized state representation to effectively use entity descriptions. Our model outperforms prior work on both transfer and multi-task scenarios in a variety of different environments. For instance, we achieve up to 14% and 11.5% absolute improvement over previously existing models in terms of average and initial rewards, respectively.

cs.CL↗

arXiv2018

The Variational Homoencoder: Learning to learn high capacity generative models from few examples

Hierarchical Bayesian methods can unify many related tasks (e.g. k-shot classification, conditional and unconditional generation) as inference within a single generative model. However, when this generative model is expressed as a powerful neural network such as a PixelCNN, we show that existing learning techniques typically fail to effectively use latent variables. To address this, we develop a modification of the Variational Autoencoder in which encoded observations are decoded to new elements from the same class. This technique, which we call a Variational Homoencoder (VHE), produces a hierarchical latent variable model which better utilises latent variables. We use the VHE framework to learn a hierarchical PixelCNN on the Omniglot dataset, which outperforms all existing models on test set likelihood and achieves strong performance on one-shot generation and classification tasks. We additionally validate the VHE on natural images from the YouTube Faces database. Finally, we develop extensions of the model that apply to richer dataset structures such as factorial and hierarchical categories.

cs.LG↗

arXiv2017

Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network

The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers from coverage and efficiency issues. In this paper, we propose a template-free approach to efficiently explore the space of product molecules by first pinpointing the reaction center -- the set of nodes and edges where graph edits occur. Since only a small number of atoms contribute to reaction center, we can directly enumerate candidate products. The generated candidates are scored by a Weisfeiler-Lehman Difference Network that models high-order interactions between changes occurring at nodes across the molecule. Our framework outperforms the top-performing template-based approach with a 10\% margin, while running orders of magnitude faster. Finally, we demonstrate that the model accuracy rivals the performance of domain experts.

cs.LG↗

arXiv2017

Style Transfer from Non-Parallel Text by Cross-Alignment

This paper focuses on style transfer on the basis of non-parallel text. This is an instance of a broad family of problems including machine translation, decipherment, and sentiment modification. The key challenge is to separate the content from other aspects such as style. We assume a shared latent content distribution across different text corpora, and propose a method that leverages refined alignment of latent representations to perform style transfer. The transferred sentences from one style should match example sentences from the other style as a population. We demonstrate the effectiveness of this cross-alignment method on three tasks: sentiment modification, decipherment of word substitution ciphers, and recovery of word order.

cs.CL↗

arXiv2017

Deriving Neural Architectures from Sequence and Graph Kernels

The design of neural architectures for structured objects is typically guided by experimental insights rather than a formal process. In this work, we appeal to kernels over combinatorial structures, such as sequences and graphs, to derive appropriate neural operations. We introduce a class of deep recurrent neural operations and formally characterize their associated kernel spaces. Our recurrent modules compare the input to virtual reference objects (cf. filters in CNN) via the kernels. Similar to traditional neural operations, these reference objects are parameterized and directly optimized in end-to-end training. We empirically evaluate the proposed class of neural architectures on standard applications such as language modeling and molecular graph regression, achieving state-of-the-art results across these applications.

cs.NE↗

arXiv2017

Aspect-augmented Adversarial Networks for Domain Adaptation

We introduce a neural method for transfer learning between two (source and target) classification tasks or aspects over the same domain. Rather than training on target labels, we use a few keywords pertaining to source and target aspects indicating sentence relevance instead of document class labels. Documents are encoded by learning to embed and softly select relevant sentences in an aspect-dependent manner. A shared classifier is trained on the source encoded documents and labels, and applied to target encoded documents. We ensure transfer through aspect-adversarial training so that encoded documents are, as sets, aspect-invariant. Experimental results demonstrate that our approach outperforms different baselines and model variants on two datasets, yielding an improvement of 27% on a pathology dataset and 5% on a review dataset.

cs.CL↗

arXiv2017

High Dimensional Inference with Random Maximum A-Posteriori Perturbations

This paper presents a new approach, called perturb-max, for high-dimensional statistical inference that is based on applying random perturbations followed by optimization. This framework injects randomness to maximum a-posteriori (MAP) predictors by randomly perturbing the potential function for the input. A classic result from extreme value statistics asserts that perturb-max operations generate unbiased samples from the Gibbs distribution using high-dimensional perturbations. Unfortunately, the computational cost of generating so many high-dimensional random variables can be prohibitive. However, when the perturbations are of low dimension, sampling the perturb-max prediction is as efficient as MAP optimization. This paper shows that the expected value of perturb-max inference with low dimensional perturbations can be used sequentially to generate unbiased samples from the Gibbs distribution. Furthermore the expected value of the maximal perturbations is a natural bound on the entropy of such perturb-max models. A measure concentration result for perturb-max values shows that the deviation of their sampled average from its expectation decays exponentially in the number of samples, allowing effective approximation of the expectation.

cs.LG↗

arXiv2017

Modeling Persistent Trends in Distributions

We present a nonparametric framework to model a short sequence of probability distributions that vary both due to underlying effects of sequential progression and confounding noise. To distinguish between these two types of variation and estimate the sequential-progression effects, our approach leverages an assumption that these effects follow a persistent trend. This work is motivated by the recent rise of single-cell RNA-sequencing experiments over a brief time course, which aim to identify genes relevant to the progression of a particular biological process across diverse cell populations. While classical statistical tools focus on scalar-response regression or order-agnostic differences between distributions, it is desirable in this setting to consider both the full distributions as well as the structure imposed by their ordering. We introduce a new regression model for ordinal covariates where responses are univariate distributions and the underlying relationship reflects consistent changes in the distributions over increasing levels of the covariate. This concept is formalized as a "trend" in distributions, which we define as an evolution that is linear under the Wasserstein metric. Implemented via a fast alternating projections algorithm, our method exhibits numerous strengths in simulations and analyses of single-cell gene expression data.

stat.ME↗

arXiv2017

Learning Optimal Interventions

Our goal is to identify beneficial interventions from observational data. We consider interventions that are narrowly focused (impacting few covariates) and may be tailored to each individual or globally enacted over a population. For applications where harmful intervention is drastically worse than proposing no change, we propose a conservative definition of the optimal intervention. Assuming the underlying relationship remains invariant under intervention, we develop efficient algorithms to identify the optimal intervention policy from limited data and provide theoretical guarantees for our approach in a Gaussian Process setting. Although our methods assume covariates can be precisely adjusted, they remain capable of improving outcomes in misspecified settings where interventions incur unintentional downstream effects. Empirically, our approach identifies good interventions in two practical applications: gene perturbation and writing improvement.

stat.ML↗

arXiv2016

Rationalizing Neural Predictions

Prediction without justification has limited applicability. As a remedy, we learn to extract pieces of input text as justifications -- rationales -- that are tailored to be short and coherent, yet sufficient for making the same prediction. Our approach combines two modular components, generator and encoder, which are trained to operate well together. The generator specifies a distribution over text fragments as candidate rationales and these are passed through the encoder for prediction. Rationales are never given during training. Instead, the model is regularized by desiderata for rationales. We evaluate the approach on multi-aspect sentiment analysis against manually annotated test cases. Our approach outperforms attention-based baseline by a significant margin. We also successfully illustrate the method on the question retrieval task.

cs.CL↗