Explainability for Deep Learning Models is especially important for clinical applications, where decisions of automated systems have far-reaching consequences. While various post-hoc explainable methods, such as attention visualization and saliency maps, already exist for common data modalities, including natural language and images, little work has been done to adapt them to the modality of Flow CytoMetry (FCM) data. In this work, we evaluate the usage of a transformer architecture called ReluFormer that ease attention visualization as well as we propose a gradient- and an attention-based visualization technique tailored for FCM. We qualitatively evaluate the visualization techniques for cell classification and polygon regression on pediatric Acute Lymphoblastic Leukemia (ALL) FCM samples. The results outline the model's decision process and demonstrate how to utilize the proposed techniques to inspect the trained model. The gradient-based visualization not only identifies cells that are most significant for a particular prediction but also indicates the directions in the FCM feature space in which changes have the most impact on the prediction. The attention visualization provides insights on the transformer's decision process when handling FCM data. We show that different attention heads specialize by attending to different biologically meaningful sub-populations in the data, even though the model retrieved solely supervised binary classification signals during training.
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Obtaining sparse, interpretable representations of observable data is crucial in many machine learning and signal processing tasks. For data representing flows along the edges of a graph, an intuitively interpretable way to obtain such representations is to lift the graph structure to a simplicial complex: The eigenvectors of the associated Hodge-Laplacian, respectively the incidence matrices of the corresponding simplicial complex then induce a Hodge decomposition, which can be used to represent the observed data in terms of gradient, curl, and harmonic flows. In this paper, we generalize this approach to cellular complexes and introduce the cell inference optimization problem, i.e., the problem of augmenting the observed graph by a set of cells, such that the eigenvectors of the associated Hodge Laplacian provide a sparse, interpretable representation of the observed edge flows on the graph. We show that this problem is NP-hard and introduce an efficient approximation algorithm for its solution. Experiments on real-world and synthetic data demonstrate that our algorithm outperforms current state-of-the-art methods while being computationally efficient.
Automatic identification of clinical trials for which a patient is eligible is complicated by the fact that trial eligibility is stated in natural language. A potential solution to this problem is to employ text classification methods for common types of eligibility criteria. In this study, we focus on seven common exclusion criteria in cancer trials: prior malignancy, human immunodeficiency virus, hepatitis B, hepatitis C, psychiatric illness, drug/substance abuse, and autoimmune illness. Our dataset consists of 764 phase III cancer trials with these exclusions annotated at the trial level. We experiment with common transformer models as well as a new pre-trained clinical trial BERT model. Our results demonstrate the feasibility of automatically classifying common exclusion criteria. Additionally, we demonstrate the value of a pre-trained language model specifically for clinical trials, which yields the highest average performance across all criteria.
The analysis of structured complex data, such as clustered graph based datasets, usually applies a variety of visual representation techniques and formats. The majority of currently available tools and approaches to exploratory visualization are built on integrated schemes for simultaneous displaying of multiple aspects of studying objects and processes. Usually, such schemes partition screen space that is composed of multiple views and adopt interaction patterns to focus on data-driven items. Widely known concepts as overview plus-detail and focus-plus-context are ambiguous in interpretation by means of technical terms. Therefore, their implementation by UI design practitioners need reviews and a classification of the basic approaches to visual composition of graphical representation modules. We propose a description of basic components of the view and focus and an overview of their multiple combinations.
Despite the general consensus in transport research community that model calibration and validation are necessary to enhance model predictive performance, there exist significant inconsistencies in the literature. This is primarily due to a lack of consistent definitions, and a unified and statistically sound framework. In this paper, we provide a general and rigorous formulation of the model calibration and validation problem, and highlight its relation to statistical inference. We also conduct a comprehensive review of the steps and challenges involved, as well as point out inconsistencies, before providing suggestions on improving the current practices. This paper is intended to help the practitioners better understand the nature of model calibration and validation, and to promote statistically rigorous and correct practices. Although the examples are drawn from a transport research background - and that is our target audience - the content in this paper is equally applicable to other modelling contexts.
We consider a decentralized formulation of the active hypothesis testing (AHT) problem, where multiple agents gather noisy observations from the environment with the purpose of identifying the correct hypothesis. At each time step, agents have the option to select a sampling action. These different actions result in observations drawn from various distributions, each associated with a specific hypothesis. The agents collaborate to accomplish the task, where message exchanges between agents are allowed over a rate-limited communications channel. The objective is to devise a multi-agent policy that minimizes the Bayes risk. This risk comprises both the cost of sampling and the joint terminal cost incurred by the agents upon making a hypothesis declaration. Deriving optimal structured policies for AHT problems is generally mathematically intractable, even in the context of a single agent. As a result, recent efforts have turned to deep learning methodologies to address these problems, which have exhibited significant success in single-agent learning scenarios. In this paper, we tackle the multi-agent AHT formulation by introducing a novel algorithm rooted in the framework of deep multi-agent reinforcement learning. This algorithm, named Multi-Agent Reinforcement Learning for AHT (MARLA), operates at each time step by having each agent map its state to an action (sampling rule or stopping rule) using a trained deep neural network with the goal of minimizing the Bayes risk. We present a comprehensive set of experimental results that effectively showcase the agents' ability to learn collaborative strategies and enhance performance using MARLA. Furthermore, we demonstrate the superiority of MARLA over single-agent learning approaches. Finally, we provide an open-source implementation of the MARLA framework, for the benefit of researchers and developers in related domains.
Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.
Benefit from the quick development of deep learning techniques, salient object detection has achieved remarkable progresses recently. However, there still exists following two major challenges that hinder its application in embedded devices, low resolution output and heavy model weight. To this end, this paper presents an accurate yet compact deep network for efficient salient object detection. More specifically, given a coarse saliency prediction in the deepest layer, we first employ residual learning to learn side-output residual features for saliency refinement, which can be achieved with very limited convolutional parameters while keep accuracy. Secondly, we further propose reverse attention to guide such side-output residual learning in a top-down manner. By erasing the current predicted salient regions from side-output features, the network can eventually explore the missing object parts and details which results in high resolution and accuracy. Experiments on six benchmark datasets demonstrate that the proposed approach compares favorably against state-of-the-art methods, and with advantages in terms of simplicity, efficiency (45 FPS) and model size (81 MB).
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis.
Detecting carried objects is one of the requirements for developing systems to reason about activities involving people and objects. We present an approach to detect carried objects from a single video frame with a novel method that incorporates features from multiple scales. Initially, a foreground mask in a video frame is segmented into multi-scale superpixels. Then the human-like regions in the segmented area are identified by matching a set of extracted features from superpixels against learned features in a codebook. A carried object probability map is generated using the complement of the matching probabilities of superpixels to human-like regions and background information. A group of superpixels with high carried object probability and strong edge support is then merged to obtain the shape of the carried object. We applied our method to two challenging datasets, and results show that our method is competitive with or better than the state-of-the-art.
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