自然语言和生物学序列之间的明显相似之处已导致最新的深层语言模型（LMS）在抗体和其他生物学序列分析中的应用激增。但是，缺乏对生物序列语言的严格语言形式化，这些语言将定义基本组成部分，例如词典（即语言的离散单元）和语法（即，将序列序列良好的规则，结构和结构和结构和结构和结构链接的规则链接在一起含义）导致了LMS的主要域无规定应用，这些应用未考虑研究的生物序列的基础结构。另一方面，语言形式化为LM应用建立了语言信息，因此适应域的组件。它将有助于更好地理解自然语言和生物序列之间的差异和相似性如何影响LMS的质量，这对于具有可解释的模型具有可解释的模型至关重要。解密抗体特异性规则对于加速有理和硅生物治疗药物设计至关重要。在这里，我们将抗体语言的特性形式化，因此不仅建立了语言工具在适应性免疫受体分析中应用的基础，而且还为免疫受体特异性的系统免疫语言学研究提供了基础。

基于神经网络的深层语言模型（LMS）越来越多地应用于大规模蛋白质序列数据以预测蛋白质功能。然而，作为黑框模型，当前的蛋白质LM方法并不促进对序列功能映射的基本理解，而阻碍了基于规则的生物治疗药物开发，因此目前的蛋白质LM方法不大。我们认为，从语言学中得出的指导是从自然语言数据中提取分析规则的领域，可以帮助构建学习相关领域特定规则的更容易解释的蛋白质LM。与自然语言LMS相比，蛋白质序列数据和语言序列数据之间的差异需要在蛋白质LMS中集成更多的域特异性知识。在这里，我们为培训数据，令牌化，令牌嵌入，序列嵌入和模型解释提供了基于语言学的路线图。将语言学与蛋白质LMS结合起来，可以发展下一代可解释的机器学习模型，并有可能发现序列功能关系基础的生物学机制。

Selecting the number of topics in LDA models is considered to be a difficult task, for which alternative approaches have been proposed. The performance of the recently developed singular Bayesian information criterion (sBIC) is evaluated and compared to the performance of alternative model selection criteria. The sBIC is a generalization of the standard BIC that can be implemented to singular statistical models. The comparison is based on Monte Carlo simulations and carried out for several alternative settings, varying with respect to the number of topics, the number of documents and the size of documents in the corpora. Performance is measured using different criteria which take into account the correct number of topics, but also whether the relevant topics from the DGPs are identified. Practical recommendations for LDA model selection in applications are derived.

Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon these advances by designing a novel deep learning architecture consisting of a 3-dimensional convolutional neural network utilizing channel-wise attention and two graph convolutional networks utilizing attention-based aggregation of node features. HAC-Net (Hybrid Attention-Based Convolutional Neural Network) obtains state-of-the-art results on the PDBbind v.2016 core set, the most widely recognized benchmark in the field. We extensively assess the generalizability of our model using multiple train-test splits, each of which maximizes differences between either protein structures, protein sequences, or ligand extended-connectivity fingerprints. Furthermore, we perform 10-fold cross-validation with a similarity cutoff between SMILES strings of ligands in the training and test sets, and also evaluate the performance of HAC-Net on lower-quality data. We envision that this model can be extended to a broad range of supervised learning problems related to structure-based biomolecular property prediction. All of our software is available as open source at https://github.com/gregory-kyro/HAC-Net/.

Counterfactual explanation is a common class of methods to make local explanations of machine learning decisions. For a given instance, these methods aim to find the smallest modification of feature values that changes the predicted decision made by a machine learning model. One of the challenges of counterfactual explanation is the efficient generation of realistic counterfactuals. To address this challenge, we propose VCNet-Variational Counter Net-a model architecture that combines a predictor and a counterfactual generator that are jointly trained, for regression or classification tasks. VCNet is able to both generate predictions, and to generate counterfactual explanations without having to solve another minimisation problem. Our contribution is the generation of counterfactuals that are close to the distribution of the predicted class. This is done by learning a variational autoencoder conditionally to the output of the predictor in a join-training fashion. We present an empirical evaluation on tabular datasets and across several interpretability metrics. The results are competitive with the state-of-the-art method.

Despite their impressive performance on diverse tasks, large language models (LMs) still struggle with tasks requiring rich world knowledge, implying the limitations of relying solely on their parameters to encode a wealth of world knowledge. This paper aims to understand LMs' strengths and limitations in memorizing factual knowledge, by conducting large-scale knowledge probing experiments of 10 models and 4 augmentation methods on PopQA, our new open-domain QA dataset with 14k questions. We find that LMs struggle with less popular factual knowledge, and that scaling fails to appreciably improve memorization of factual knowledge in the tail. We then show that retrieval-augmented LMs largely outperform orders of magnitude larger LMs, while unassisted LMs remain competitive in questions about high-popularity entities. Based on those findings, we devise a simple, yet effective, method for powerful and efficient retrieval-augmented LMs, which retrieves non-parametric memories only when necessary. Experimental results show that this significantly improves models' performance while reducing the inference costs.

We introduce the Conditional Independence Regression CovariancE (CIRCE), a measure of conditional independence for multivariate continuous-valued variables. CIRCE applies as a regularizer in settings where we wish to learn neural features $\varphi(X)$ of data $X$ to estimate a target $Y$, while being conditionally independent of a distractor $Z$ given $Y$. Both $Z$ and $Y$ are assumed to be continuous-valued but relatively low dimensional, whereas $X$ and its features may be complex and high dimensional. Relevant settings include domain-invariant learning, fairness, and causal learning. The procedure requires just a single ridge regression from $Y$ to kernelized features of $Z$, which can be done in advance. It is then only necessary to enforce independence of $\varphi(X)$ from residuals of this regression, which is possible with attractive estimation properties and consistency guarantees. By contrast, earlier measures of conditional feature dependence require multiple regressions for each step of feature learning, resulting in more severe bias and variance, and greater computational cost. When sufficiently rich features are used, we establish that CIRCE is zero if and only if $\varphi(X) \perp \!\!\! \perp Z \mid Y$. In experiments, we show superior performance to previous methods on challenging benchmarks, including learning conditionally invariant image features.

This paper describes Waymo's Collision Avoidance Testing (CAT) methodology: a scenario-based testing method that evaluates the safety of the Waymo Driver Automated Driving Systems' (ADS) intended functionality in conflict situations initiated by other road users that require urgent evasive maneuvers. Because SAE Level 4 ADS are responsible for the dynamic driving task (DDT), when engaged, without immediate human intervention, evaluating a Level 4 ADS using scenario-based testing is difficult due to the potentially infinite number of operational scenarios in which hazardous situations may unfold. To that end, in this paper we first describe the safety test objectives for the CAT methodology, including the collision and serious injury metrics and the reference behavior model representing a non-impaired eyes on conflict human driver used to form an acceptance criterion. Afterward, we introduce the process for identifying potentially hazardous situations from a combination of human data, ADS testing data, and expert knowledge about the product design and associated Operational Design Domain (ODD). The test allocation and execution strategy is presented next, which exclusively utilize simulations constructed from sensor data collected on a test track, real-world driving, or from simulated sensor data. The paper concludes with the presentation of results from applying CAT to the fully autonomous ride-hailing service that Waymo operates in San Francisco, California and Phoenix, Arizona. The iterative nature of scenario identification, combined with over ten years of experience of on-road testing, results in a scenario database that converges to a representative set of responder role scenarios for a given ODD. Using Waymo's virtual test platform, which is calibrated to data collected as part of many years of ADS development, the CAT methodology provides a robust and scalable safety evaluation.

Training a Neural Radiance Field (NeRF) without pre-computed camera poses is challenging. Recent advances in this direction demonstrate the possibility of jointly optimising a NeRF and camera poses in forward-facing scenes. However, these methods still face difficulties during dramatic camera movement. We tackle this challenging problem by incorporating undistorted monocular depth priors. These priors are generated by correcting scale and shift parameters during training, with which we are then able to constrain the relative poses between consecutive frames. This constraint is achieved using our proposed novel loss functions. Experiments on real-world indoor and outdoor scenes show that our method can handle challenging camera trajectories and outperforms existing methods in terms of novel view rendering quality and pose estimation accuracy.

The integration of data and knowledge from several sources is known as data fusion. When data is available in a distributed fashion or when different sensors are used to infer a quantity of interest, data fusion becomes essential. In Bayesian settings, a priori information of the unknown quantities is available and, possibly, shared among the distributed estimators. When the local estimates are fused, such prior might be overused unless it is accounted for. This paper explores the effects of shared priors in Bayesian data fusion contexts, providing fusion rules and analysis to understand the performance of such fusion as a function of the number of collaborative agents and the uncertainty of the priors. Analytical results are corroborated through experiments in a variety of estimation and classification problems.