In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.

Temporal graph link prediction aims to predict future interactions between nodes in a graph based on their historical interactions, which are encoded in node embeddings. We observe that heterogeneity naturally appears in temporal interactions, e.g., a few node pairs can make most interaction events, and interaction events happen at varying intervals. This leads to the problems of ineffective temporal information encoding and forgetting of past interactions for a pair of nodes that interact intermittently for their link prediction. Existing methods, however, do not consider such heterogeneity in their learning process, and thus their learned temporal node embeddings are less effective, especially when predicting the links for infrequently interacting node pairs. To cope with the heterogeneity, we propose a novel framework called TAMI, which contains two effective components, namely log time encoding function (LTE) and link history aggregation (LHA). LTE better encodes the temporal information through transforming interaction intervals into more balanced ones, and LHA prevents the historical interactions for each target node pair from being forgotten. State-of-the-art temporal graph neural networks can be seamlessly and readily integrated into TAMI to improve their effectiveness. Experiment results on 13 classic datasets and three newest temporal graph benchmark (TGB) datasets show that TAMI consistently improves the link prediction performance of the underlying models in both transductive and inductive settings.

Vehicle aerodynamics optimization has become critical for automotive electrification, where drag reduction directly determines electric vehicle range and energy efficiency. Traditional approaches face an intractable trade-off: computationally expensive Computational Fluid Dynamics (CFD) simulations requiring weeks per design iteration, or simplified models that sacrifice production-grade accuracy. While machine learning offers transformative potential, existing datasets exhibit fundamental limitations--inadequate mesh resolution, missing vehicle components, and validation errors exceeding 5%--preventing deployment in industrial workflows. We present DrivAerStar, comprising 12,000 industrial-grade automotive CFD simulations generated using STAR-CCM+ software. The dataset systematically explores three vehicle configurations through 20 Computer Aided Design (CAD) parameters via Free Form Deformation (FFD) algorithms, including complete engine compartments and cooling systems with realistic internal airflow. DrivAerStar achieves wind tunnel validation accuracy below 1.04%-- a five-fold improvement over existing datasets--through refined mesh strategies with strict wall y` control. Benchmarks demonstrate that models trained on this data achieve production-ready accuracy while reducing computational costs from weeks to minutes. This represents the first dataset bridging academic machine learning research and industrial CFD practice, establishing a new standard for data-driven aerodynamic optimization in automotive development. Beyond automotive applications, DrivAerStardemonstrates a paradigm for integrating highfidelity physics simulations with Artificial Intelligence (AI) across engineering disciplines where computational constraints currently limit innovation.

Encoding models using word embeddings or artificial neural network (ANN) features reliably predict brain responses to naturalistic stimuli, yet interpreting these models remains challenging. A central limitation is superposition: distinct semantic features become entangled along correlated directions in dense embeddings when latent features outnumber embedding dimensions. This entanglement renders regression weights non-identifiable--different combinations of semantic directions can produce identical predictions, precluding principled interpretation of voxel selectivity. To address this, we introduce the Sparse Concept Encoding Model, which transforms dense embeddings into a higher-dimensional, sparse, non-negative space of learned concept atoms.

Transformers have proven highly effective across various applications, especially in handling sequential data such as natural languages and time series. However, transformer models often lack clear interpretability, and the success of transformers has not been well understood in theory. In this paper, we study the capability and interpretability of transformers in learning a family of classic statistical models, namely random walks on circles. We theoretically demonstrate that, after training with gradient descent, a one-layer transformer model can achieve optimal accuracy in predicting random walks. Importantly, our analysis reveals that the trained model is interpretable: the trained softmax attention serves as a token selector, focusing on the direct parent state; subsequently, the value matrix executes a onestep probability transition to predict the location of the next state based on this parent state. We also show that certain edge cases not covered by our theory are indeed failure cases, demonstrating that our theoretical conditions are tight. By investigating these success and failure cases, it is revealed that gradient descent with small initialization may fail or struggle to converge to a good solution in certain simple tasks even beyond random walks. Experiments are conducted to support our theoretical findings.

In multi-modal biomedical research, integrating high-dimensional genomic data with clinical baselines is essential for precision medicine. However, standard deep neural network approaches often entangle these modalities, obscuring the specific predictive impact of genetic features and leading to possibly suboptimal predictive performance. Motivated by the landmark METABRIC cohort primary breast tumors study, we propose the Stein-Encoder, a white-box supervised framework designed to isolate the genetic signal driving clinical outcomes conditional on nuisance covariates. By leveraging Stein's method and residualization techniques, our approach constructs an interpretable single index that summarizes relevant biological heterogeneity while flexibly incorporating clinical factors and can be used to improve downstream prediction. We establish theoretical guarantees for identification, consistency and efficiency improvement. Applied to the METABRIC cohort, the Stein-Encoder outperforms unsupervised benchmarks in predictive accuracy. Crucially, it achieves structural disentanglement by revealing response-specific biological mechanisms: we find that tumor size is driven primarily by mitotic networks, whereas prognostic indices rely on a distinct proliferation-versus-immune axis. This work contributes a unified, computationally efficient framework that bridges statistical rigor with the representational power of neural networks, enabling interpretable, task-specific and efficient compression of multi-modal health data for a wide range of precision medicine applications, beyond biomarker discovery.

S1.1 Step-by-step derivation of min-max optimization in Section 2.2.1 By substituting Eq. 2 into Eq. 1 in the main manuscript, we can obtain the objective function of subscript z (we temporarily drop ifor clarity): J(z) = max Since z might be in high dimensional space, solving such a large system of linear equations under the constraint |z| 1is oftentimes computationally challenging. In order to find a practical solution for z that satisfies the constrained minimization problem in Eq. By setting zl as point of coincidence, we can find a separable majorizer of M(z) by adding the non-negative function (z zl) (βI Gx Gx)(z zl) (S6) 37th Conference on Neural Information Processing Systems (NeurIPS 2023). Note, to unify the format, we use the matrix transpose property in Eq. Then, the next step is to find z RN that minimizes z z 2bz subject to the constraint |z| 1. Let's first consider the simplest case where z is a scalar: argmin If b 1, then the solution is z = b.

In this appendix, we first introduce the datasets and evaluation metrics used in the experiments in Section A. Then, we provide extra experimental results in Section B. In Section C, we present details of network design, training scheme, and hyper-parameter tuning. We conduct experiments on 11 popular time series datasets: (1) Electricity Transformer Temperature [42] (ETTh(1,2),ETTm1) 3consists of 2 year electric power data collected from two separated counties of China. Each data point includes an "oil temperature" value and 6 power load features. The data is aggregated into 5-minutes windows, resulting in 12 points per hour and 288 points per day. A.1 Electricity Transformer Temperature (ETT) For data pre-processing, we perform zero-mean normalization, i.e., X We use Mean Absolute Errors (MAE) [17] and Mean Squared Errors (MSE) [26] for model comparison.