Finding Regions of Interest in Whole Slide Images Using Multiple Instance Learning

Whole Slide Images (WSI), obtained by high-resolution digital scanning of microscope slides at multiple scales, are the cornerstone of modern Digital Pathology. However, they represent a particular challenge to AI-based/AI-mediated analysis because pathology labeling is typically done at slide-level, instead of tile-level. It is not just that medical diagnostics is recorded at the specimen level, the detection of oncogene mutation is also experimentally obtained, and recorded by initiatives like The Cancer Genome Atlas (TCGA), at the slide level. This configures a dual challenge: a) accurately predicting the overall cancer phenotype and b) finding out what cellular morphologies are associated with it at the tile level. To address these challenges, a weakly supervised Multiple Instance Learning (MIL) approach was explored for two prevalent cancer types, Invasive Breast Carcinoma (TCGA-BRCA) and Lung Squamous Cell Carcinoma (TCGA-LUSC). This approach was explored for tumor detection at low magnification levels and TP53 mutations at various levels. Our results show that a novel additive implementation of MIL matched the performance of reference implementation (AUC 0.96), and was only slightly outperformed by Attention MIL (AUC 0.97). More interestingly from the perspective of the molecular pathologist, these different AI architectures identify distinct sensitivities to morphological features (through the detection of Regions of Interest, RoI) at different amplification levels. Tellingly, TP53 mutation was most sensitive to features at the higher applications where cellular morphology is resolved.

DE-COP: Detecting Copyrighted Content in Language Models Training Data

How can we detect if copyrighted content was used in the training process of a language model, considering that the training data is typically undisclosed? We are motivated by the premise that a language model is likely to identify verbatim excerpts from its training text. We propose DE-COP, a method to determine whether a piece of copyrighted content was included in training. DE-COP's core approach is to probe an LLM with multiple-choice questions, whose options include both verbatim text and their paraphrases. We construct BookTection, a benchmark with excerpts from 165 books published prior and subsequent to a model's training cutoff, along with their paraphrases. Our experiments show that DE-COP surpasses the prior best method by 9.6% in detection performance (AUC) on models with logits available. Moreover, DE-COP also achieves an average accuracy of 72% for detecting suspect books on fully black-box models where prior methods give $\approx$ 4% accuracy. Our code and datasets are available at https://github.com/avduarte333/DE-COP_Method

DeepThought: An Architecture for Autonomous Self-motivated Systems

The ability of large language models (LLMs) to engage in credible dialogues with humans, taking into account the training data and the context of the conversation, has raised discussions about their ability to exhibit intrinsic motivations, agency, or even some degree of consciousness. We argue that the internal architecture of LLMs and their finite and volatile state cannot support any of these properties. By combining insights from complementary learning systems, global neuronal workspace, and attention schema theories, we propose to integrate LLMs and other deep learning systems into an architecture for cognitive language agents able to exhibit properties akin to agency, self-motivation, even some features of meta-cognition.

Matching the Neuronal Representations of V1 is Necessary to Improve Robustness in CNNs with V1-like Front-ends

While some convolutional neural networks (CNNs) have achieved great success in object recognition, they struggle to identify objects in images corrupted with different types of common noise patterns. Recently, it was shown that simulating computations in early visual areas at the front of CNNs leads to improvements in robustness to image corruptions. Here, we further explore this result and show that the neuronal representations that emerge from precisely matching the distribution of RF properties found in primate V1 is key for this improvement in robustness. We built two variants of a model with a front-end modeling the primate primary visual cortex (V1): one sampling RF properties uniformly and the other sampling from empirical biological distributions. The model with the biological sampling has a considerably higher robustness to image corruptions that the uniform variant (relative difference of 8.72%). While similar neuronal sub-populations across the two variants have similar response properties and learn similar downstream weights, the impact on downstream processing is strikingly different. This result sheds light on the origin of the improvements in robustness observed in some biologically-inspired models, pointing to the need of precisely mimicking the neuronal representations found in the primate brain.

Improving Address Matching using Siamese Transformer Networks

Matching addresses is a critical task for companies and post offices involved in the processing and delivery of packages. The ramifications of incorrectly delivering a package to the wrong recipient are numerous, ranging from harm to the company's reputation to economic and environmental costs. This research introduces a deep learning-based model designed to increase the efficiency of address matching for Portuguese addresses. The model comprises two parts: (i) a bi-encoder, which is fine-tuned to create meaningful embeddings of Portuguese postal addresses, utilized to retrieve the top 10 likely matches of the un-normalized target address from a normalized database, and (ii) a cross-encoder, which is fine-tuned to accurately rerank the 10 addresses obtained by the bi-encoder. The model has been tested on a real-case scenario of Portuguese addresses and exhibits a high degree of accuracy, exceeding 95% at the door level. When utilized with GPU computations, the inference speed is about 4.5 times quicker than other traditional approaches such as BM25. An implementation of this system in a real-world scenario would substantially increase the effectiveness of the distribution process. Such an implementation is currently under investigation.

Connecting metrics for shape-texture knowledge in computer vision

Modern artificial neural networks, including convolutional neural networks and vision transformers, have mastered several computer vision tasks, including object recognition. However, there are many significant differences between the behavior and robustness of these systems and of the human visual system. Deep neural networks remain brittle and susceptible to many changes in the image that do not cause humans to misclassify images. Part of this different behavior may be explained by the type of features humans and deep neural networks use in vision tasks. Humans tend to classify objects according to their shape while deep neural networks seem to rely mostly on texture. Exploring this question is relevant, since it may lead to better performing neural network architectures and to a better understanding of the workings of the vision system of primates. In this work, we advance the state of the art in our understanding of this phenomenon, by extending previous analyses to a much larger set of deep neural network architectures. We found that the performance of models in image classification tasks is highly correlated with their shape bias measured at the output and penultimate layer. Furthermore, our results showed that the number of neurons that represent shape and texture are strongly anti-correlated, thus providing evidence that there is competition between these two types of features. Finally, we observed that while in general there is a correlation between performance and shape bias, there are significant variations between architecture families.

Pretraining the Vision Transformer using self-supervised methods for vision based Deep Reinforcement Learning

The Vision Transformer architecture has shown to be competitive in the computer vision (CV) space where it has dethroned convolution-based networks in several benchmarks. Nevertheless, Convolutional Neural Networks (CNN) remain the preferential architecture for the representation module in Reinforcement Learning. In this work, we study pretraining a Vision Transformer using several state-of-the-art self-supervised methods and assess data-efficiency gains from this training framework. We propose a new self-supervised learning method called TOV-VICReg that extends VICReg to better capture temporal relations between observations by adding a temporal order verification task. Furthermore, we evaluate the resultant encoders with Atari games in a sample-efficiency regime. Our results show that the vision transformer, when pretrained with TOV-VICReg, outperforms the other self-supervised methods but still struggles to overcome a CNN. Nevertheless, we were able to outperform a CNN in two of the ten games where we perform a 100k steps evaluation. Ultimately, we believe that such approaches in Deep Reinforcement Learning (DRL) might be the key to achieving new levels of performance as seen in natural language processing and computer vision. Source code will be available at: https://github.com/mgoulao/TOV-VICReg

Assessing Policy, Loss and Planning Combinations in Reinforcement Learning using a New Modular Architecture

The model-based reinforcement learning paradigm, which uses planning algorithms and neural network models, has recently achieved unprecedented results in diverse applications, leading to what is now known as deep reinforcement learning. These agents are quite complex and involve multiple components, factors that can create challenges for research. In this work, we propose a new modular software architecture suited for these types of agents, and a set of building blocks that can be easily reused and assembled to construct new model-based reinforcement learning agents. These building blocks include planning algorithms, policies, and loss functions. We illustrate the use of this architecture by combining several of these building blocks to implement and test agents that are optimized to three different test environments: Cartpole, Minigrid, and Tictactoe. One particular planning algorithm, made available in our implementation and not previously used in reinforcement learning, which we called averaged minimax, achieved good results in the three tested environments. Experiments performed with this architecture have shown that the best combination of planning algorithm, policy, and loss function is heavily problem dependent. This result provides evidence that the proposed architecture, which is modular and reusable, is useful for reinforcement learning researchers who want to study new environments and techniques.

Assessing the Impact of Attention and Self-Attention Mechanisms on the Classification of Skin Lesions

Attention mechanisms have raised significant interest in the research community, since they promise significant improvements in the performance of neural network architectures. However, in any specific problem, we still lack a principled way to choose specific mechanisms and hyper-parameters that lead to guaranteed improvements. More recently, self-attention has been proposed and widely used in transformer-like architectures, leading to significant breakthroughs in some applications. In this work we focus on two forms of attention mechanisms: attention modules and self-attention. Attention modules are used to reweight the features of each layer input tensor. Different modules have different ways to perform this reweighting in fully connected or convolutional layers. The attention models studied are completely modular and in this work they will be used with the popular ResNet architecture. Self-Attention, originally proposed in the area of Natural Language Processing makes it possible to relate all the items in an input sequence. Self-Attention is becoming increasingly popular in Computer Vision, where it is sometimes combined with convolutional layers, although some recent architectures do away entirely with convolutions. In this work, we study and perform an objective comparison of a number of different attention mechanisms in a specific computer vision task, the classification of samples in the widely used Skin Cancer MNIST dataset. The results show that attention modules do sometimes improve the performance of convolutional neural network architectures, but also that this improvement, although noticeable and statistically significant, is not consistent in different settings. The results obtained with self-attention mechanisms, on the other hand, show consistent and significant improvements, leading to the best results even in architectures with a reduced number of parameters.

Using Soft Labels to Model Uncertainty in Medical Image Segmentation

Medical image segmentation is inherently uncertain. For a given image, there may be multiple plausible segmentation hypotheses, and physicians will often disagree on lesion and organ boundaries. To be suited to real-world application, automatic segmentation systems must be able to capture this uncertainty and variability. Thus far, this has been addressed by building deep learning models that, through dropout, multiple heads, or variational inference, can produce a set - infinite, in some cases - of plausible segmentation hypotheses for any given image. However, in clinical practice, it may not be practical to browse all hypotheses. Furthermore, recent work shows that segmentation variability plateaus after a certain number of independent annotations, suggesting that a large enough group of physicians may be able to represent the whole space of possible segmentations. Inspired by this, we propose a simple method to obtain soft labels from the annotations of multiple physicians and train models that, for each image, produce a single well-calibrated output that can be thresholded at multiple confidence levels, according to each application's precision-recall requirements. We evaluated our method on the MICCAI 2021 QUBIQ challenge, showing that it performs well across multiple medical image segmentation tasks, produces well-calibrated predictions, and, on average, performs better at matching physicians' predictions than other physicians.