Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many potential applications and can be modelled using a continuous-time Markov chain (CTMC). Here we present ViDa, a new visualization approach for DNA reaction trajectories that uses a 2D embedding of the secondary structure state space underlying the CTMC model. To this end, we integrate a scattering transform of the secondary structure adjacency, a variational autoencoder, and a nonlinear dimensionality reduction method. We augment the training loss with domain-specific supervised terms that capture both thermodynamic and kinetic features. We assess ViDa on two well-studied DNA hybridization reactions. Our results demonstrate that the domain-specific features lead to significant quality improvements over the state-of-the-art in DNA state space visualization, successfully separating different folding pathways and thus providing useful insights into dominant reaction mechanisms.

Single-cell RNA sequencing (scRNA-seq) is important to transcriptomic analysis of gene expression. Recently, deep learning has facilitated the analysis of high-dimensional single-cell data. Unfortunately, deep learning models may leak sensitive information about users. As a result, Differential Privacy (DP) is increasingly used to protect privacy. However, existing DP methods usually perturb whole neural networks to achieve differential privacy, and hence result in great performance overheads. To address this challenge, in this paper, we take advantage of the uniqueness of the autoencoder that it outputs only the dimension-reduced vector in the middle of the network, and design a Differentially Private Deep Contrastive Autoencoder Network (DP-DCAN) by partial network perturbation for single-cell clustering. Since only partial network is added with noise, the performance improvement is obvious and twofold: one part of network is trained with less noise due to a bigger privacy budget, and the other part is trained without any noise. Experimental results of six datasets have verified that DP-DCAN is superior to the traditional DP scheme with whole network perturbation. Moreover, DP-DCAN demonstrates strong robustness to adversarial attacks. The code is available at https://github.com/LFD-byte/DP-DCAN.

Machine learning (ML) has employed various discretization methods to partition numerical attributes into intervals. However, an effective discretization technique remains elusive in many ML applications, such as association rule mining. Moreover, the existing discretization techniques do not reflect best the impact of the independent numerical factor on the dependent numerical target factor. This research aims to establish a benchmark approach for numerical attribute partitioning. We conduct an extensive analysis of human perceptions of partitioning a numerical attribute and compare these perceptions with the results obtained from our two proposed measures. We also examine the perceptions of experts in data science, statistics, and engineering by employing numerical data visualization techniques. The analysis of collected responses reveals that $68.7\%$ of human responses approximately closely align with the values generated by our proposed measures. Based on these findings, our proposed measures may be used as one of the methods for discretizing the numerical attributes.

In recent years, process mining emerged as a proven technology to analyze and improve operational processes. An expanding range of organizations using process mining in their daily operation brings a broader spectrum of processes to be analyzed. Some of these processes are highly unstructured, making it difficult for traditional process discovery approaches to discover a start-to-end model describing the entire process. Therefore, the subdiscipline of Local Process Model (LPM) discovery tries to build a set of LPMs, i.e., smaller models that explain sub-behaviors of the process. However, like other pattern mining approaches, LPM discovery algorithms also face the problems of model explosion and model repetition, i.e., the algorithms may create hundreds if not thousands of models, and subsets of them are close in structure or behavior. This work proposes a three-step pipeline for grouping similar LPMs using various process model similarity measures. We demonstrate the usefulness of grouping through a real-life case study, and analyze the impact of different measures, the gravity of repetition in the discovered LPMs, and how it improves after grouping on multiple real event logs.

We present HUME, a simple model-agnostic framework for inferring human labeling of a given dataset without any external supervision. The key insight behind our approach is that classes defined by many human labelings are linearly separable regardless of the representation space used to represent a dataset. HUME utilizes this insight to guide the search over all possible labelings of a dataset to discover an underlying human labeling. We show that the proposed optimization objective is strikingly well-correlated with the ground truth labeling of the dataset. In effect, we only train linear classifiers on top of pretrained representations that remain fixed during training, making our framework compatible with any large pretrained and self-supervised model. Despite its simplicity, HUME outperforms a supervised linear classifier on top of self-supervised representations on the STL-10 dataset by a large margin and achieves comparable performance on the CIFAR-10 dataset. Compared to the existing unsupervised baselines, HUME achieves state-of-the-art performance on four benchmark image classification datasets including the large-scale ImageNet-1000 dataset. Altogether, our work provides a fundamentally new view to tackle unsupervised learning by searching for consistent labelings between different representation spaces.

Benefiting from the strong view-consistent information mining capacity, multi-view contrastive clustering has attracted plenty of attention in recent years. However, we observe the following drawback, which limits the clustering performance from further improvement. The existing multi-view models mainly focus on the consistency of the same samples in different views while ignoring the circumstance of similar but different samples in cross-view scenarios. To solve this problem, we propose a novel Dual contrastive calibration network for Multi-View Clustering (DealMVC). Specifically, we first design a fusion mechanism to obtain a global cross-view feature. Then, a global contrastive calibration loss is proposed by aligning the view feature similarity graph and the high-confidence pseudo-label graph. Moreover, to utilize the diversity of multi-view information, we propose a local contrastive calibration loss to constrain the consistency of pair-wise view features. The feature structure is regularized by reliable class information, thus guaranteeing similar samples have similar features in different views. During the training procedure, the interacted cross-view feature is jointly optimized at both local and global levels. In comparison with other state-of-the-art approaches, the comprehensive experimental results obtained from eight benchmark datasets provide substantial validation of the effectiveness and superiority of our algorithm. We release the code of DealMVC at https://github.com/xihongyang1999/DealMVC on GitHub.

Due to the high heterogeneity and clinical characteristics of cancer, there are significant differences in multi-omics data and clinical features among subtypes of different cancers. Therefore, the identification and discovery of cancer subtypes are crucial for the diagnosis, treatment, and prognosis of cancer. In this study, we proposed a generalization framework based on attention mechanisms for unsupervised contrastive learning to analyze cancer multi-omics data for the identification and characterization of cancer subtypes. The framework contains a symmetric unsupervised multi-head attention encoder, which can deeply extract contextual features and long-range dependencies of multi-omics data, reducing the impact of noise in multi-omics data. Importantly, the proposed framework includes a decoupled contrastive learning model (DEDUCE) based on a multi-head attention mechanism to learn multi-omics data features and clustering and identify cancer subtypes. This method clusters subtypes by calculating the similarity between samples in the feature space and sample space of multi-omics data. The basic idea is to decouple different attributes of multi-omics data features and learn them as contrasting terms. Construct a contrastive loss function to measure the difference between positive examples and negative examples, and minimize this difference, thereby encouraging the model to learn better feature representation. The DEDUCE model conducts large-scale experiments on simulated multi-omics data sets, single-cell multi-omics data sets and cancer multi-omics data sets, and the results are better than 10 deep learning models. Finally, we used the DEDUCE model to reveal six cancer subtypes of AML. By analyzing GO functional enrichment, subtype-specific biological functions and GSEA of AML,

Current self-supervised learning (SSL) methods (e.g., SimCLR, DINO, VICReg,MOCOv3) target primarily on representations at instance level and do not generalize well to dense prediction tasks, such as object detection and segmentation.Towards aligning SSL with dense predictions, this paper demonstrates for the first time the underlying mean-shift clustering process of Vision Transformers (ViT), which aligns well with natural image semantics (e.g., a world of objects and stuffs). By employing transformer for joint embedding and clustering, we propose a two-level feature clustering SSL method, coined Feature-Level Self-supervised Learning (FLSL). We present the formal definition of the FLSL problem and construct the objectives from the mean-shift and k-means perspectives. We show that FLSL promotes remarkable semantic cluster representations and learns an embedding scheme amenable to intra-view and inter-view feature clustering. Experiments show that FLSL yields significant improvements in dense prediction tasks, achieving 44.9 (+2.8)% AP and 46.5% AP in object detection, as well as 40.8 (+2.3)% AP and 42.1% AP in instance segmentation on MS-COCO, using Mask R-CNN with ViT-S/16 and ViT-S/8 as backbone, respectively. FLSL consistently outperforms existing SSL methods across additional benchmarks, including UAV17 object detection on UAVDT, and video instance segmentation on DAVIS 2017.We conclude by presenting visualization and various ablation studies to better understand the success of FLSL. The source code is available at https://github.com/ISL-CV/FLSL.

We introduce a differentiable clustering method based on stochastic perturbations of minimum-weight spanning forests. This allows us to include clustering in end-to-end trainable pipelines, with efficient gradients. We show that our method performs well even in difficult settings, such as data sets with high noise and challenging geometries. We also formulate an ad hoc loss to efficiently learn from partial clustering data using this operation. We demonstrate its performance on several data sets for supervised and semi-supervised tasks.

Evaluating and optimizing policies in the presence of unobserved confounders is a problem of growing interest in offline reinforcement learning. Using conventional methods for offline RL in the presence of confounding can not only lead to poor decisions and poor policies, but also have disastrous effects in critical applications such as healthcare and education. We map out the landscape of offline policy evaluation for confounded MDPs, distinguishing assumptions on confounding based on whether they are memoryless and on their effect on the data-collection policies. We characterize settings where consistent value estimates are provably not achievable, and provide algorithms with guarantees to instead estimate lower bounds on the value. When consistent estimates are achievable, we provide algorithms for value estimation with sample complexity guarantees. We also present new algorithms for offline policy improvement and prove local convergence guarantees. Finally, we experimentally evaluate our algorithms on both a gridworld environment and a simulated healthcare setting of managing sepsis patients. In gridworld, our model-based method provides tighter lower bounds than existing methods, while in the sepsis simulator, our methods significantly outperform confounder-oblivious benchmarks.