Advances in single-cell omics allow for unprecedented insights into the transcription profiles of individual cells. When combined with large-scale perturbation screens, through which specific biological mechanisms can be targeted, these technologies allow for measuring the effect of targeted perturbations on the whole transcriptome. These advances provide an opportunity to better understand the causative role of genes in complex biological processes such as gene regulation, disease progression or cellular development. However, the high-dimensional nature of the data, coupled with the intricate complexity of biological systems renders this task nontrivial. Within the machine learning community, there has been a recent increase of interest in causality, with a focus on adapting established causal techniques and algorithms to handle high-dimensional data. In this perspective, we delineate the application of these methodologies within the realm of single-cell genomics and their challenges. We first present the model that underlies most of current causal approaches to single-cell biology and discuss and challenge the assumptions it entails from the biological point of view. We then identify open problems in the application of causal approaches to single-cell data: generalising to unseen environments, learning interpretable models, and learning causal models of dynamics. For each problem, we discuss how various research directions - including the development of computational approaches and the adaptation of experimental protocols - may offer ways forward, or on the contrary pose some difficulties. With the advent of single cell atlases and increasing perturbation data, we expect causal models to become a crucial tool for informed experimental design.

Explainable artificial intelligence (XAI) is one of the most intensively developed are of AI in recent years. It is also one of the most fragmented one with multiple methods that focus on different aspects of explanations. This makes difficult to obtain the full spectrum of explanation at once in a compact and consistent way. To address this issue, we present Local Universal Explainer (LUX) that is a rule-based explainer which can generate factual, counterfactual and visual explanations. It is based on a modified version of decision tree algorithms that allows for oblique splits and integration with feature importance XAI methods such as SHAP or LIME. It does not use data generation in opposite to other algorithms, but is focused on selecting local concepts in a form of high-density clusters of real data that have the highest impact on forming the decision boundary of the explained model. We tested our method on real and synthetic datasets and compared it with state-of-the-art rule-based explainers such as LORE, EXPLAN and Anchor. Our method outperforms currently existing approaches in terms of simplicity, global fidelity and representativeness.

The posterior in probabilistic programs with stochastic support decomposes as a weighted sum of the local posterior distributions associated with each possible program path. We show that making predictions with this full posterior implicitly performs a Bayesian model averaging (BMA) over paths. This is potentially problematic, as model misspecification can cause the BMA weights to prematurely collapse onto a single path, leading to sub-optimal predictions in turn. To remedy this issue, we propose alternative mechanisms for path weighting: one based on stacking and one based on ideas from PAC-Bayes. We show how both can be implemented as a cheap post-processing step on top of existing inference engines. In our experiments, we find them to be more robust and lead to better predictions compared to the default BMA weights.

Graph data structures are widely used to store relational information between several entities. With data being generated worldwide on a large scale, we see a significant growth in the generation of knowledge graphs. Thing in the future is Orange's take on a knowledge graph in the domain of the Web Of Things (WoT), where the main objective of the platform is to provide a digital representation of the physical world and enable cross-domain applications to be built upon this massive and highly connected graph of things. In this context, as the knowledge graph grows in size, it is prone to have noisy and messy data. In this paper, we explore state-of-the-art knowledge graph embedding (KGE) methods to learn numerical representations of the graph entities and, subsequently, explore downstream tasks like link prediction, node classification, and triple classification. We also investigate Graph neural networks (GNN) alongside KGEs and compare their performance on the same downstream tasks. Our evaluation highlights the encouraging performance of both KGE and GNN-based methods on node classification, and the superiority of GNN approaches in the link prediction task. Overall, we show that state-of-the-art approaches are relevant in a WoT context, and this preliminary work provides insights to implement and evaluate them in this context.

With the rapid advancement of artificial intelligence technology, the usage of machine learning models is gradually becoming part of our daily lives. High-quality models rely not only on efficient optimization algorithms but also on the training and learning processes built upon vast amounts of data and computational power. However, in practice, due to various challenges such as limited computational resources and data privacy concerns, users in need of models often cannot train machine learning models locally. This has led them to explore alternative approaches such as outsourced learning and federated learning. While these methods address the feasibility of model training effectively, they introduce concerns about the trustworthiness of the training process since computations are not performed locally. Similarly, there are trustworthiness issues associated with outsourced model inference. These two problems can be summarized as the trustworthiness problem of model computations: How can one verify that the results computed by other participants are derived according to the specified algorithm, model, and input data? To address this challenge, verifiable machine learning (VML) has emerged. This paper presents a comprehensive survey of zero-knowledge proof-based verifiable machine learning (ZKP-VML) technology. We first analyze the potential verifiability issues that may exist in different machine learning scenarios. Subsequently, we provide a formal definition of ZKP-VML. We then conduct a detailed analysis and classification of existing works based on their technical approaches. Finally, we discuss the key challenges and future directions in the field of ZKP-based VML.

First-order gradient descent has been the base of the most successful optimization algorithms ever implemented. On supervised learning problems with very high dimensionality, such as neural network optimization, it is almost always the algorithm of choice, mainly due to its memory and computational efficiency. However, it is a classical result in optimization that gradient descent converges to local minima on non-convex functions. Even more importantly, in certain high-dimensional cases, escaping the plateaus of large saddle points becomes intractable. On the other hand, black-box optimization methods are not sensitive to the local structure of a loss function's landscape but suffer the curse of dimensionality. Instead, memetic algorithms aim to combine the benefits of both. Inspired by this, we present Population Descent, a memetic algorithm focused on hyperparameter optimization. We show that an adaptive m-elitist selection approach combined with a normalized-fitness-based randomization scheme outperforms more complex state-of-the-art algorithms by up to 13% on common benchmark tasks.

k-nearest-neighbor machine translation has demonstrated remarkable improvements in machine translation quality by creating a datastore of cached examples. However, these improvements have been limited to high-resource language pairs, with large datastores, and remain a challenge for low-resource languages. In this paper, we address this issue by combining representations from multiple languages into a single datastore. Our results consistently demonstrate substantial improvements not only in low-resource translation quality (up to +3.6 BLEU), but also for high-resource translation quality (up to +0.5 BLEU). Our experiments show that it is possible to create multilingual datastores that are a quarter of the size, achieving a 5.3x speed improvement, by using linguistic similarities for datastore creation.

Deep hashing has been intensively studied and successfully applied in large-scale image retrieval systems due to its efficiency and effectiveness. Recent studies have recognized that the existence of adversarial examples poses a security threat to deep hashing models, that is, adversarial vulnerability. Notably, it is challenging to efficiently distill reliable semantic representatives for deep hashing to guide adversarial learning, and thereby it hinders the enhancement of adversarial robustness of deep hashing-based retrieval models. Moreover, current researches on adversarial training for deep hashing are hard to be formalized into a unified minimax structure. In this paper, we explore Semantic-Aware Adversarial Training (SAAT) for improving the adversarial robustness of deep hashing models. Specifically, we conceive a discriminative mainstay features learning (DMFL) scheme to construct semantic representatives for guiding adversarial learning in deep hashing. Particularly, our DMFL with the strict theoretical guarantee is adaptively optimized in a discriminative learning manner, where both discriminative and semantic properties are jointly considered. Moreover, adversarial examples are fabricated by maximizing the Hamming distance between the hash codes of adversarial samples and mainstay features, the efficacy of which is validated in the adversarial attack trials. Further, we, for the first time, formulate the formalized adversarial training of deep hashing into a unified minimax optimization under the guidance of the generated mainstay codes. Extensive experiments on benchmark datasets show superb attack performance against the state-of-the-art algorithms, meanwhile, the proposed adversarial training can effectively eliminate adversarial perturbations for trustworthy deep hashing-based retrieval. Our code is available at https://github.com/xandery-geek/SAAT.

In machining processes, monitoring the condition of the tool is a crucial aspect to ensure high productivity and quality of the product. Using different machine learning techniques in Tool Condition Monitoring (TCM) enables a better analysis of the large amount of data of different signals acquired during the machining processes. The real-time force signals encountered during the process were acquired by performing numerous experiments. Different tool wear conditions were considered during the experimentation. A comprehensive statistical analysis of the data and feature selection using decision trees was conducted, and the KNN algorithm was used to perform classification. Hyperparameter tuning of the model was done to improve the model's performance. Much research has been done to employ machine learning approaches in tool condition monitoring systems; however, a model-agnostic approach to increase the interpretability of the process and get an in-depth understanding of how the decision-making is done is not implemented by many. This research paper presents a KNN-based white box model, which allows us to dive deep into how the model performs the classification and how it prioritizes the different features included. This approach helps in detecting why the tool is in a certain condition and allows the manufacturer to make an informed decision about the tool's maintenance.

Accurate 3D object detection and understanding for self-driving cars heavily relies on LiDAR point clouds, necessitating large amounts of labeled data to train. In this work, we introduce an innovative pre-training approach, Grounded Point Colorization (GPC), to bridge the gap between data and labels by teaching the model to colorize LiDAR point clouds, equipping it with valuable semantic cues. To tackle challenges arising from color variations and selection bias, we incorporate color as "context" by providing ground-truth colors as hints during colorization. Even with limited labeled data, GPC significantly improves finetuning performance; notably, on just 20% of the KITTI dataset, GPC outperforms training from scratch with the entire dataset. In sum, we introduce a fresh perspective on pre-training for 3D object detection, aligning the objective with the model's intended role and ultimately advancing the accuracy and efficiency of 3D object detection for autonomous vehicles. Detecting objects such as vehicles and pedestrians in 3D is crucial for self-driving cars to operate safely. Mainstream 3D object detectors (Shi et al., 2019; 2020b; Zhu et al., 2020; He et al., 2020a) take LiDAR point clouds as input, which provide precise 3D signals of the surrounding environment. However, training a detector needs a lot of labeled data. The expensive process of curating annotated data has motivated the community to investigate model pre-training using unlabeled data that can be collected easily. Most of the existing pre-training methods are built upon contrastive learning (Yin et al., 2022; Xie et al., 2020; Zhang et al., 2021; Huang et al., 2021; Liang et al., 2021), inspired by its success in 2D recognition (Chen et al., 2020a; He et al., 2020b). The key novelties, however, are often limited to how the positive and negative data pairs are constructed. This paper attempts to go beyond contrastive learning by providing a new perspective on pre-training 3D object detectors. We rethink pre-training's role in how it could facilitate the downstream fine-tuning with labeled data.