arXiv subjects

Neil D. Lawrence

Publications and source records attributed to Neil D. Lawrence.

At least 37 records · Page 2Linked to original sources

arXiv2023

Causal fault localisation in dataflow systems

Dataflow computing was shown to bring significant benefits to multiple niches of systems engineering and has the potential to become a general-purpose paradigm of choice for data-driven application development. One of the characteristic features of dataflow computing is the natural access to the dataflow graph of the entire system. Recently it has been observed that these dataflow graphs can be treated as complete graphical causal models, opening opportunities to apply causal inference techniques to dataflow systems. In this demonstration paper we aim to provide the first practical validation of this idea with a particular focus on causal fault localisation. We provide multiple demonstrations of how causal inference can be used to detect software bugs and data shifts in multiple scenarios with three modern dataflow engines.

cs.SE↗

arXiv2023

Dataflow graphs as complete causal graphs

Component-based development is one of the core principles behind modern software engineering practices. Understanding of causal relationships between components of a software system can yield significant benefits to developers. Yet modern software design approaches make it difficult to track and discover such relationships at system scale, which leads to growing intellectual debt. In this paper we consider an alternative approach to software design, flow-based programming (FBP), and draw the attention of the community to the connection between dataflow graphs produced by FBP and structural causal models. With expository examples we show how this connection can be leveraged to improve day-to-day tasks in software projects, including fault localisation, business analysis and experimentation.

cs.SE↗

arXiv2023

AI for Science: An Emerging Agenda

This report documents the programme and the outcomes of Dagstuhl Seminar 22382 "Machine Learning for Science: Bridging Data-Driven and Mechanistic Modelling". Today's scientific challenges are characterised by complexity. Interconnected natural, technological, and human systems are influenced by forces acting across time- and spatial-scales, resulting in complex interactions and emergent behaviours. Understanding these phenomena -- and leveraging scientific advances to deliver innovative solutions to improve society's health, wealth, and well-being -- requires new ways of analysing complex systems. The transformative potential of AI stems from its widespread applicability across disciplines, and will only be achieved through integration across research domains. AI for science is a rendezvous point. It brings together expertise from $\mathrm{AI}$ and application domains; combines modelling knowledge with engineering know-how; and relies on collaboration across disciplines and between humans and machines. Alongside technical advances, the next wave of progress in the field will come from building a community of machine learning researchers, domain experts, citizen scientists, and engineers working together to design and deploy effective AI tools. This report summarises the discussions from the seminar and provides a roadmap to suggest how different communities can collaborate to deliver a new wave of progress in AI and its application for scientific discovery.

cs.AI↗

arXiv2022

Behavioral Experiments for Understanding Catastrophic Forgetting

In this paper we explore whether the fundamental tool of experimental psychology, the behavioral experiment, has the power to generate insight not only into humans and animals, but artificial systems too. We apply the techniques of experimental psychology to investigating catastrophic forgetting in neural networks. We present a series of controlled experiments with two-layer ReLU networks, and exploratory results revealing a new understanding of the behavior of catastrophic forgetting. Alongside our empirical findings, we demonstrate an alternative, behavior-first approach to investigating neural network phenomena.

cs.LG↗

arXiv2022

Modelling Technical and Biological Effects in scRNA-seq data with Scalable GPLVMs

Single-cell RNA-seq datasets are growing in size and complexity, enabling the study of cellular composition changes in various biological/clinical contexts. Scalable dimensionality reduction techniques are in need to disentangle biological variation in them, while accounting for technical and biological confounders. In this work, we extend a popular approach for probabilistic non-linear dimensionality reduction, the Gaussian process latent variable model, to scale to massive single-cell datasets while explicitly accounting for technical and biological confounders. The key idea is to use an augmented kernel which preserves the factorisability of the lower bound allowing for fast stochastic variational inference. We demonstrate its ability to reconstruct latent signatures of innate immunity recovered in Kumasaka et al. (2021) with 9x lower training time. We further analyze a COVID dataset and demonstrate across a cohort of 130 individuals, that this framework enables data integration while capturing interpretable signatures of infection. Specifically, we explore COVID severity as a latent dimension to refine patient stratification and capture disease-specific gene expression.

cs.LG↗

arXiv2022

Ice Core Dating using Probabilistic Programming

Ice cores record crucial information about past climate. However, before ice core data can have scientific value, the chronology must be inferred by estimating the age as a function of depth. Under certain conditions, chemicals locked in the ice display quasi-periodic cycles that delineate annual layers. Manually counting these noisy seasonal patterns to infer the chronology can be an imperfect and time-consuming process, and does not capture uncertainty in a principled fashion. In addition, several ice cores may be collected from a region, introducing an aspect of spatial correlation between them. We present an exploration of the use of probabilistic models for automatic dating of ice cores, using probabilistic programming to showcase its use for prototyping, automatic inference and maintainability, and demonstrate common failure modes of these tools.

stat.ML↗

arXiv2022

Bayesian Learning via Neural Schrödinger-Föllmer Flows

In this work we explore a new framework for approximate Bayesian inference in large datasets based on stochastic control (i.e. Schrödinger bridges). We advocate stochastic control as a finite time and low variance alternative to popular steady-state methods such as stochastic gradient Langevin dynamics (SGLD). Furthermore, we discuss and adapt the existing theoretical guarantees of this framework and establish connections to already existing VI routines in SDE-based models.

stat.ML↗

arXiv2022

Modeling the Machine Learning Multiverse

Amid mounting concern about the reliability and credibility of machine learning research, we present a principled framework for making robust and generalizable claims: the multiverse analysis. Our framework builds upon the multiverse analysis (Steegen et al., 2016) introduced in response to psychology's own reproducibility crisis. To efficiently explore high-dimensional and often continuous ML search spaces, we model the multiverse with a Gaussian Process surrogate and apply Bayesian experimental design. Our framework is designed to facilitate drawing robust scientific conclusions about model performance, and thus our approach focuses on exploration rather than conventional optimization. In the first of two case studies, we investigate disputed claims about the relative merit of adaptive optimizers. Second, we synthesize conflicting research on the effect of learning rate on the large batch training generalization gap. For the machine learning community, the multiverse analysis is a simple and effective technique for identifying robust claims, for increasing transparency, and a step toward improved reproducibility.

cs.LG↗

arXiv2022

Solving Schrödinger Bridges via Maximum Likelihood

The Schrödinger bridge problem (SBP) finds the most likely stochastic evolution between two probability distributions given a prior stochastic evolution. As well as applications in the natural sciences, problems of this kind have important applications in machine learning such as dataset alignment and hypothesis testing. Whilst the theory behind this problem is relatively mature, scalable numerical recipes to estimate the Schrödinger bridge remain an active area of research. We prove an equivalence between the SBP and maximum likelihood estimation enabling direct application of successful machine learning techniques. We propose a numerical procedure to estimate SBPs using Gaussian process and demonstrate the practical usage of our approach in numerical simulations and experiments.

stat.ML↗

arXiv2022

The Effect of Task Ordering in Continual Learning

We investigate the effect of task ordering on continual learning performance. We conduct an extensive series of empirical experiments on synthetic and naturalistic datasets and show that reordering tasks significantly affects the amount of catastrophic forgetting. Connecting to the field of curriculum learning, we show that the effect of task ordering can be exploited to modify continual learning performance, and present a simple approach for doing so. Our method computes the distance between all pairs of tasks, where distance is defined as the source task curvature of a gradient step toward the target task. Using statistically rigorous methods and sound experimental design, we show that task ordering is an important aspect of continual learning that can be modified for improved performance.

cs.LG↗

arXiv2022

Challenges in Deploying Machine Learning: a Survey of Case Studies

In recent years, machine learning has transitioned from a field of academic research interest to a field capable of solving real-world business problems. However, the deployment of machine learning models in production systems can present a number of issues and concerns. This survey reviews published reports of deploying machine learning solutions in a variety of use cases, industries and applications and extracts practical considerations corresponding to stages of the machine learning deployment workflow. By mapping found challenges to the steps of the machine learning deployment workflow we show that practitioners face issues at each stage of the deployment process. The goal of this paper is to lay out a research agenda to explore approaches addressing these challenges.

cs.LG↗

arXiv2022

An Empirical Evaluation of Flow Based Programming in the Machine Learning Deployment Context

As use of data driven technologies spreads, software engineers are more often faced with the task of solving a business problem using data-driven methods such as machine learning (ML) algorithms. Deployment of ML within large software systems brings new challenges that are not addressed by standard engineering practices and as a result businesses observe high rate of ML deployment project failures. Data Oriented Architecture (DOA) is an emerging approach that can support data scientists and software developers when addressing such challenges. However, there is a lack of clarity about how DOA systems should be implemented in practice. This paper proposes to consider Flow-Based Programming (FBP) as a paradigm for creating DOA applications. We empirically evaluate FBP in the context of ML deployment on four applications that represent typical data science projects. We use Service Oriented Architecture (SOA) as a baseline for comparison. Evaluation is done with respect to different application domains, ML deployment stages, and code quality metrics. Results reveal that FBP is a suitable paradigm for data collection and data science tasks, and is able to simplify data collection and discovery when compared with SOA. We discuss the advantages of FBP as well as the gaps that need to be addressed to increase FBP adoption as a standard design paradigm for DOA.

cs.SE↗

arXiv2022

Generalised Gaussian Process Latent Variable Models (GPLVM) with Stochastic Variational Inference

Gaussian process latent variable models (GPLVM) are a flexible and non-linear approach to dimensionality reduction, extending classical Gaussian processes to an unsupervised learning context. The Bayesian incarnation of the GPLVM Titsias and Lawrence, 2010] uses a variational framework, where the posterior over latent variables is approximated by a well-behaved variational family, a factorized Gaussian yielding a tractable lower bound. However, the non-factories ability of the lower bound prevents truly scalable inference. In this work, we study the doubly stochastic formulation of the Bayesian GPLVM model amenable with minibatch training. We show how this framework is compatible with different latent variable formulations and perform experiments to compare a suite of models. Further, we demonstrate how we can train in the presence of massively missing data and obtain high-fidelity reconstructions. We demonstrate the model's performance by benchmarking against the canonical sparse GPLVM for high-dimensional data examples.

cs.LG↗

arXiv2022

Scalable Bigraphical Lasso: Two-way Sparse Network Inference for Count Data

Classically, statistical datasets have a larger number of data points than features ($n > p$). The standard model of classical statistics caters for the case where data points are considered conditionally independent given the parameters. However, for $n\approx p$ or $p > n$ such models are poorly determined. Kalaitzis et al. (2013) introduced the Bigraphical Lasso, an estimator for sparse precision matrices based on the Cartesian product of graphs. Unfortunately, the original Bigraphical Lasso algorithm is not applicable in case of large p and n due to memory requirements. We exploit eigenvalue decomposition of the Cartesian product graph to present a more efficient version of the algorithm which reduces memory requirements from $O(n^2p^2)$ to $O(n^2 + p^2)$. Many datasets in different application fields, such as biology, medicine and social science, come with count data, for which Gaussian based models are not applicable. Our multi-way network inference approach can be used for discrete data. Our methodology accounts for the dependencies across both instances and features, reduces the computational complexity for high dimensional data and enables to deal with both discrete and continuous data. Numerical studies on both synthetic and real datasets are presented to showcase the performance of our method.

stat.ML↗

arXiv2021

Towards better data discovery and collection with flow-based programming

Despite huge successes reported by the field of machine learning, such as voice assistants or self-driving cars, businesses still observe very high failure rate when it comes to deployment of ML in production. We argue that part of the reason is infrastructure that was not designed for data-oriented activities. This paper explores the potential of flow-based programming (FBP) for simplifying data discovery and collection in software systems. We compare FBP with the currently prevalent service-oriented paradigm to assess characteristics of each paradigm in the context of ML deployment. We develop a data processing application, formulate a subsequent ML deployment task, and measure the impact of the task implementation within both programming paradigms. Our main conclusion is that FBP shows great potential for providing data-centric infrastructural benefits for deployment of ML. Additionally, we provide an insight into the current trend that prioritizes model development over data quality management.

cs.SE↗

arXiv2021

Emulation of physical processes with Emukit

Decision making in uncertain scenarios is an ubiquitous challenge in real world systems. Tools to deal with this challenge include simulations to gather information and statistical emulation to quantify uncertainty. The machine learning community has developed a number of methods to facilitate decision making, but so far they are scattered in multiple different toolkits, and generally rely on a fixed backend. In this paper, we present Emukit, a highly adaptable Python toolkit for enriching decision making under uncertainty. Emukit allows users to: (i) use state of the art methods including Bayesian optimization, multi-fidelity emulation, experimental design, Bayesian quadrature and sensitivity analysis; (ii) easily prototype new decision making methods for new problems. Emukit is agnostic to the underlying modeling framework and enables users to use their own custom models. We show how Emukit can be used on three exemplary case studies.

cs.LG↗

arXiv2021

Inconsistency in Conference Peer Review: Revisiting the 2014 NeurIPS Experiment

In this paper we revisit the 2014 NeurIPS experiment that examined inconsistency in conference peer review. We determine that 50\% of the variation in reviewer quality scores was subjective in origin. Further, with seven years passing since the experiment we find that for \emph{accepted} papers, there is no correlation between quality scores and impact of the paper as measured as a function of citation count. We trace the fate of rejected papers, recovering where these papers were eventually published. For these papers we find a correlation between quality scores and impact. We conclude that the reviewing process for the 2014 conference was good for identifying poor papers, but poor for identifying good papers. We give some suggestions for improving the reviewing process but also warn against removing the subjective element. Finally, we suggest that the real conclusion of the experiment is that the community should place less onus on the notion of `top-tier conference publications' when assessing the quality of individual researchers. For NeurIPS 2021, the PCs are repeating the experiment, as well as conducting new ones.

cs.DL↗

arXiv2020

Empirical Bayes Transductive Meta-Learning with Synthetic Gradients

We propose a meta-learning approach that learns from multiple tasks in a transductive setting, by leveraging the unlabeled query set in addition to the support set to generate a more powerful model for each task. To develop our framework, we revisit the empirical Bayes formulation for multi-task learning. The evidence lower bound of the marginal log-likelihood of empirical Bayes decomposes as a sum of local KL divergences between the variational posterior and the true posterior on the query set of each task. We derive a novel amortized variational inference that couples all the variational posteriors via a meta-model, which consists of a synthetic gradient network and an initialization network. Each variational posterior is derived from synthetic gradient descent to approximate the true posterior on the query set, although where we do not have access to the true gradient. Our results on the Mini-ImageNet and CIFAR-FS benchmarks for episodic few-shot classification outperform previous state-of-the-art methods. Besides, we conduct two zero-shot learning experiments to further explore the potential of the synthetic gradient.

cs.LG↗