Mahesan Niranjan

Keqiang Fan, Xiaohao Cai, Mahesan Niranjan

Automated medical report generation has become increasingly important in medical analysis. It can produce computer-aided diagnosis descriptions and thus significantly alleviate the doctors' work. Inspired by the huge success of neural machine translation and image captioning, various deep learning methods have been proposed for medical report generation. However, due to the inherent properties of medical data, including data imbalance and the length and correlation between report sequences, the generated reports by existing methods may exhibit linguistic fluency but lack adequate clinical accuracy. In this work, we propose an image-to-indicator hierarchical transformer (IIHT) framework for medical report generation. It consists of three modules, i.e., a classifier module, an indicator expansion module and a generator module. The classifier module first extracts image features from the input medical images and produces disease-related indicators with their corresponding states. The disease-related indicators are subsequently utilised as input for the indicator expansion module, incorporating the "data-text-data" strategy. The transformer-based generator then leverages these extracted features along with image features as auxiliary information to generate final reports. Furthermore, the proposed IIHT method is feasible for radiologists to modify disease indicators in real-world scenarios and integrate the operations into the indicator expansion module for fluent and accurate medical report generation. Extensive experiments and comparisons with state-of-the-art methods under various evaluation metrics demonstrate the great performance of the proposed method.

Yihong Wu, Yuwen Heng, Mahesan Niranjan et al.

Depth estimation from a single image is a challenging problem in computer vision because binocular disparity or motion information is absent. Whereas impressive performances have been reported in this area recently using end-to-end trained deep neural architectures, as to what cues in the images that are being exploited by these black box systems is hard to know. To this end, in this work, we quantify the relative contributions of the known cues of depth in a monocular depth estimation setting using an indoor scene data set. Our work uses feature extraction techniques to relate the single features of shape, texture, colour and saturation, taken in isolation, to predict depth. We find that the shape of objects extracted by edge detection substantially contributes more than others in the indoor setting considered, while the other features also have contributions in varying degrees. These insights will help optimise depth estimation models, boosting their accuracy and robustness. They promise to broaden the practical applications of vision-based depth estimation. The project code is attached to the supplementary material and will be published on GitHub.

Ethan Harris, Antonia Marcu, Matthew Painter et al.

Mixed Sample Data Augmentation (MSDA) has received increasing attention in recent years, with many successful variants such as MixUp and CutMix. By studying the mutual information between the function learned by a VAE on the original data and on the augmented data we show that MixUp distorts learned functions in a way that CutMix does not. We further demonstrate this by showing that MixUp acts as a form of adversarial training, increasing robustness to attacks such as Deep Fool and Uniform Noise which produce examples similar to those generated by MixUp. We argue that this distortion prevents models from learning about sample specific features in the data, aiding generalisation performance. In contrast, we suggest that CutMix works more like a traditional augmentation, improving performance by preventing memorisation without distorting the data distribution. However, we argue that an MSDA which builds on CutMix to include masks of arbitrary shape, rather than just square, could further prevent memorisation whilst preserving the data distribution in the same way. To this end, we propose FMix, an MSDA that uses random binary masks obtained by applying a threshold to low frequency images sampled from Fourier space. These random masks can take on a wide range of shapes and can be generated for use with one, two, and three dimensional data. FMix improves performance over MixUp and CutMix, without an increase in training time, for a number of models across a range of data sets and problem settings, obtaining a new single model state-of-the-art result on CIFAR-10 without external data. Finally, we show that a consequence of the difference between interpolating MSDA such as MixUp and masking MSDA such as FMix is that the two can be combined to improve performance even further. Code for all experiments is provided at https://github.com/ecs-vlc/FMix .

Keqiang Fan, Xiaohao Cai, Mahesan Niranjan

Diffusion probabilistic models (DPMs) have exhibited significant effectiveness in computer vision tasks, particularly in image generation. However, their notable performance heavily relies on labelled datasets, which limits their application in medical images due to the associated high-cost annotations. Current DPM-related methods for lesion detection in medical imaging, which can be categorized into two distinct approaches, primarily rely on image-level annotations. The first approach, based on anomaly detection, involves learning reference healthy brain representations and identifying anomalies based on the difference in inference results. In contrast, the second approach, resembling a segmentation task, employs only the original brain multi-modalities as prior information for generating pixel-level annotations. In this paper, our proposed model - discrepancy distribution medical diffusion (DDMD) - for lesion detection in brain MRI introduces a novel framework by incorporating distinctive discrepancy features, deviating from the conventional direct reliance on image-level annotations or the original brain modalities. In our method, the inconsistency in image-level annotations is translated into distribution discrepancies among heterogeneous samples while preserving information within homogeneous samples. This property retains pixel-wise uncertainty and facilitates an implicit ensemble of segmentation, ultimately enhancing the overall detection performance. Thorough experiments conducted on the BRATS2020 benchmark dataset containing multimodal MRI scans for brain tumour detection demonstrate the great performance of our approach in comparison to state-of-the-art methods.

Deshani Geethika Poddenige, Sachith Seneviratne, Damith Senanayake et al.

Unsupervised representation learning has been widely explored across various modalities, including neural architectures, where it plays a key role in downstream applications like Neural Architecture Search (NAS). These methods typically learn an unsupervised representation space before generating/ sampling architectures for the downstream search. A common approach involves the use of Variational Autoencoders (VAEs) to map discrete architectures onto a continuous representation space, however, sampling from these spaces often leads to a high percentage of invalid or duplicate neural architectures. This could be due to the unnatural mapping of inherently discrete architectural space onto a continuous space, which emphasizes the need for a robust discrete representation of these architectures. To address this, we introduce a Vector Quantized Variational Autoencoder (VQ-VAE) to learn a discrete latent space more naturally aligned with the discrete neural architectures. In contrast to VAEs, VQ-VAEs (i) map each architecture into a discrete code sequence and (ii) allow the prior to be learned by any generative model rather than assuming a normal distribution. We then represent these architecture latent codes as numerical sequences and train a text-to-text model leveraging a Large Language Model to learn and generate sequences representing architectures. We experiment our method with Inception/ ResNet-like cell-based search spaces, namely NAS-Bench-101 and NAS-Bench-201. Compared to VAE-based methods, our approach improves the generation of valid and unique architectures by over 80% on NASBench-101 and over 8% on NASBench-201. Finally, we demonstrate the applicability of our method in NAS employing a sequence-modeling-based NAS algorithm.

Mona Alawadh, Mahesan Niranjan, Hansung Kim

Semantic Scene Completion (SSC) is a critical task in computer vision, that utilized in applications such as virtual reality (VR). SSC aims to construct detailed 3D models from partial views by transforming a single 2D image into a 3D representation, assigning each voxel a semantic label. The main challenge lies in completing 3D volumes with limited information, compounded by data imbalance, inter-class ambiguity, and intra-class diversity in indoor scenes. To address this, we propose the Multi-Feature Data Balancing Network (MDBNet), a dual-head model for RGB and depth data (F-TSDF) inputs. Our hybrid encoder-decoder architecture with identity transformation in a pre-activation residual module (ITRM) effectively manages diverse signals within F-TSDF. We evaluate RGB feature fusion strategies and use a combined loss function cross entropy for 2D RGB features and weighted cross-entropy for 3D SSC predictions. MDBNet results surpass comparable state-of-the-art (SOTA) methods on NYU datasets, demonstrating the effectiveness of our approach.

Keqiang Fan, Xiaohao Cai, Mahesan Niranjan

Unlike typical visual scene recognition domains, in which massive datasets are accessible to deep neural networks, medical image interpretations are often obstructed by the paucity of data. In this paper, we investigate the effectiveness of data-based few-shot learning in medical imaging by exploring different data attribute representations in a low-dimensional space. We introduce different types of non-negative matrix factorization (NMF) in few-shot learning, addressing the data scarcity issue in medical image classification. Extensive empirical studies are conducted in terms of validating the effectiveness of NMF, especially its supervised variants (e.g., discriminative NMF, and supervised and constrained NMF with sparseness), and the comparison with principal component analysis (PCA), i.e., the collaborative representation-based dimensionality reduction technique derived from eigenvectors. With 14 different datasets covering 11 distinct illness categories, thorough experimental results and comparison with related techniques demonstrate that NMF is a competitive alternative to PCA for few-shot learning in medical imaging, and the supervised NMF algorithms are more discriminative in the subspace with greater effectiveness. Furthermore, we show that the part-based representation of NMF, especially its supervised variants, is dramatically impactful in detecting lesion areas in medical imaging with limited samples.

Jiahui Liu, Xiaohao Cai, Mahesan Niranjan

There is growing concern that the potential of black box AI may exacerbate health-related disparities and biases such as gender and ethnicity in clinical decision-making. Biased decisions can arise from data availability and collection processes, as well as from the underlying confounding effects of the protected attributes themselves. This work proposes a machine learning-based orthogonal approach aiming to analyze and suppress the effect of the confounder through discriminant dimensionality reduction and orthogonalization of the protected attributes against the primary attribute information. By doing so, the impact of the protected attributes on disease diagnosis can be realized, undesirable feature correlations can be mitigated, and the model prediction performance can be enhanced.

Jiahui Liu, Xiaohao Cai, Mahesan Niranjan

Linear discriminant analysis (LDA) has been a useful tool in pattern recognition and data analysis research and practice. While linearity of class boundaries cannot always be expected, nonlinear projections through pre-trained deep neural networks have served to map complex data onto feature spaces in which linear discrimination has served well. The solution to binary LDA is obtained by eigenvalue analysis of within-class and between-class scatter matrices. It is well known that the multiclass LDA is solved by an extension to the binary LDA, a generalised eigenvalue problem, from which the largest subspace that can be extracted is of dimension one lower than the number of classes in the given problem. In this paper, we show that, apart from the first of the discriminant directions, the generalised eigenanalysis solution to multiclass LDA does neither yield orthogonal discriminant directions nor maximise discrimination of projected data along them. Surprisingly, to the best of our knowledge, this has not been noted in decades of literature on LDA. To overcome this drawback, we present a derivation with a strict theoretical support for sequentially obtaining discriminant directions that are orthogonal to previously computed ones and maximise in each step the Fisher criterion. We show distributions of projections along these axes and demonstrate that discrimination of data projected onto these discriminant directions has optimal separation, which is much higher than those from the generalised eigenvectors of the multiclass LDA. Using a wide range of benchmark tasks, we present a comprehensive empirical demonstration that on a number of pattern recognition and classification problems, the optimal discriminant subspaces obtained by the proposed method, referred to as GO-LDA (Generalised Optimal LDA), can offer superior accuracy.

Junyu Mao, Stuart E. Middleton, Mahesan Niranjan

Prompt-based models have gathered a lot of attention from researchers due to their remarkable advancements in the fields of zero-shot and few-shot learning. Developing an effective prompt template plays a critical role. However, prior studies have mainly focused on prompt vocabulary searching or embedding initialization within a predefined template with the prompt position fixed. In this empirical study, we conduct the most comprehensive analysis to date of prompt position for diverse Natural Language Processing (NLP) tasks. Our findings quantify the substantial impact prompt position has on model performance. We observe that the prompt positions used in prior studies are often sub-optimal, and this observation is consistent even in widely used instruction-tuned models. These findings suggest prompt position optimisation as a valuable research direction to augment prompt engineering methodologies and prompt position-aware instruction tuning as a potential way to build more robust models in the future.

Manuel Nunes, Enrico Gerding, Frank McGroarty et al.

Modern decision-making in fixed income asset management benefits from intelligent systems, which involve the use of state-of-the-art machine learning models and appropriate methodologies. We conduct the first study of bond yield forecasting using long short-term memory (LSTM) networks, validating its potential and identifying its memory advantage. Specifically, we model the 10-year bond yield using univariate LSTMs with three input sequences and five forecasting horizons. We compare those with multilayer perceptrons (MLP), univariate and with the most relevant features. To demystify the notion of black box associated with LSTMs, we conduct the first internal study of the model. To this end, we calculate the LSTM signals through time, at selected locations in the memory cell, using sequence-to-sequence architectures, uni and multivariate. We then proceed to explain the states' signals using exogenous information, for what we develop the LSTM-LagLasso methodology. The results show that the univariate LSTM model with additional memory is capable of achieving similar results as the multivariate MLP using macroeconomic and market information. Furthermore, shorter forecasting horizons require smaller input sequences and vice-versa. The most remarkable property found consistently in the LSTM signals, is the activation/deactivation of units through time, and the specialisation of units by yield range or feature. Those signals are complex but can be explained by exogenous variables. Additionally, some of the relevant features identified via LSTM-LagLasso are not commonly used in forecasting models. In conclusion, our work validates the potential of LSTMs and methodologies for bonds, providing additional tools for financial practitioners.

Steven Squires, Adam Prügel Bennett, Mahesan Niranjan

We introduce and demonstrate the variational autoencoder (VAE) for probabilistic non-negative matrix factorisation (PAE-NMF). We design a network which can perform non-negative matrix factorisation (NMF) and add in aspects of a VAE to make the coefficients of the latent space probabilistic. By restricting the weights in the final layer of the network to be non-negative and using the non-negative Weibull distribution we produce a probabilistic form of NMF which allows us to generate new data and find a probability distribution that effectively links the latent and input variables. We demonstrate the effectiveness of PAE-NMF on three heterogeneous datasets: images, financial time series and genomic.

Francisco Belchí, Jacek Brodzki, Matthew Burfitt et al.

Mapper is an unsupervised machine learning algorithm generalising the notion of clustering to obtain a geometric description of a dataset. The procedure splits the data into possibly overlapping bins which are then clustered. The output of the algorithm is a graph where nodes represent clusters and edges represent the sharing of data points between two clusters. However, several parameters must be selected before applying Mapper and the resulting graph may vary dramatically with the choice of parameters. We define an intrinsic notion of Mapper instability that measures the variability of the output as a function of the choice of parameters required to construct a Mapper output. Our results and discussion are general and apply to all Mapper-type algorithms. We derive theoretical results that provide estimates for the instability and suggest practical ways to control it. We provide also experiments to illustrate our results and in particular we demonstrate that a reliable candidate Mapper output can be identified as a local minimum of instability regarded as a function of Mapper input parameters.

Steven Squires, Adam Prugel Bennett, Mahesan Niranjan

Non-negative matrix factorization (NMF) is a dimensionality reduction technique which tends to produce a sparse representation of data. Commonly, the error between the actual and recreated matrices is used as an objective function, but this method may not produce the type of representation we desire as it allows for the complexity of the model to grow, constrained only by the size of the subspace and the non-negativity requirement. If additional constraints, such as sparsity, are imposed the question of parameter selection becomes critical. Instead of adding sparsity constraints in an ad-hoc manner we propose a novel objective function created by using the principle of minimum description length (MDL). Our formulation, MDL-NMF, automatically trades off between the complexity and accuracy of the model using a principled approach with little parameter selection or the need for domain expertise. We demonstrate our model works effectively on three heterogeneous data-sets and on a range of semi-synthetic data showing the broad applicability of our method.

Ethan Harris, Mahesan Niranjan, Jonathon Hare

The ability to look multiple times through a series of pose-adjusted glimpses is fundamental to human vision. This critical faculty allows us to understand highly complex visual scenes. Short term memory plays an integral role in aggregating the information obtained from these glimpses and informing our interpretation of the scene. Computational models have attempted to address glimpsing and visual attention but have failed to incorporate the notion of memory. We introduce a novel, biologically inspired visual working memory architecture that we term the Hebb-Rosenblatt memory. We subsequently introduce a fully differentiable Short Term Attentive Working Memory model (STAWM) which uses transformational attention to learn a memory over each image it sees. The state of our Hebb-Rosenblatt memory is embedded in STAWM as the weights space of a layer. By projecting different queries through this layer we can obtain goal-oriented latent representations for tasks including classification and visual reconstruction. Our model obtains highly competitive classification performance on MNIST and CIFAR-10. As demonstrated through the CelebA dataset, to perform reconstruction the model learns to make a sequence of updates to a canvas which constitute a parts-based representation. Classification with the self supervised representation obtained from MNIST is shown to be in line with the state of the art models (none of which use a visual attention mechanism). Finally, we show that STAWM can be trained under the dual constraints of classification and reconstruction to provide an interpretable visual sketchpad which helps open the 'black-box' of deep learning.

Xin Liu, Mahesan Niranjan

We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken from in vitro experiments, or are hand-tuned during the model development process to reproduces observations from the system. We consider the family of algorithms coming under the Bayesian formulation of Approximate Bayesian Computation (ABC), and show that sensitivity analysis could be deployed to quantify the relative roles of different parameters in the system. Parameters to which a system is relatively less sensitive (known as sloppy parameters) need not be estimated to high precision, while the values of parameters that are more critical (stiff parameters) need to be determined with care. A tradeoff between computational complexity and the accuracy with which the posterior distribution may be probed is an important characteristic of this class of algorithms.