3,979 research outputs found

    Undergraduate Catalog of Studies, 2023-2024

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    Neuromodulatory effects on early visual signal processing

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    Understanding how the brain processes information and generates simple to complex behavior constitutes one of the core objectives in systems neuroscience. However, when studying different neural circuits, their dynamics and interactions researchers often assume fixed connectivity, overlooking a crucial factor - the effect of neuromodulators. Neuromodulators can modulate circuit activity depending on several aspects, such as different brain states or sensory contexts. Therefore, considering the modulatory effects of neuromodulators on the functionality of neural circuits is an indispensable step towards a more complete picture of the brain’s ability to process information. Generally, this issue affects all neural systems; hence this thesis tries to address this with an experimental and computational approach to resolve neuromodulatory effects on cell type-level in a well-define system, the mouse retina. In the first study, we established and applied a machine-learning-based classification algorithm to identify individual functional retinal ganglion cell types, which enabled detailed cell type-resolved analyses. We applied the classifier to newly acquired data of light-evoked retinal ganglion cell responses and successfully identified their functional types. Here, the cell type-resolved analysis revealed that a particular principle of efficient coding applies to all types in a similar way. In a second study, we focused on the issue of inter-experimental variability that can occur during the process of pooling datasets. As a result, further downstream analyses may be complicated by the subtle variations between the individual datasets. To tackle this, we proposed a theoretical framework based on an adversarial autoencoder with the objective to remove inter-experimental variability from the pooled dataset, while preserving the underlying biological signal of interest. In the last study of this thesis, we investigated the functional effects of the neuromodulator nitric oxide on the retinal output signal. To this end, we used our previously developed retinal ganglion cell type classifier to unravel type-specific effects and established a paired recording protocol to account for type-specific time-dependent effects. We found that certain retinal ganglion cell types showed adaptational type-specific changes and that nitric oxide had a distinct modulation of a particular group of retinal ganglion cells. In summary, I first present several experimental and computational methods that allow to study functional neuromodulatory effects on the retinal output signal in a cell type-resolved manner and, second, use these tools to demonstrate their feasibility to study the neuromodulator nitric oxide

    Undergraduate Catalog of Studies, 2023-2024

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    On the Generation of Realistic and Robust Counterfactual Explanations for Algorithmic Recourse

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    This recent widespread deployment of machine learning algorithms presents many new challenges. Machine learning algorithms are usually opaque and can be particularly difficult to interpret. When humans are involved, algorithmic and automated decisions can negatively impact people’s lives. Therefore, end users would like to be insured against potential harm. One popular way to achieve this is to provide end users access to algorithmic recourse, which gives end users negatively affected by algorithmic decisions the opportunity to reverse unfavorable decisions, e.g., from a loan denial to a loan acceptance. In this thesis, we design recourse algorithms to meet various end user needs. First, we propose methods for the generation of realistic recourses. We use generative models to suggest recourses likely to occur under the data distribution. To this end, we shift the recourse action from the input space to the generative model’s latent space, allowing to generate counterfactuals that lie in regions with data support. Second, we observe that small changes applied to the recourses prescribed to end users likely invalidate the suggested recourse after being nosily implemented in practice. Motivated by this observation, we design methods for the generation of robust recourses and for assessing the robustness of recourse algorithms to data deletion requests. Third, the lack of a commonly used code-base for counterfactual explanation and algorithmic recourse algorithms and the vast array of evaluation measures in literature make it difficult to compare the per formance of different algorithms. To solve this problem, we provide an open source benchmarking library that streamlines the evaluation process and can be used for benchmarking, rapidly developing new methods, and setting up new experiments. In summary, our work contributes to a more reliable interaction of end users and machine learned models by covering fundamental aspects of the recourse process and suggests new solutions towards generating realistic and robust counterfactual explanations for algorithmic recourse

    Lip2Speech : lightweight multi-speaker speech reconstruction with Gabor features

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    In environments characterised by noise or the absence of audio signals, visual cues, notably facial and lip movements, serve as valuable substitutes for missing or corrupted speech signals. In these scenarios, speech reconstruction can potentially generate speech from visual data. Recent advancements in this domain have predominantly relied on end-to-end deep learning models, like Convolutional Neural Networks (CNN) or Generative Adversarial Networks (GAN). However, these models are encumbered by their intricate and opaque architectures, coupled with their lack of speaker independence. Consequently, achieving multi-speaker speech reconstruction without supplementary information is challenging. This research introduces an innovative Gabor-based speech reconstruction system tailored for lightweight and efficient multi-speaker speech restoration. Using our Gabor feature extraction technique, we propose two novel models: GaborCNN2Speech and GaborFea2Speech. These models employ a rapid Gabor feature extraction method to derive lowdimensional mouth region features, encompassing filtered Gabor mouth images and low-dimensional Gabor features as visual inputs. An encoded spectrogram serves as the audio target, and a Long Short-Term Memory (LSTM)-based model is harnessed to generate coherent speech output. Through comprehensive experiments conducted on the GRID corpus, our proposed Gabor-based models have showcased superior performance in sentence and vocabulary reconstruction when compared to traditional end-to-end CNN models. These models stand out for their lightweight design and rapid processing capabilities. Notably, the GaborFea2Speech model presented in this study achieves robust multi-speaker speech reconstruction without necessitating supplementary information, thereby marking a significant milestone in the field of speech reconstruction

    Bayesian inference for challenging scientific models

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    Advances in technology and computation have led to ever more complicated scientific models of phenomena across a wide variety of fields. Many of these models present challenges for Bayesian inference, as a result of computationally intensive likelihoods, high-dimensional parameter spaces or large dataset sizes. In this thesis we show how we can apply developments in probabilistic machine learning and statistics to do inference with examples of these types of models. As a demonstration of an applied inference problem involving a non-trivial likelihood computation, we show how a combination of optimisation and MCMC methods along with careful consideration of priors can be used to infer the parameters of an ODE model of the cardiac action potential. We then consider the problem of pileup, a phenomenon that occurs in astronomy when using CCD detectors to observe bright sources. It complicates the fitting of even simple spectral models by introducing an observation model with a large number of continuous and discrete latent variables that scales with the size of the dataset. We develop an MCMC-based method that can work in the presence of pileup by explicitly marginalising out discrete variables and using adaptive HMC on the remaining continuous variables. We show with synthetic experiments that it allows us to fit spectral models in the presence of pileup without biasing the results. We also compare it to neural Simulation- Based Inference approaches, and find that they perform comparably to the MCMC-based approach whilst being able to scale to larger datasets. As an example of a problem where we wish to do inference with extremely large datasets, we consider the Extreme Deconvolution method. The method fits a probability density to a dataset where each observation has Gaussian noise added with a known sample-specific covariance, originally intended for use with astronomical datasets. The existing fitting method is batch EM, which would not normally be applied to large datasets such as the Gaia catalog containing noisy observations of a billion stars. In this thesis we propose two minibatch variants of extreme deconvolution, based on an online variation of the EM algorithm, and direct gradient-based optimisation of the log-likelihood, both of which can run on GPUs. We demonstrate that these methods provide faster fitting, whilst being able to scale to much larger models for use with larger datasets. We then extend the extreme deconvolution approach to work with non- Gaussian noise, and to use more flexible density estimators such as normalizing flows. Since both adjustments lead to an intractable likelihood, we resort to amortized variational inference in order to fit them. We show that for some datasets that flows can outperform Gaussian mixtures for extreme deconvolution, and that fitting with non-Gaussian noise is now possible

    Self-supervised learning for transferable representations

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    Machine learning has undeniably achieved remarkable advances thanks to large labelled datasets and supervised learning. However, this progress is constrained by the labour-intensive annotation process. It is not feasible to generate extensive labelled datasets for every problem we aim to address. Consequently, there has been a notable shift in recent times toward approaches that solely leverage raw data. Among these, self-supervised learning has emerged as a particularly powerful approach, offering scalability to massive datasets and showcasing considerable potential for effective knowledge transfer. This thesis investigates self-supervised representation learning with a strong focus on computer vision applications. We provide a comprehensive survey of self-supervised methods across various modalities, introducing a taxonomy that categorises them into four distinct families while also highlighting practical considerations for real-world implementation. Our focus thenceforth is on the computer vision modality, where we perform a comprehensive benchmark evaluation of state-of-the-art self supervised models against many diverse downstream transfer tasks. Our findings reveal that self-supervised models often outperform supervised learning across a spectrum of tasks, albeit with correlations weakening as tasks transition beyond classification, particularly for datasets with distribution shifts. Digging deeper, we investigate the influence of data augmentation on the transferability of contrastive learners, uncovering a trade-off between spatial and appearance-based invariances that generalise to real-world transformations. This begins to explain the differing empirical performances achieved by self-supervised learners on different downstream tasks, and it showcases the advantages of specialised representations produced with tailored augmentation. Finally, we introduce a novel self-supervised pre-training algorithm for object detection, aligning pre-training with downstream architecture and objectives, leading to reduced localisation errors and improved label efficiency. In conclusion, this thesis contributes a comprehensive understanding of self-supervised representation learning and its role in enabling effective transfer across computer vision tasks

    The persistent shadow of the supermassive black hole of M 87

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    In April 2019, the Event Horizon Telescope (EHT) Collaboration reported the first-ever event-horizon-scale images of a black hole, resolving the central compact radio source in the giant elliptical galaxy M 87. These images reveal a ring with a southerly brightness distribution and a diameter of ∼42 μas, consistent with the predicted size and shape of a shadow produced by the gravitationally lensed emission around a supermassive black hole. These results were obtained as part of the April 2017 EHT observation campaign, using a global very long baseline interferometric radio array operating at a wavelength of 1.3 mm. Here, we present results based on the second EHT observing campaign, taking place in April 2018 with an improved array, wider frequency coverage, and increased bandwidth. In particular, the additional baselines provided by the Greenland telescope improved the coverage of the array. Multiyear EHT observations provide independent snapshots of the horizon-scale emission, allowing us to confirm the persistence, size, and shape of the black hole shadow, and constrain the intrinsic structural variability of the accretion flow. We have confirmed the presence of an asymmetric ring structure, brighter in the southwest, with a median diameter of 43.3−3.1+1.5 μas. The diameter of the 2018 ring is remarkably consistent with the diameter obtained from the previous 2017 observations. On the other hand, the position angle of the brightness asymmetry in 2018 is shifted by about 30° relative to 2017. The perennial persistence of the ring and its diameter robustly support the interpretation that the ring is formed by lensed emission surrounding a Kerr black hole with a mass ∼6.5 × 109 M⊙. The significant change in the ring brightness asymmetry implies a spin axis that is more consistent with the position angle of the large-scale jet

    A Benchmark Generative Probabilistic Model for Weak Supervised Learning

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    Finding relevant and high-quality datasets to train machine learning models is a major bottleneck for practitioners. Furthermore, to address ambitious real-world use-cases there is usually the requirement that the data come labelled with high-quality annotations that can facilitate the training of a supervised model. Manually labelling data with high-quality labels is generally a time-consuming and challenging task and often this turns out to be the bottleneck in a machine learning project. Weak Supervised Learning (WSL) approaches have been developed to alleviate the annotation burden by offering an automatic way of assigning approximate labels (pseudo-labels) to unlabelled data based on heuristics, distant supervision and knowledge bases. We apply probabilistic generative latent variable models (PLVMs), trained on heuristic labelling representations of the original dataset, as an accurate, fast and cost-effective way to generate pseudo-labels. We show that the PLVMs achieve state-of-the-art performance across four datasets. For example, they achieve 22% points higher F1 score than Snorkel in the class-imbalanced Spouse dataset. PLVMs are plug-and-playable and are a drop-in replacement to existing WSL frameworks (e.g. Snorkel) or they can be used as benchmark models for more complicated algorithms, giving practitioners a compelling accuracy boost

    A brief review of contrastive learning applied to astrophysics

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    Reliable tools to extract patterns from high-dimensionality spaces are becoming more necessary as astronomical datasets increase both in volume and complexity. Contrastive Learning is a self-supervised machine learning algorithm that extracts informative measurements from multi-dimensional datasets, which has become increasingly popular in the computer vision and Machine Learning communities in recent years. To do so, it maximizes the agreement between the information extracted from augmented versions of the same input data, making the final representation invariant to the applied transformations. Contrastive Learning is particularly useful in astronomy for removing known instrumental effects and for performing supervised classifications and regressions with a limited amount of available labels, showing a promising avenue towards \emph{Foundation Models}. This short review paper briefly summarizes the main concepts behind contrastive learning and reviews the first promising applications to astronomy. We include some practical recommendations on which applications are particularly attractive for contrastive learning.Comment: Invited review to be published in RAST
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