In the field of biological research, it is essential to comprehend the characteristics and functions of molecular sequences. The classification of molecular sequences has seen widespread use of neural network-based techniques. Despite their astounding accuracy, these models often require a substantial number of parameters and more data collection. In this work, we present a novel approach based on the compression-based Model, motivated from \cite{jiang2023low}, which combines the simplicity of basic compression algorithms like Gzip and Bz2, with Normalized Compression Distance (NCD) algorithm to achieve better performance on classification tasks without relying on handcrafted features or pre-trained models. Firstly, we compress the molecular sequence using well-known compression algorithms, such as Gzip and Bz2. By leveraging the latent structure encoded in compressed files, we compute the Normalized Compression Distance between each pair of molecular sequences, which is derived from the Kolmogorov complexity. This gives us a distance matrix, which is the input for generating a kernel matrix using a Gaussian kernel. Next, we employ kernel Principal Component Analysis (PCA) to get the vector representations for the corresponding molecular sequence, capturing important structural and functional information. The resulting vector representations provide an efficient yet effective solution for molecular sequence analysis and can be used in ML-based downstream tasks. The proposed approach eliminates the need for computationally intensive Deep Neural Networks (DNNs), with their large parameter counts and data requirements. Instead, it leverages a lightweight and universally accessible compression-based model.

Graph Neural Networks (GNNs) can be trained to detect communities within a graph by learning from the duality of feature and connectivity information. Currently, the common approach for optimisation of GNNs is to use comparisons to ground-truth for hyperparameter tuning and model selection. In this work, we show that nodes can be clustered into communities with GNNs by solely optimising for modularity, without any comparison to ground-truth. Although modularity is a graph partitioning quality metric, we show that this can be used to optimise GNNs that also encode features without a drop in performance. We take it a step further and also study whether the unsupervised metric performance can predict ground-truth performance. To investigate why modularity can be used to optimise GNNs, we design synthetic experiments that show the limitations of this approach. The synthetic graphs are created to highlight current capabilities in distinct, random and zero information space partitions in attributed graphs. We conclude that modularity can be used for hyperparameter optimisation and model selection on real-world datasets as well as being a suitable proxy for predicting ground-truth performance, however, GNNs fail to balance the information duality when the spaces contain conflicting signals.

Lung cancer is the primary cause of cancer-related mortality, claiming approximately 1.79 million lives globally in 2020, with an estimated 2.21 million new cases diagnosed within the same period. Among these, Non-Small Cell Lung Cancer (NSCLC) is the predominant subtype, characterized by a notably bleak prognosis and low overall survival rate of approximately 25% over five years across all disease stages. However, survival outcomes vary considerably based on the stage at diagnosis and the therapeutic interventions administered. Recent advancements in artificial intelligence (AI) have revolutionized the landscape of lung cancer prognosis. AI-driven methodologies, including machine learning and deep learning algorithms, have shown promise in enhancing survival prediction accuracy by efficiently analyzing complex multi-omics data and integrating diverse clinical variables. By leveraging AI techniques, clinicians can harness comprehensive prognostic insights to tailor personalized treatment strategies, ultimately improving patient outcomes in NSCLC. Overviewing AI-driven data processing can significantly help bolster the understanding and provide better directions for using such systems.

In recent years, machine learning algorithms have been used in high-stakes decision-making settings, such as healthcare, loan approval, or parole decisions (Baesens et al., 2003; Zeng et al., 2022, 2017). Consequently, there is a growing interest and necessity in their explainability and interpretability (Du et al., 2019; Jung et al., 2020; Molnar et al., 2020; Rudin et al., 2022; Zhang et al., 2019). Once a supervised classification model has been trained, one may be interested in knowing the changes needed to be made in the features of an instance to change the prediction made by the classifier. These changes are the so-called counterfactual explanations (Martens and Provost, 2014; Wachter et al., 2017). There is a growing literature on the development of algorithms to generate counterfactual explanations, see Artelt and Hammer (2019); Guidotti (2022); Karimi et al. (2022); Sokol and Flach (2019); Stepin et al. (2021); Verma et al. (2022) for recent surveys on Counterfactual Analysis. Nevertheless, they mainly focus on the single-instance, single-counterfactual case, where for one specific instance, a single counterfactual is provided (Wachter et al., 2017; Parmentier and Vidal, 2021).

Accurate prediction of pedestrians' future motions is critical for intelligent driving systems. Developing models for this task requires rich datasets containing diverse sets of samples. However, the existing naturalistic trajectory prediction datasets are generally imbalanced in favor of simpler samples and lack challenging scenarios. Such a long-tail effect causes prediction models to underperform on the tail portion of the data distribution containing safety-critical scenarios. Previous methods tackle the long-tail problem using methods such as contrastive learning and class-conditioned hypernetworks. These approaches, however, are not modular and cannot be applied to many machine learning architectures. In this work, we propose a modular model-agnostic framework for trajectory prediction that leverages a specialized mixture of experts. In our approach, each expert is trained with a specialized skill with respect to a particular part of the data. To produce predictions, we utilise a router network that selects the best expert by generating relative confidence scores. We conduct experimentation on common pedestrian trajectory prediction datasets and show that besides achieving state-of-the-art performance, our method significantly performs better on long-tail scenarios. We further conduct ablation studies to highlight the contribution of different proposed components.

The discovery of small molecules with therapeutic potential is a long-standing challenge in chemistry and biology. Researchers have increasingly leveraged novel computational techniques to streamline the drug development process to increase hit rates and reduce the costs associated with bringing a drug to market. To this end, we introduce a quantum-classical generative model that seamlessly integrates the computational power of quantum algorithms trained on a 16-qubit IBM quantum computer with the established reliability of classical methods for designing small molecules. Our hybrid generative model was applied to designing new KRAS inhibitors, a crucial target in cancer therapy. We synthesized 15 promising molecules during our investigation and subjected them to experimental testing to assess their ability to engage with the target. Notably, among these candidates, two molecules, ISM061-018-2 and ISM061-22, each featuring unique scaffolds, stood out by demonstrating effective engagement with KRAS. ISM061-018-2 was identified as a broad-spectrum KRAS inhibitor, exhibiting a binding affinity to KRAS-G12D at $1.4 \mu M$. Concurrently, ISM061-22 exhibited specific mutant selectivity, displaying heightened activity against KRAS G12R and Q61H mutants. To our knowledge, this work shows for the first time the use of a quantum-generative model to yield experimentally confirmed biological hits, showcasing the practical potential of quantum-assisted drug discovery to produce viable therapeutics. Moreover, our findings reveal that the efficacy of distribution learning correlates with the number of qubits utilized, underlining the scalability potential of quantum computing resources. Overall, we anticipate our results to be a stepping stone towards developing more advanced quantum generative models in drug discovery.

Data cleansing aims to improve model performance by removing a set of harmful instances from the training dataset. Data Shapley is a common theoretically guaranteed method to evaluate the contribution of each instance to model performance; however, it requires training on all subsets of the training data, which is computationally expensive. In this paper, we propose an iterativemethod to fast identify a subset of instances with low data Shapley values by using the thresholding bandit algorithm. We provide a theoretical guarantee that the proposed method can accurately select harmful instances if a sufficiently large number of iterations is conducted. Empirical evaluation using various models and datasets demonstrated that the proposed method efficiently improved the computational speed while maintaining the model performance.

The class imbalance problem is a classic classification problem, which arises because the number of negative samples (i.e., majority class) in the data set is much larger than the number of positive samples (i.e., minority class)[4]. This type of problem is common in many fields. For example, in the field of financial fraud, the occurrence of occasional small-probability fraud will cause huge economic losses. Therefore, accurately identifying positive samples will be the key to the class imbalance problem. The first difficulty in the class imbalance problem is mainly due to the rarity of positive samples, which has two connotations[2]: One is absolutely rare, which makes the data not representative enough and has a lot of noise; the other is relatively rare, which causes the feature space to overlap seriously, making it hard for the model to accurately separate the two classes. The second reason is the potential discrimination toward positive samples by current mainstream classifiers. Many current models treat the majority and minority classes equally when evaluating classification accuracy, resulting in the direction of model evaluation being naturally biased towards the majorities; the third reason is the potential discrimination toward important samples in positive samples by the oversampling model. SMOTE, as a classic oversampling method to solve class imbalance[1], only selects the data randomly when expanding the minorities, which may result in more serious feature space overlap because of the ignoration of important samples in minorities. To solve the various problems mentioned above, we propose a hierarchical Smote Based on Marginalized Minorities(MM-SMOTE). First, we use the basic SVM classifier to roughly classify the data, and obtain the support vectors in minorities as important samples for sampling; then assign weights to those support vectors based on their distance to the decision hyperplane; and then based on the k-nearest neighbors of support vectors, we used an adaptive oversampling to generate synthetic samples; finally, synthetic samples are used to augment the original kernel function of the basic SVM to form a new classifier.

This paper studies online structured prediction with full-information feedback. For online multiclass classification, van der Hoeven (2020) has obtained surrogate regret bounds independent of the time horizon, or \emph{finite}, by introducing an elegant \emph{exploit-the-surrogate-gap} framework. However, this framework has been limited to multiclass classification primarily because it relies on a classification-specific procedure for converting estimated scores to outputs. We extend the exploit-the-surrogate-gap framework to online structured prediction with \emph{Fenchel--Young losses}, a large family of surrogate losses including the logistic loss for multiclass classification, obtaining finite surrogate regret bounds in various structured prediction problems. To this end, we propose and analyze \emph{randomized decoding}, which converts estimated scores to general structured outputs. Moreover, by applying our decoding to online multiclass classification with the logistic loss, we obtain a surrogate regret bound of $O(B^2)$, where $B$ is the $\ell_2$-diameter of the domain. This bound is tight up to logarithmic factors and improves the previous bound of $O(dB^2)$ due to van der Hoeven (2020) by a factor of $d$, the number of classes.

Learning positional information of nodes in a graph is important for link prediction tasks. We propose a representation of positional information using representative nodes called landmarks. A small number of nodes with high degree centrality are selected as landmarks, which serve as reference points for the nodes' positions. We justify this selection strategy for well-known random graph models and derive closed-form bounds on the average path lengths involving landmarks. In a model for power-law graphs, we prove that landmarks provide asymptotically exact information on inter-node distances. We apply theoretical insights to practical networks and propose Hierarchical Position embedding with Landmarks and Clustering (HPLC). HPLC combines landmark selection and graph clustering, where the graph is partitioned into densely connected clusters in which nodes with the highest degree are selected as landmarks. HPLC leverages the positional information of nodes based on landmarks at various levels of hierarchy such as nodes' distances to landmarks, inter-landmark distances and hierarchical grouping of clusters. Experiments show that HPLC achieves state-of-the-art performances of link prediction on various datasets in terms of HIT@K, MRR, and AUC. The code is available at \url{https://github.com/kmswin1/HPLC}.