On Feature Learning for Titi Monkey Activity Detection

This paper, a technical summary of our preceding publication, introduces a robust machine learning framework for the detection of vocal activities of Coppery titi monkeys. Utilizing a combination of MFCC features and a bidirectional LSTM-based classifier, we effectively address the challenges posed by the small amount of expert-annotated vocal data available. Our approach significantly reduces false positives and improves the accuracy of call detection in bioacoustic research. Initial results demonstrate an accuracy of 95\% on instance predictions, highlighting the effectiveness of our model in identifying and classifying complex vocal patterns in environmental audio recordings. Moreover, we show how call classification can be done downstream, paving the way for real-world monitoring.

Towards One Model for Classical Dimensionality Reduction: A Probabilistic Perspective on UMAP and t-SNE

This paper shows that the dimensionality reduction methods, UMAP and t-SNE, can be approximately recast as MAP inference methods corresponding to a generalized Wishart-based model introduced in ProbDR. This interpretation offers deeper theoretical insights into these algorithms, while introducing tools with which similar dimensionality reduction methods can be studied.

Scalable Amortized GPLVMs for Single Cell Transcriptomics Data

Dimensionality reduction is crucial for analyzing large-scale single-cell RNA-seq data. Gaussian Process Latent Variable Models (GPLVMs) offer an interpretable dimensionality reduction method, but current scalable models lack effectiveness in clustering cell types. We introduce an improved model, the amortized stochastic variational Bayesian GPLVM (BGPLVM), tailored for single-cell RNA-seq with specialized encoder, kernel, and likelihood designs. This model matches the performance of the leading single-cell variational inference (scVI) approach on synthetic and real-world COVID datasets and effectively incorporates cell-cycle and batch information to reveal more interpretable latent structures as we demonstrate on an innate immunity dataset.

Self-sustaining Software Systems (S4): Towards Improved Interpretability and Adaptation

Software systems impact society at different levels as they pervasively solve real-world problems. Modern software systems are often so sophisticated that their complexity exceeds the limits of human comprehension. These systems must respond to changing goals, dynamic data, unexpected failures, and security threats, among other variable factors in real-world environments. Systems' complexity challenges their interpretability and requires autonomous responses to dynamic changes. Two main research areas explore autonomous systems' responses: evolutionary computing and autonomic computing. Evolutionary computing focuses on software improvement based on iterative modifications to the source code. Autonomic computing focuses on optimising systems' performance by changing their structure, behaviour, or environment variables. Approaches from both areas rely on feedback loops that accumulate knowledge from the system interactions to inform autonomous decision-making. However, this knowledge is often limited, constraining the systems' interpretability and adaptability. This paper proposes a new concept for interpretable and adaptable software systems: self-sustaining software systems (S4). S4 builds knowledge loops between all available knowledge sources that define modern software systems to improve their interpretability and adaptability. This paper introduces and discusses the S4 concept.

Automated discovery of trade-off between utility, privacy and fairness in machine learning models

Machine learning models are deployed as a central component in decision making and policy operations with direct impact on individuals' lives. In order to act ethically and comply with government regulations, these models need to make fair decisions and protect the users' privacy. However, such requirements can come with decrease in models' performance compared to their potentially biased, privacy-leaking counterparts. Thus the trade-off between fairness, privacy and performance of ML models emerges, and practitioners need a way of quantifying this trade-off to enable deployment decisions. In this work we interpret this trade-off as a multi-objective optimization problem, and propose PFairDP, a pipeline that uses Bayesian optimization for discovery of Pareto-optimal points between fairness, privacy and utility of ML models. We show how PFairDP can be used to replicate known results that were achieved through manual constraint setting process. We further demonstrate effectiveness of PFairDP with experiments on multiple models and datasets.

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.

Dimensionality Reduction as Probabilistic Inference

Dimensionality reduction (DR) algorithms compress high-dimensional data into a lower dimensional representation while preserving important features of the data. DR is a critical step in many analysis pipelines as it enables visualisation, noise reduction and efficient downstream processing of the data. In this work, we introduce the ProbDR variational framework, which interprets a wide range of classical DR algorithms as probabilistic inference algorithms in this framework. ProbDR encompasses PCA, CMDS, LLE, LE, MVU, diffusion maps, kPCA, Isomap, (t-)SNE, and UMAP. In our framework, a low-dimensional latent variable is used to construct a covariance, precision, or a graph Laplacian matrix, which can be used as part of a generative model for the data. Inference is done by optimizing an evidence lower bound. We demonstrate the internal consistency of our framework and show that it enables the use of probabilistic programming languages (PPLs) for DR. Additionally, we illustrate that the framework facilitates reasoning about unseen data and argue that our generative models approximate Gaussian processes (GPs) on manifolds. By providing a unified view of DR, our framework facilitates communication, reasoning about uncertainties, model composition, and extensions, particularly when domain knowledge is present.

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.

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.

Real-world Machine Learning Systems: A survey from a Data-Oriented Architecture Perspective

With the upsurge of interest in artificial intelligence machine learning (ML) algorithms, originally developed in academic environments, are now being deployed as parts of real-life systems that deal with large amounts of heterogeneous, dynamic, and high-dimensional data. Deployment of ML methods in real life is prone to challenges across the whole system life-cycle from data management to systems deployment, monitoring, and maintenance. Data-Oriented Architecture (DOA) is an emerging software engineering paradigm that has the potential to mitigate these challenges by proposing a set of principles to create data-driven, loosely coupled, decentralised, and open systems. However DOA as a concept is not widespread yet, and there is no common understanding of how it can be realised in practice. This review addresses that problem by contextualising the principles that underpin the DOA paradigm through the ML system challenges. We explore the extent to which current architectures of ML-based real-world systems have implemented the DOA principles. We also formulate open research challenges and directions for further development of the DOA paradigm.