We show that TKRR can achieve a fast rate of convergence in the over-aligned regime.

Selecting high-quality candidates from large datasets is critical in applications such as drug discovery, precision medicine, and alignment of large language models (LLMs). While Conformal Selection (CS) provides rigorous uncertainty quantification, it is limited to univariate responses and scalar criteria. To address this issue, we propose Multivariate Conformal Selection (mCS), a generalization of CS designed for multivariate response settings. Our method introduces regional monotonicity and employs multivariate nonconformity scores to construct conformal p-values, enabling finite-sample False Discovery Rate (FDR) control. We present two variants: mCS-dist, using distance-based scores, and mCS-learn, which learns optimal scores via differentiable optimization. Experiments on simulated and real-world datasets demonstrate that mCS significantly improves selection power while maintaining FDR control, establishing it as a robust framework for multivariate selection tasks.

We report the development of a knowledge representation and reasoning (KRR) system built on hybrid SHACL-SKOS ontologies for globally harmonized system (GHS) material Safety Data Sheets (SDS) to enhance chemical safety communication and regulatory compliance. SDS are comprehensive documents containing safety and handling information for chemical substances. Thus, they are an essential part of workplace safety and risk management. However, the vast number of Safety Data Sheets from multiple organizations, manufacturers, and suppliers that produce and distribute chemicals makes it challenging to centralize and access SDS documents through a single repository. To accomplish the underlying issues of data exchange related to chemical shipping and handling, we construct SDS related controlled vocabulary and conditions validated by SHACL, and knowledge systems of similar domains linked via SKOS. The resulting hybrid ontologies aim to provide standardized yet adaptable representations of SDS information, facilitating better data sharing, retrieval, and integration across various platforms. This paper outlines our SHACL-SKOS system architectural design and showcases our implementation for an industrial application streamlining the generation of a composite shipping cover sheet.

Survival analysis is a key area of statistics that focuses on modeling time-to-event data, with applications in many fields including clinical trials, engineering, and marketing. For example, in a clinical trial, researchers may aim to predict how long a cancer patient is likely to survive based on individual characteristics and treatments received. Two central goals are modeling the probability that an event will not occur before a given time and predicting the actual event time. These tasks are typically complicated by the fact that the data are censored--the exact event time may be unknown due to study limitations or participant withdrawal. While traditional methods, such as the Kaplan-Meier estimator and parametric models like the Cox proportional hazards model (Cox, 1972), are valued for their interpretability, they tend to struggle in high-dimensional settings or when their assumptions are violated. As a result, machine learning (ML) approaches are gaining popularity (Ishwaran et al., 2008; Katzman et al., 2018), despite the difficulty of obtaining uncertainty estimates and statistical guarantees. A promising approach to integrating ML models with rigorous statistical guarantees in survival analysis was recently introduced by Candès et al. (2023) and refined by Gui et al. (2024). Their conformal inference (Vovk et al., 2005; Lei & Wasserman, 2014) framework can use any survival

It is increasingly common in a wide variety of applied settings to collect data of multiple different types on the same set of samples. Our particular focus in this article is on studying relationships between such multiview features and responses. A motivating application arises in the context of precision medicine where multi-omics data are collected to correlate with clinical outcomes. It is of interest to infer dependence within and across views while combining multimodal information to improve the prediction of outcomes. The signal-to-noise ratio can vary substantially across views, motivating more nuanced statistical tools beyond standard late and early fusion. This challenge comes with the need to preserve interpretability, select features, and obtain accurate uncertainty quantification. We propose a joint additive factor regression model (JAFAR) with a structured additive design, accounting for shared and view-specific components. We ensure identifiability via a novel dependent cumulative shrinkage process (D-CUSP) prior. We provide an efficient implementation via a partially collapsed Gibbs sampler and extend our approach to allow flexible feature and outcome distributions. Prediction of time-to-labor onset from immunome, metabolome, and proteome data illustrates performance gains against state-of-the-art competitors. Our open-source software (R package) is available at https://github.com/niccoloanceschi/jafar.

In drug discovery, in vitro and in vivo experiments reveal biochemical activities related to the efficacy and toxicity of compounds. The experimental data accumulate into massive, ever-evolving, and sparse datasets. Quantitative Structure-Activity Relationship (QSAR) models, which predict biochemical activities using only the structural information of compounds, face challenges in integrating the evolving experimental data as studies progress. We develop QSAR-Complete (QComp), a data completion framework to address this issue. Based on pre-existing QSAR models, QComp utilizes the correlation inherent in experimental data to enhance prediction accuracy across various tasks. Moreover, QComp emerges as a promising tool for guiding the optimal sequence of experiments by quantifying the reduction in statistical uncertainty for specific endpoints, thereby aiding in rational decision-making throughout the drug discovery process.

General purpose Large Language Models (LLM) such as the Generative Pretrained Transformer (GPT) and Large Language Model Meta AI (LLaMA) have attracted much attention in recent years. There is strong evidence that these models can perform remarkably well in various natural language processing tasks. However, how to leverage them to approach domain-specific use cases and drive value remains an open question. In this work, we focus on a specific use case, pharmaceutical manufacturing investigations, and propose that leveraging historical records of manufacturing incidents and deviations in an organization can be beneficial for addressing and closing new cases, or de-risking new manufacturing campaigns. Using a small but diverse dataset of real manufacturing deviations selected from different product lines, we evaluate and quantify the power of three general purpose LLMs (GPT-3.5, GPT-4, and Claude-2) in performing tasks related to the above goal. In particular, (1) the ability of LLMs in automating the process of extracting specific information such as root cause of a case from unstructured data, as well as (2) the possibility of identifying similar or related deviations by performing semantic search on the database of historical records are examined. While our results point to the high accuracy of GPT-4 and Claude-2 in the information extraction task, we discuss cases of complex interplay between the apparent reasoning and hallucination behavior of LLMs as a risk factor. Furthermore, we show that semantic search on vector embedding of deviation descriptions can be used to identify similar records, such as those with a similar type of defect, with a high level of accuracy. We discuss further improvements to enhance the accuracy of similar record identification.

Variable importance plays a pivotal role in interpretable machine learning as it helps measure the impact of factors on the output of the prediction model. Model agnostic methods based on the generation of "null" features via permutation (or related approaches) can be applied. Such analysis is often utilized in pharmaceutical applications due to its ability to interpret black-box models, including tree-based ensembles. A major challenge and significant confounder in variable importance estimation however is the presence of between-feature correlation. Recently, several adjustments to marginal permutation utilizing feature knockoffs were proposed to address this issue, such as the variable importance measure known as conditional predictive impact (CPI). Assessment and evaluation of such approaches is the focus of our work. We first present a comprehensive simulation study investigating the impact of feature correlation on the assessment of variable importance. We then theoretically prove the limitation that highly correlated features pose for the CPI through the knockoff construction. While we expect that there is always no correlation between knockoff variables and its corresponding predictor variables, we prove that the correlation increases linearly beyond a certain correlation threshold between the predictor variables. Our findings emphasize the absence of free lunch when dealing with high feature correlation, as well as the necessity of understanding the utility and limitations behind methods in variable importance estimation.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

Both Minsky's "society of mind" and Schmidhuber's "learning to think" inspire diverse societies of large multimodal neural networks (NNs) that solve problems by interviewing each other in a "mindstorm." Recent implementations of NN-based societies of minds consist of large language models (LLMs) and other NN-based experts communicating through a natural language interface. In doing so, they overcome the limitations of single LLMs, improving multimodal zero-shot reasoning. In these natural language-based societies of mind (NLSOMs), new agents -- all communicating through the same universal symbolic language -- are easily added in a modular fashion. To demonstrate the power of NLSOMs, we assemble and experiment with several of them (having up to 129 members), leveraging mindstorms in them to solve some practical AI tasks: visual question answering, image captioning, text-to-image synthesis, 3D generation, egocentric retrieval, embodied AI, and general language-based task solving. We view this as a starting point towards much larger NLSOMs with billions of agents-some of which may be humans. And with this emergence of great societies of heterogeneous minds, many new research questions have suddenly become paramount to the future of artificial intelligence. What should be the social structure of an NLSOM? What would be the (dis)advantages of having a monarchical rather than a democratic structure? How can principles of NN economies be used to maximize the total reward of a reinforcement learning NLSOM? In this work, we identify, discuss, and try to answer some of these questions.