Aaron Smith

Nameyeh Alam, Jake Basilico, Daniele Bertolini et al.

A patient's digital twin is a computational model that describes the evolution of their health over time. Digital twins have the potential to revolutionize medicine by enabling individual-level computer simulations of human health, which can be used to conduct more efficient clinical trials or to recommend personalized treatment options. Due to the overwhelming complexity of human biology, machine learning approaches that leverage large datasets of historical patients' longitudinal health records to generate patients' digital twins are more tractable than potential mechanistic models. In this manuscript, we describe a neural network architecture that can learn conditional generative models of clinical trajectories, which we call Digital Twin Generators (DTGs), that can create digital twins of individual patients. We show that the same neural network architecture can be trained to generate accurate digital twins for patients across 13 different indications simply by changing the training set and tuning hyperparameters. By introducing a general purpose architecture, we aim to unlock the ability to scale machine learning approaches to larger datasets and across more indications so that a digital twin could be created for any patient in the world.

Aaron Smith, Bernd Bohnet, Miryam de Lhoneux et al.

We present the Uppsala system for the CoNLL 2018 Shared Task on universal dependency parsing. Our system is a pipeline consisting of three components: the first performs joint word and sentence segmentation; the second predicts part-of- speech tags and morphological features; the third predicts dependency trees from words and tags. Instead of training a single parsing model for each treebank, we trained models with multiple treebanks for one language or closely related languages, greatly reducing the number of models. On the official test run, we ranked 7th of 27 teams for the LAS and MLAS metrics. Our system obtained the best scores overall for word segmentation, universal POS tagging, and morphological features.

Aaron Smith, Miryam de Lhoneux, Sara Stymne et al.

We provide a comprehensive analysis of the interactions between pre-trained word embeddings, character models and POS tags in a transition-based dependency parser. While previous studies have shown POS information to be less important in the presence of character models, we show that in fact there are complex interactions between all three techniques. In isolation each produces large improvements over a baseline system using randomly initialised word embeddings only, but combining them quickly leads to diminishing returns. We categorise words by frequency, POS tag and language in order to systematically investigate how each of the techniques affects parsing quality. For many word categories, applying any two of the three techniques is almost as good as the full combined system. Character models tend to be more important for low-frequency open-class words, especially in morphologically rich languages, while POS tags can help disambiguate high-frequency function words. We also show that large character embedding sizes help even for languages with small character sets, especially in morphologically rich languages.

Oren Mangoubi, Natesh S. Pillai, Aaron Smith

Hamiltonian Monte Carlo (HMC) is a very popular and generic collection of Markov chain Monte Carlo (MCMC) algorithms. One explanation for the popularity of HMC algorithms is their excellent performance as the dimension $d$ of the target becomes large: under conditions that are satisfied for many common statistical models, optimally-tuned HMC algorithms have a running time that scales like $d^{0.25}$. In stark contrast, the running time of the usual Random-Walk Metropolis (RWM) algorithm, optimally tuned, scales like $d$. This superior scaling of the HMC algorithm with dimension is attributed to the fact that it, unlike RWM, incorporates the gradient information in the proposal distribution. In this paper, we investigate a different scaling question: does HMC beat RWM for highly $\textit{multimodal}$ targets? We find that the answer is often $\textit{no}$. We compute the spectral gaps for both the algorithms for a specific class of multimodal target densities, and show that they are identical. The key reason is that, within one mode, the gradient is effectively ignorant about other modes, thus negating the advantage the HMC algorithm enjoys in unimodal targets. We also give heuristic arguments suggesting that the above observation may hold quite generally. Our main tool for answering this question is a novel simple formula for the conductance of HMC using Liouville's theorem. This result allows us to compute the spectral gap of HMC algorithms, for both the classical HMC with isotropic momentum and the recent Riemannian HMC, for multimodal targets.

Sara Stymne, Miryam de Lhoneux, Aaron Smith et al.

How to make the most of multiple heterogeneous treebanks when training a monolingual dependency parser is an open question. We start by investigating previously suggested, but little evaluated, strategies for exploiting multiple treebanks based on concatenating training sets, with or without fine-tuning. We go on to propose a new method based on treebank embeddings. We perform experiments for several languages and show that in many cases fine-tuning and treebank embeddings lead to substantial improvements over single treebanks or concatenation, with average gains of 2.0--3.5 LAS points. We argue that treebank embeddings should be preferred due to their conceptual simplicity, flexibility and extensibility.