arXiv subjects

Efstratios Gavves

Publications and source records attributed to Efstratios Gavves.

At least 73 records · Page 4Linked to original sources

arXiv2023

DeepSMILE: Contrastive self-supervised pre-training benefits MSI and HRD classification directly from H&E whole-slide images in colorectal and breast cancer

We propose a Deep learning-based weak label learning method for analyzing whole slide images (WSIs) of Hematoxylin and Eosin (H&E) stained tumor tissue not requiring pixel-level or tile-level annotations using Self-supervised pre-training and heterogeneity-aware deep Multiple Instance LEarning (DeepSMILE). We apply DeepSMILE to the task of Homologous recombination deficiency (HRD) and microsatellite instability (MSI) prediction. We utilize contrastive self-supervised learning to pre-train a feature extractor on histopathology tiles of cancer tissue. Additionally, we use variability-aware deep multiple instance learning to learn the tile feature aggregation function while modeling tumor heterogeneity. For MSI prediction in a tumor-annotated and color normalized subset of TCGA-CRC (n=360 patients), contrastive self-supervised learning improves the tile supervision baseline from 0.77 to 0.87 AUROC, on par with our proposed DeepSMILE method. On TCGA-BC (n=1041 patients) without any manual annotations, DeepSMILE improves HRD classification performance from 0.77 to 0.81 AUROC compared to tile supervision with either a self-supervised or ImageNet pre-trained feature extractor. Our proposed methods reach the baseline performance using only 40% of the labeled data on both datasets. These improvements suggest we can use standard self-supervised learning techniques combined with multiple instance learning in the histopathology domain to improve genomic label classification performance with fewer labeled data.

eess.IV↗

arXiv2023

BISCUIT: Causal Representation Learning from Binary Interactions

Identifying the causal variables of an environment and how to intervene on them is of core value in applications such as robotics and embodied AI. While an agent can commonly interact with the environment and may implicitly perturb the behavior of some of these causal variables, often the targets it affects remain unknown. In this paper, we show that causal variables can still be identified for many common setups, e.g., additive Gaussian noise models, if the agent's interactions with a causal variable can be described by an unknown binary variable. This happens when each causal variable has two different mechanisms, e.g., an observational and an interventional one. Using this identifiability result, we propose BISCUIT, a method for simultaneously learning causal variables and their corresponding binary interaction variables. On three robotic-inspired datasets, BISCUIT accurately identifies causal variables and can even be scaled to complex, realistic environments for embodied AI.

cs.LG↗

arXiv2023

Graph Switching Dynamical Systems

Dynamical systems with complex behaviours, e.g. immune system cells interacting with a pathogen, are commonly modelled by splitting the behaviour into different regimes, or modes, each with simpler dynamics, and then learning the switching behaviour from one mode to another. Switching Dynamical Systems (SDS) are a powerful tool that automatically discovers these modes and mode-switching behaviour from time series data. While effective, these methods focus on independent objects, where the modes of one object are independent of the modes of the other objects. In this paper, we focus on the more general interacting object setting for switching dynamical systems, where the per-object dynamics also depends on an unknown and dynamically changing subset of other objects and their modes. To this end, we propose a novel graph-based approach for switching dynamical systems, GRAph Switching dynamical Systems (GRASS), in which we use a dynamic graph to characterize interactions between objects and learn both intra-object and inter-object mode-switching behaviour. We introduce two new datasets for this setting, a synthesized ODE-driven particles dataset and a real-world Salsa Couple Dancing dataset. Experiments show that GRASS can consistently outperforms previous state-of-the-art methods.

cs.CV↗

arXiv2023

Modelling Long Range Dependencies in $N$D: From Task-Specific to a General Purpose CNN

Performant Convolutional Neural Network (CNN) architectures must be tailored to specific tasks in order to consider the length, resolution, and dimensionality of the input data. In this work, we tackle the need for problem-specific CNN architectures. We present the Continuous Convolutional Neural Network (CCNN): a single CNN able to process data of arbitrary resolution, dimensionality and length without any structural changes. Its key component are its continuous convolutional kernels which model long-range dependencies at every layer, and thus remove the need of current CNN architectures for task-dependent downsampling and depths. We showcase the generality of our method by using the same architecture for tasks on sequential ($1{\rm D}$), visual ($2{\rm D}$) and point-cloud ($3{\rm D}$) data. Our CCNN matches and often outperforms the current state-of-the-art across all tasks considered.

cs.CV↗

arXiv2023

Few-shot Semantic Segmentation with Support-induced Graph Convolutional Network

Few-shot semantic segmentation (FSS) aims to achieve novel objects segmentation with only a few annotated samples and has made great progress recently. Most of the existing FSS models focus on the feature matching between support and query to tackle FSS. However, the appearance variations between objects from the same category could be extremely large, leading to unreliable feature matching and query mask prediction. To this end, we propose a Support-induced Graph Convolutional Network (SiGCN) to explicitly excavate latent context structure in query images. Specifically, we propose a Support-induced Graph Reasoning (SiGR) module to capture salient query object parts at different semantic levels with a Support-induced GCN. Furthermore, an instance association (IA) module is designed to capture high-order instance context from both support and query instances. By integrating the proposed two modules, SiGCN can learn rich query context representation, and thus being more robust to appearance variations. Extensive experiments on PASCAL-5i and COCO-20i demonstrate that our SiGCN achieves state-of-the-art performance.

cs.CV↗

arXiv2023

Causal Representation Learning for Instantaneous and Temporal Effects in Interactive Systems

Causal representation learning is the task of identifying the underlying causal variables and their relations from high-dimensional observations, such as images. Recent work has shown that one can reconstruct the causal variables from temporal sequences of observations under the assumption that there are no instantaneous causal relations between them. In practical applications, however, our measurement or frame rate might be slower than many of the causal effects. This effectively creates "instantaneous" effects and invalidates previous identifiability results. To address this issue, we propose iCITRIS, a causal representation learning method that allows for instantaneous effects in intervened temporal sequences when intervention targets can be observed, e.g., as actions of an agent. iCITRIS identifies the potentially multidimensional causal variables from temporal observations, while simultaneously using a differentiable causal discovery method to learn their causal graph. In experiments on three datasets of interactive systems, iCITRIS accurately identifies the causal variables and their causal graph.

cs.LG↗

arXiv2023

Batch Bayesian Optimization on Permutations using the Acquisition Weighted Kernel

In this work we propose a batch Bayesian optimization method for combinatorial problems on permutations, which is well suited for expensive-to-evaluate objectives. We first introduce LAW, an efficient batch acquisition method based on determinantal point processes using the acquisition weighted kernel. Relying on multiple parallel evaluations, LAW enables accelerated search on combinatorial spaces. We then apply the framework to permutation problems, which have so far received little attention in the Bayesian Optimization literature, despite their practical importance. We call this method LAW2ORDER. On the theoretical front, we prove that LAW2ORDER has vanishing simple regret by showing that the batch cumulative regret is sublinear. Empirically, we assess the method on several standard combinatorial problems involving permutations such as quadratic assignment, flowshop scheduling and the traveling salesman, as well as on a structure learning task.

stat.ML↗

arXiv2022

Fake It Till You Make It: Towards Accurate Near-Distribution Novelty Detection

We aim for image-based novelty detection. Despite considerable progress, existing models either fail or face a dramatic drop under the so-called "near-distribution" setting, where the differences between normal and anomalous samples are subtle. We first demonstrate existing methods experience up to 20% decrease in performance in the near-distribution setting. Next, we propose to exploit a score-based generative model to produce synthetic near-distribution anomalous data. Our model is then fine-tuned to distinguish such data from the normal samples. We provide a quantitative as well as qualitative evaluation of this strategy, and compare the results with a variety of GAN-based models. Effectiveness of our method for both the near-distribution and standard novelty detection is assessed through extensive experiments on datasets in diverse applications such as medical images, object classification, and quality control. This reveals that our method considerably improves over existing models, and consistently decreases the gap between the near-distribution and standard novelty detection performance. The code repository is available at https://github.com/rohban-lab/FITYMI.

cs.CV↗

arXiv2022

Differentiable Mathematical Programming for Object-Centric Representation Learning

We propose topology-aware feature partitioning into $k$ disjoint partitions for given scene features as a method for object-centric representation learning. To this end, we propose to use minimum $s$-$t$ graph cuts as a partitioning method which is represented as a linear program. The method is topologically aware since it explicitly encodes neighborhood relationships in the image graph. To solve the graph cuts our solution relies on an efficient, scalable, and differentiable quadratic programming approximation. Optimizations specific to cut problems allow us to solve the quadratic programs and compute their gradients significantly more efficiently compared with the general quadratic programming approach. Our results show that our approach is scalable and outperforms existing methods on object discovery tasks with textured scenes and objects.

cs.LG↗

arXiv2022

Mixed Variable Bayesian Optimization with Frequency Modulated Kernels

The sample efficiency of Bayesian optimization(BO) is often boosted by Gaussian Process(GP) surrogate models. However, on mixed variable spaces, surrogate models other than GPs are prevalent, mainly due to the lack of kernels which can model complex dependencies across different types of variables. In this paper, we propose the frequency modulated (FM) kernel flexibly modeling dependencies among different types of variables, so that BO can enjoy the further improved sample efficiency. The FM kernel uses distances on continuous variables to modulate the graph Fourier spectrum derived from discrete variables. However, the frequency modulation does not always define a kernel with the similarity measure behavior which returns higher values for pairs of more similar points. Therefore, we specify and prove conditions for FM kernels to be positive definite and to exhibit the similarity measure behavior. In experiments, we demonstrate the improved sample efficiency of GP BO using FM kernels (BO-FM).On synthetic problems and hyperparameter optimization problems, BO-FM outperforms competitors consistently. Also, the importance of the frequency modulation principle is empirically demonstrated on the same problems. On joint optimization of neural architectures and SGD hyperparameters, BO-FM outperforms competitors including Regularized evolution(RE) and BOHB. Remarkably, BO-FM performs better even than RE and BOHB using three times as many evaluations.

stat.ML↗

arXiv2022

Towards a General Purpose CNN for Long Range Dependencies in $N$D

The use of Convolutional Neural Networks (CNNs) is widespread in Deep Learning due to a range of desirable model properties which result in an efficient and effective machine learning framework. However, performant CNN architectures must be tailored to specific tasks in order to incorporate considerations such as the input length, resolution, and dimentionality. In this work, we overcome the need for problem-specific CNN architectures with our Continuous Convolutional Neural Network (CCNN): a single CNN architecture equipped with continuous convolutional kernels that can be used for tasks on data of arbitrary resolution, dimensionality and length without structural changes. Continuous convolutional kernels model long range dependencies at every layer, and remove the need for downsampling layers and task-dependent depths needed in current CNN architectures. We show the generality of our approach by applying the same CCNN to a wide set of tasks on sequential (1$\mathrm{D}$) and visual data (2$\mathrm{D}$). Our CCNN performs competitively and often outperforms the current state-of-the-art across all tasks considered.

cs.LG↗

arXiv2022

Continual Learning of Dynamical Systems with Competitive Federated Reservoir Computing

Machine learning recently proved efficient in learning differential equations and dynamical systems from data. However, the data is commonly assumed to originate from a single never-changing system. In contrast, when modeling real-world dynamical processes, the data distribution often shifts due to changes in the underlying system dynamics. Continual learning of these processes aims to rapidly adapt to abrupt system changes without forgetting previous dynamical regimes. This work proposes an approach to continual learning based on reservoir computing, a state-of-the-art method for training recurrent neural networks on complex spatiotemporal dynamical systems. Reservoir computing fixes the recurrent network weights - hence these cannot be forgotten - and only updates linear projection heads to the output. We propose to train multiple competitive prediction heads concurrently. Inspired by neuroscience's predictive coding, only the most predictive heads activate, laterally inhibiting and thus protecting the inactive heads from forgetting induced by interfering parameter updates. We show that this multi-head reservoir minimizes interference and catastrophic forgetting on several dynamical systems, including the Van-der-Pol oscillator, the chaotic Lorenz attractor, and the high-dimensional Lorenz-96 weather model. Our results suggest that reservoir computing is a promising candidate framework for the continual learning of dynamical systems. We provide our code for data generation, method, and comparisons at \url{https://github.com/leonardbereska/multiheadreservoir}.

cs.LG↗

arXiv2022

CITRIS: Causal Identifiability from Temporal Intervened Sequences

Understanding the latent causal factors of a dynamical system from visual observations is considered a crucial step towards agents reasoning in complex environments. In this paper, we propose CITRIS, a variational autoencoder framework that learns causal representations from temporal sequences of images in which underlying causal factors have possibly been intervened upon. In contrast to the recent literature, CITRIS exploits temporality and observing intervention targets to identify scalar and multidimensional causal factors, such as 3D rotation angles. Furthermore, by introducing a normalizing flow, CITRIS can be easily extended to leverage and disentangle representations obtained by already pretrained autoencoders. Extending previous results on scalar causal factors, we prove identifiability in a more general setting, in which only some components of a causal factor are affected by interventions. In experiments on 3D rendered image sequences, CITRIS outperforms previous methods on recovering the underlying causal variables. Moreover, using pretrained autoencoders, CITRIS can even generalize to unseen instantiations of causal factors, opening future research areas in sim-to-real generalization for causal representation learning.

cs.LG↗

arXiv2022

Dynamic Prototype Convolution Network for Few-Shot Semantic Segmentation

The key challenge for few-shot semantic segmentation (FSS) is how to tailor a desirable interaction among support and query features and/or their prototypes, under the episodic training scenario. Most existing FSS methods implement such support-query interactions by solely leveraging plain operations - e.g., cosine similarity and feature concatenation - for segmenting the query objects. However, these interaction approaches usually cannot well capture the intrinsic object details in the query images that are widely encountered in FSS, e.g., if the query object to be segmented has holes and slots, inaccurate segmentation almost always happens. To this end, we propose a dynamic prototype convolution network (DPCN) to fully capture the aforementioned intrinsic details for accurate FSS. Specifically, in DPCN, a dynamic convolution module (DCM) is firstly proposed to generate dynamic kernels from support foreground, then information interaction is achieved by convolution operations over query features using these kernels. Moreover, we equip DPCN with a support activation module (SAM) and a feature filtering module (FFM) to generate pseudo mask and filter out background information for the query images, respectively. SAM and FFM together can mine enriched context information from the query features. Our DPCN is also flexible and efficient under the k-shot FSS setting. Extensive experiments on PASCAL-5i and COCO-20i show that DPCN yields superior performances under both 1-shot and 5-shot settings.

cs.CV↗

arXiv2022

NFormer: Robust Person Re-identification with Neighbor Transformer

Person re-identification aims to retrieve persons in highly varying settings across different cameras and scenarios, in which robust and discriminative representation learning is crucial. Most research considers learning representations from single images, ignoring any potential interactions between them. However, due to the high intra-identity variations, ignoring such interactions typically leads to outlier features. To tackle this issue, we propose a Neighbor Transformer Network, or NFormer, which explicitly models interactions across all input images, thus suppressing outlier features and leading to more robust representations overall. As modelling interactions between enormous amount of images is a massive task with lots of distractors, NFormer introduces two novel modules, the Landmark Agent Attention, and the Reciprocal Neighbor Softmax. Specifically, the Landmark Agent Attention efficiently models the relation map between images by a low-rank factorization with a few landmarks in feature space. Moreover, the Reciprocal Neighbor Softmax achieves sparse attention to relevant -- rather than all -- neighbors only, which alleviates interference of irrelevant representations and further relieves the computational burden. In experiments on four large-scale datasets, NFormer achieves a new state-of-the-art. The code is released at \url{https://github.com/haochenheheda/NFormer}.

cs.CV↗

arXiv2022

3D Equivariant Graph Implicit Functions

In recent years, neural implicit representations have made remarkable progress in modeling of 3D shapes with arbitrary topology. In this work, we address two key limitations of such representations, in failing to capture local 3D geometric fine details, and to learn from and generalize to shapes with unseen 3D transformations. To this end, we introduce a novel family of graph implicit functions with equivariant layers that facilitates modeling fine local details and guaranteed robustness to various groups of geometric transformations, through local $k$-NN graph embeddings with sparse point set observations at multiple resolutions. Our method improves over the existing rotation-equivariant implicit function from 0.69 to 0.89 (IoU) on the ShapeNet reconstruction task. We also show that our equivariant implicit function can be extended to other types of similarity transformations and generalizes to unseen translations and scaling.

cs.CV↗

arXiv2022

Delta Distillation for Efficient Video Processing

This paper aims to accelerate video stream processing, such as object detection and semantic segmentation, by leveraging the temporal redundancies that exist between video frames. Instead of propagating and warping features using motion alignment, such as optical flow, we propose a novel knowledge distillation schema coined as Delta Distillation. In our proposal, the student learns the variations in the teacher's intermediate features over time. We demonstrate that these temporal variations can be effectively distilled due to the temporal redundancies within video frames. During inference, both teacher and student cooperate for providing predictions: the former by providing initial representations extracted only on the key-frame, and the latter by iteratively estimating and applying deltas for the successive frames. Moreover, we consider various design choices to learn optimal student architectures including an end-to-end learnable architecture search. By extensive experiments on a wide range of architectures, including the most efficient ones, we demonstrate that delta distillation sets a new state of the art in terms of accuracy vs. efficiency trade-off for semantic segmentation and object detection in videos. Finally, we show that, as a by-product, delta distillation improves the temporal consistency of the teacher model.

cs.CV↗

arXiv2022

Reliably Re-Acting to Partner's Actions with the Social Intrinsic Motivation of Transfer Empowerment

We consider multi-agent reinforcement learning (MARL) for cooperative communication and coordination tasks. MARL agents can be brittle because they can overfit their training partners' policies. This overfitting can produce agents that adopt policies that act under the expectation that other agents will act in a certain way rather than react to their actions. Our objective is to bias the learning process towards finding reactive strategies towards other agents' behaviors. Our method, transfer empowerment, measures the potential influence between agents' actions. Results from three simulated cooperation scenarios support our hypothesis that transfer empowerment improves MARL performance. We discuss how transfer empowerment could be a useful principle to guide multi-agent coordination by ensuring reactiveness to one's partner.

cs.AI↗