Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use publicly available datasets, there is however no adopted standard for citing the datasets used in scientific papers, leading to difficulty in tracking dataset usage. In this work, we present two open-source tools we created that could help with the detection of dataset usage, a pipeline \url{//github.com/TheoSourget/Public_Medical_Datasets_References} using OpenAlex and full-text analysis, and a PDF annotation software \url{//github.com/TheoSourget/pdf_annotator} used in our study to manually label the presence of datasets. We applied both tools on a study of the usage of 20 publicly available medical datasets in papers from MICCAI and MIDL. We compute the proportion and the evolution between 2013 and 2023 of 3 types of presence in a paper: cited, mentioned in the full text, cited and mentioned. Our findings demonstrate the concentration of the usage of a limited set of datasets. We also highlight different citing practices, making the automation of tracking difficult.
Compared to other techniques, particle swarm optimization is more frequently utilized because of its ease of use and low variability. However, it is complicated to find the best possible solution in the search space in large-scale optimization problems. Moreover, changing algorithm variables does not influence algorithm convergence much. The PSO algorithm can be combined with other algorithms. It can use their advantages and operators to solve this problem. Therefore, this paper proposes the onlooker multi-parent crossover discrete particle swarm optimization (OMPCDPSO). To improve the efficiency of the DPSO algorithm, we utilized multi-parent crossover on the best solutions. We performed an independent and intensive neighborhood search using the onlooker bees of the bee algorithm. The algorithm uses onlooker bees and crossover. They do local search (exploitation) and global search (exploration). Each of these searches is among the best solutions (employed bees). The proposed algorithm was tested on the allocation problem, which is an NP-hard optimization problem. Also, we used two types of simulated data. They were used to test the scalability and complexity of the better algorithm. Also, fourteen 2D test functions and thirteen 30D test functions were used. They also used twenty IEEE CEC2005 benchmark functions to test the efficiency of OMPCDPSO. Also, to test OMPCDPSO's performance, we compared it to four new binary optimization algorithms and three classic ones. The results show that the OMPCDPSO version had high capability. It performed better than other algorithms. The developed algorithm in this research (OMCDPSO) in 36 test functions out of 47 (76.60%) is better than other algorithms. The Onlooker bees and multi-parent operators significantly impact the algorithm's performance.
In this paper, we propose two algorithms for a hybrid construction of all $n\times n$ MDS and involutory MDS matrices over a finite field $\mathbb{F}_{p^m}$, respectively. The proposed algorithms effectively narrow down the search space to identify $(n-1) \times (n-1)$ MDS matrices, facilitating the generation of all $n \times n$ MDS and involutory MDS matrices over $\mathbb{F}_{p^m}$. To the best of our knowledge, existing literature lacks methods for generating all $n\times n$ MDS and involutory MDS matrices over $\mathbb{F}_{p^m}$. In our approach, we introduce a representative matrix form for generating all $n\times n$ MDS and involutory MDS matrices over $\mathbb{F}_{p^m}$. The determination of these representative MDS matrices involves searching through all $(n-1)\times (n-1)$ MDS matrices over $\mathbb{F}_{p^m}$. Our contributions extend to proving that the count of all $3\times 3$ MDS matrices over $\mathbb{F}_{2^m}$ is precisely $(2^m-1)^5(2^m-2)(2^m-3)(2^{2m}-9\cdot 2^m+21)$. Furthermore, we explicitly provide the count of all $4\times 4$ MDS and involutory MDS matrices over $\mathbb{F}_{2^m}$ for $m=2, 3, 4$.
Uncertainty is a key feature of any machine learning model and is particularly important in neural networks, which tend to be overconfident. This overconfidence is worrying under distribution shifts, where the model performance silently degrades as the data distribution diverges from the training data distribution. Uncertainty estimation offers a solution to overconfident models, communicating when the output should (not) be trusted. Although methods for uncertainty estimation have been developed, they have not been explicitly linked to the field of explainable artificial intelligence (XAI). Furthermore, literature in operations research ignores the actionability component of uncertainty estimation and does not consider distribution shifts. This work proposes a general uncertainty framework, with contributions being threefold: (i) uncertainty estimation in ML models is positioned as an XAI technique, giving local and model-specific explanations; (ii) classification with rejection is used to reduce misclassifications by bringing a human expert in the loop for uncertain observations; (iii) the framework is applied to a case study on neural networks in educational data mining subject to distribution shifts. Uncertainty as XAI improves the model's trustworthiness in downstream decision-making tasks, giving rise to more actionable and robust machine learning systems in operations research.
We explore the training dynamics of neural networks in a structured non-IID setting where documents are presented cyclically in a fixed, repeated sequence. Typically, networks suffer from catastrophic interference when training on a sequence of documents; however, we discover a curious and remarkable property of LLMs fine-tuned sequentially in this setting: they exhibit anticipatory behavior, recovering from the forgetting on documents before encountering them again. The behavior emerges and becomes more robust as the architecture scales up its number of parameters. Through comprehensive experiments and visualizations, we uncover new insights into training over-parameterized networks in structured environments.
Clustering of publication networks is an efficient way to obtain classifications of large collections of research publications. Such classifications can be used to, e.g., detect research topics, normalize citation relations, or explore the publication output of a unit. Citation networks can be created using a variety of approaches. Best practices to obtain classifications using clustering have been investigated, in particular the performance of different publication-publication relatedness measures. However, evaluation of different approaches to normalization of citation relations have not been explored to the same extent. In this paper, we evaluate five approaches to normalization of direct citation relations with respect to clustering solution quality in four data sets. A sixth approach is evaluated using no normalization. To assess the quality of clustering solutions, we use three measures. (1) We compare the clustering solution to the reference lists of a set of publications using the Adjusted Rand Index. (2) Using the Sihouette width measure, we quantity to which extent the publications have relations to other clusters than the one they have been assigned to. (3) We propose a measure that captures publications that have probably been inaccurately assigned. The results clearly show that normalization is preferred over unnormalized direct citation relations. Furthermore, the results indicate that the fractional normalization approach, which can be considered the standard approach, causes inaccurate assignments. The geometric normalization approach has a similar performance as the fractional approach regarding Adjusted Rand Index and Silhouette width but leads to fewer inaccurate assignments. We therefore believe that the geometric approach may be preferred over the fractional approach.
Conversation demands attention. Speakers must call words to mind, listeners must make sense of them, and both together must negotiate this flow of information, all in fractions of a second. We used large language models to study how this works in a large-scale dataset of English-language conversation, the CANDOR corpus. We provide a new estimate of the information density of unstructured conversation, of approximately 13 bits/second, and find significant effects associated with the cognitive load of both retrieving, and presenting, that information. We also reveal a role for backchannels -- the brief yeahs, uh-huhs, and mhmms that listeners provide -- in regulating the production of novelty: the lead-up to a backchannel is associated with declining information rate, while speech downstream rebounds to previous rates. Our results provide new insights into long-standing theories of how we respond to fluctuating demands on cognitive resources, and how we negotiate those demands in partnership with others.
Marginal structural models have been increasingly used by analysts in recent years to account for confounding bias in studies with time-varying treatments. The parameters of these models are often estimated using inverse probability of treatment weighting. To ensure that the estimated weights adequately control confounding, it is possible to check for residual imbalance between treatment groups in the weighted data. Several balance metrics have been developed and compared in the cross-sectional case but have not yet been evaluated and compared in longitudinal studies with time-varying treatment. We have first extended the definition of several balance metrics to the case of a time-varying treatment, with or without censoring. We then compared the performance of these balance metrics in a simulation study by assessing the strength of the association between their estimated level of imbalance and bias. We found that the Mahalanobis balance performed best.Finally, the method was illustrated for estimating the cumulative effect of statins exposure over one year on the risk of cardiovascular disease or death in people aged 65 and over in population-wide administrative data. This illustration confirms the feasibility of employing our proposed metrics in large databases with multiple time-points.
Markov networks are probabilistic graphical models that employ undirected graphs to depict conditional independence relationships among variables. Our focus lies in constraint-based structure learning, which entails learning the undirected graph from data through the execution of conditional independence tests. We establish theoretical limits concerning two critical aspects of constraint-based learning of Markov networks: the number of tests and the sizes of the conditioning sets. These bounds uncover an exciting interplay between the structural properties of the graph and the amount of tests required to learn a Markov network. The starting point of our work is that the graph parameter maximum pairwise connectivity, $\kappa$, that is, the maximum number of vertex-disjoint paths connecting a pair of vertices in the graph, is responsible for the sizes of independence tests required to learn the graph. On one hand, we show that at least one test with the size of the conditioning set at least $\kappa$ is always necessary. On the other hand, we prove that any graph can be learned by performing tests of size at most $\kappa$. This completely resolves the question of the minimum size of conditioning sets required to learn the graph. When it comes to the number of tests, our upper bound on the sizes of conditioning sets implies that every $n$-vertex graph can be learned by at most $n^{\kappa}$ tests with conditioning sets of sizes at most $\kappa$. We show that for any upper bound $q$ on the sizes of the conditioning sets, there exist graphs with $O(n q)$ vertices that require at least $n^{\Omega(\kappa)}$ tests to learn. This lower bound holds even when the treewidth and the maximum degree of the graph are at most $\kappa+2$. On the positive side, we prove that every graph of bounded treewidth can be learned by a polynomial number of tests with conditioning sets of sizes at most $2\kappa$.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.