占用预测

Uncertainty quantification is an important prerequisite for the deployment of deep learning models in safety-critical areas. Yet, this hinges on the uncertainty estimates being useful to the extent the prediction intervals are well-calibrated and sharp. In the absence of inherent uncertainty estimates (e.g. pretrained models predicting only point estimates), popular approaches that operate post-hoc include Laplace’s method and split conformal prediction (split-CP). However, Laplace’s method can be miscalibrated when the model is misspecified and split-CP requires sample splitting, and thus comes at the expense of statistical efficiency. In this work, we construct prediction intervals for neural network regressors post-hoc without held-out data. This is achieved by approximating the full conformal prediction method (full-CP). Whilst full-CP nominally requires retraining the model for every test point and candidate label, we propose to train just once and locally perturb model parameters using Gauss-Newton influence to approximate the effect of retraining. Coupled with linearization of the network, we express the absolute residual nonconformity score as a piecewise linear function of the candidate label allowing for an efficient procedure that avoids the exhaustive search over the output space. On standard regression benchmarks and bounding box localization, we show the resulting prediction intervals are locally-adaptive and often tighter than those of split-CP.

Predicting variations in complex traffic environments is crucial for the safety of autonomous driving. Recent advancements in occupancy forecasting have enabled forecasting future 3D occupied status in driving environments by observing historical 2D images. However, high computational demands make occupancy forecasting less efficient during training and inference stages, hindering its feasibility for deployment on edge agents. In this paper, we propose a novel framework, \textit{i.e.}, OccProphet, to efficiently and effectively learn occupancy forecasting with significantly lower computational requirements while improving forecasting accuracy. OccProphet comprises three lightweight components: Observer, Forecaster, and Refiner. The Observer extracts spatio-temporal features from 3D multi-frame voxels using the proposed Efficient 4D Aggregation with Tripling-Attention Fusion, while the Forecaster and Refiner conditionally predict and refine future occupancy inferences. Experimental results on nuScenes, Lyft-Level5, and nuScenes-Occupancy datasets demonstrate that OccProphet is both training- and inference-friendly. OccProphet reduces 58\%$\sim$78\% of the computational cost with a 2.6$\times$ speedup compared with the state-of-the-art Cam4DOcc. Moreover, it achieves 4\%$\sim$18\% relatively higher forecasting accuracy. Code and models are publicly available at https://github.com/JLChen-C/OccProphet.

The rising interest in Bayesian deep learning (BDL) has led to a plethora of methods for estimating the posterior distribution. However, efficient computation of inferences, such as predictions, has been largely overlooked with Monte Carlo integration remaining the standard. In this work we examine streamlining prediction in BDL through a single forward pass without sampling. For this, we use local linearisation of activation functions and local Gaussian approximations at linear layers. Thus allowing us to analytically compute an approximation of the posterior predictive distribution. We showcase our approach for both MLP and transformers, such as ViT and GPT-2, and assess its performance on regression and classification tasks. Open-source library: https://github.com/AaltoML/SUQ.

Density estimation and reliable prediction regions for outputs are crucial in supervised and unsupervised learning. While conformal prediction effectively generates coverage-guaranteed regions, it struggles with multi-dimensional outputs due to reliance on one-dimensional nonconformity scores. To address this, we introduce CONTRA: CONformal prediction region via normalizing flow TRAnsformation. CONTRA utilizes the latent spaces of normalizing flows to define nonconformity scores based on distances from the center. This allows for the mapping of high-density regions in latent space to sharp prediction regions in the output space, surpassing traditional hyperrectangular or elliptical conformal regions. Further, for scenarios where other predictive models are favored over flow-based models, we extend CONTRA to enhance any such model with a reliable prediction region by training a simple normalizing flow on the residuals. We demonstrate that both CONTRA and its extension maintain guaranteed coverage probability and outperform existing methods in generating accurate prediction regions across various datasets. We conclude that CONTRA is an effective tool for (conditional) density estimation, addressing the under-explored challenge of delivering multi-dimensional prediction regions.

Conformal prediction has been a popular distribution-free framework for uncertainty quantification. In this work, we present a novel conformal prediction method for time-series, which we call Kernel-based Optimally Weighted Conformal Prediction Intervals ($\texttt{KOWCPI}$). Specifically, $\texttt{KOWCPI}$ adapts the classic Reweighted Nadaraya-Watson (RNW) estimator for quantile regression on dependent data and learns optimal data-adaptive weights. Theoretically, we tackle the challenge of establishing a conditional coverage guarantee for non-exchangeable data under strong mixing conditions on the non-conformity scores. We demonstrate the superior performance of $\texttt{KOWCPI}$ on real time-series against state-of-the-art methods, where $\texttt{KOWCPI}$ achieves narrower confidence intervals without losing coverage.

Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their specific types is therefore essential for elucidating protein function and understanding disease mechanisms. Existing computational approaches predominantly focus on protein sequences to predict PTM sites, driven by the recognition of sequence-dependent motifs. However, these approaches often overlook protein structural contexts. In this work, we first compile a large-scale sequence-structure PTM dataset, which serves as the foundation for fair comparison. We introduce the MeToken model, which tokenizes the micro-environment of each amino acid, integrating both sequence and structural information into unified discrete tokens. This model not only captures the typical sequence motifs associated with PTMs but also leverages the spatial arrangements dictated by protein tertiary structures, thus providing a holistic view of the factors influencing PTM sites. Designed to address the long-tail distribution of PTM types, MeToken employs uniform sub-codebooks that ensure even the rarest PTMs are adequately represented and distinguished. We validate the effectiveness and generalizability of MeToken across multiple datasets, demonstrating its superior performance in accurately identifying PTM types. The results underscore the importance of incorporating structural data and highlight MeToken's potential in facilitating accurate and comprehensive PTM predictions, which could significantly impact proteomics research.

Leveraging machine learning (ML) to predict an initial solution for mixed-integer linear programming (MILP) has gained considerable popularity in recent years. These methods predict a solution and fix a subset of variables to reduce the problem dimension. Then, they solve the reduced problem to obtain the final solutions. However, directly fixing variable values can lead to low-quality solutions or even infeasible reduced problems if the predicted solution is not accurate enough. To address this challenge, we propose an Alternating prediction-correction neural solving framework (Apollo-MILP) that can identify and select accurate and reliable predicted values to fix. In each iteration, Apollo-MILP conducts a prediction step for the unfixed variables, followed by a correction step to obtain an improved solution (called reference solution) through a trust-region search. By incorporating the predicted and reference solutions, we introduce a novel Uncertainty-based Error upper BOund (UEBO) to evaluate the uncertainty of the predicted values and fix those with high confidence. A notable feature of Apollo-MILP is the superior ability for problem reduction while preserving optimality, leading to high-quality final solutions. Experiments on commonly used benchmarks demonstrate that our proposed Apollo-MILP significantly outperforms other ML-based approaches in terms of solution quality, achieving over a 50% reduction in the solution gap.

Conformal prediction (CP) converts any model's output to prediction sets with a guarantee to cover the true label with (adjustable) high probability. Robust CP extends this guarantee to worst-case (adversarial) inputs. Existing baselines achieve robustness by bounding randomly smoothed conformity scores. In practice, they need expensive Monte-Carlo (MC) sampling (e.g. $\sim10^4$ samples per point) to maintain an acceptable set size. We propose a robust conformal prediction that produces smaller sets even with significantly lower MC samples (e.g. 150 for CIFAR10). Our approach binarizes samples with an adjustable (or automatically adjusted) threshold selected to preserve the coverage guarantee. Remarkably, we prove that robustness can be achieved by computing only one binary certificate, unlike previous methods that certify each calibration (or test) point. Thus, our method is faster and returns smaller robust sets. We also eliminate a previous limitation that requires a bounded score function.

Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce VenusVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 7000 antigen sequences, structures, and immunogenicity labels from bacteria, viruses, and tumors. Extensive experiments demonstrate that VenusVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research. The implementation is at \url{https://github.com/songleee/VenusVaccine}.

The prohibitive training costs of Large Language Models (LLMs) have emerged as a significant bottleneck in the development of next-generation LLMs. In this paper, we show that it is possible to significantly reduce the training costs of LLMs without sacrificing their performance. Specifically, we introduce patch-level training for LLMs, in which multiple tokens are aggregated into a unit of higher information density, referred to as a `patch', to serve as the fundamental text unit for training LLMs. During patch-level training, we feed the language model shorter sequences of patches and train it to predict the next patch, thereby processing the majority of the training data at a significantly reduced cost. Following this, the model continues token-level training on the remaining training data to align with the inference mode. Experiments on a diverse range of models (370M-2.7B parameters) demonstrate that patch-level training can reduce the overall training costs to 0.5$\times$, without compromising the model performance compared to token-level training. Source code: \url{https://github.com/shaochenze/PatchTrain}.

To predict future trajectories of pedestrians, scene is as important as the history trajectory since i) scene reflects the position of possible goals of the pedestrian ii) trajectories are affected by the semantic information of the scene. It requires the model to capture scene information and learn the relation between scenes and trajectories. However, existing methods either apply Convolutional Neural Networks (CNNs) to summarize the scene to a feature vector, which raises the feature misalignment issue, or convert trajectory to heatmaps to align with the scene map, which ignores the interactions among different pedestrians. In this work, we introduce the trajectory-scene-cell feature to represent both trajectories and scenes in one feature space. By decoupling the trajectory in temporal domain and the scene in spatial domain, trajectory feature and scene feature are re-organized in different types of cell feature, which well aligns trajectory and scene, and allows the framework to model both human-human and human-scene interactions. Moreover, the Trajectory-Scene-Cell Network (TSC-Net) with new trajectory prediction manner is proposed, where both goal and intermediate positions of the trajectory are predict by cell classification and offset regression. Comparative experiments show that TSC-Net achieves the SOTA performance on several datasets with most of the metrics. Especially for the goal estimation, TSC-Net is demonstrated better on predicting goals for trajectories with irregular speed.

We develop a new method for generating prediction sets that combines the flexibility of conformal methods with an estimate of the conditional distribution $\textup{P}_{Y \mid X}$. Existing methods, such as conformalized quantile regression and probabilistic conformal prediction, usually provide only a marginal coverage guarantee. In contrast, our approach extends these frameworks to achieve approximately conditional coverage, which is crucial for many practical applications. Our prediction sets adapt to the behavior of the predictive distribution, making them effective even under high heteroscedasticity. While exact conditional guarantees are infeasible without assumptions on the underlying data distribution, we derive non-asymptotic bounds that depend on the total variation distance of the conditional distribution and its estimate. Using extensive simulations, we show that our method consistently outperforms existing approaches in terms of conditional coverage, leading to more reliable statistical inference in a variety of applications.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

RNA secondary structure prediction is critical for understanding RNA function but remains challenging due to complex structural elements like pseudoknots and limited training data. We introduce DEPfold, a novel deep learning approach that re-frames RNA secondary structure prediction as a dependency parsing problem. DEPfold presents three key innovations: (1) a biologically motivated transformation of RNA structures into labeled dependency trees, (2) a biaffine attention mechanism for joint prediction of base pairings and their types, and (3) an optimal tree decoding algorithm that enforces valid RNA structural constraints. Unlike traditional energy-based methods, DEPfold learns directly from annotated data and leverages pretrained language models to predict RNA structure. We evaluate DEPfold on both within-family and cross-family RNA datasets, demonstrating significant performance improvements over existing methods. DEPfold shows strong performance in cross-family generalization when trained on data augmented by traditional energy-based models, outperforming existing methods on the bpRNAnew dataset. This demonstrates DEPfold’s ability to effectively learn structural information beyond what traditional methods capture. Our approach bridges natural language processing (NLP) with RNA biology, providing a computationally efficient and adaptable tool for advancing RNA structure prediction and analysis

Missing values are prevalent across various fields, posing challenges for training and deploying predictive models. In this context, imputation is a common practice, driven by the hope that accurate imputations will enhance predictions. However, recent theoretical and empirical studies indicate that simple constant imputation can be consistent and competitive. This empirical study aims at clarifying *if* and *when* investing in advanced imputation methods yields significantly better predictions. Relating imputation and predictive accuracies across combinations of imputation and predictive models on 19 datasets, we show that imputation accuracy matters less i) when using expressive models, ii) when incorporating missingness indicators as complementary inputs, iii) matters much more for generated linear outcomes than for real-data outcomes. Interestingly, we also show that the use of the missingness indicator is beneficial to the prediction performance, even in MCAR scenarios. Overall, on real-data with powerful models, imputation quality has only a minor effect on prediction performance. Thus, investing in better imputations for improved predictions often offers limited benefits.

Conformal prediction (CP) is an important tool for distribution-free predictive uncertainty quantification. Yet, a major challenge is to balance computational efficiency and prediction accuracy, particularly for multiple predictions. We propose **L**eave-**O**ne-**O**ut **Stab**le **C**onformal **P**rediction (LOO-StabCP), a novel method to speed up full conformal using algorithmic stability without sample splitting. By leveraging *leave-one-out* stability, our method is much faster in handling a large number of prediction requests compared to existing method RO-StabCP based on *replace-one* stability. We derived stability bounds for several popular machine learning tools: regularized loss minimization (RLM) and stochastic gradient descent (SGD), as well as kernel method, neural networks and bagging. Our method is theoretically justified and demonstrates superior numerical performance on synthetic and real-world data. We applied our method to a screening problem, where its effective exploitation of training data led to improved test power compared to state-of-the-art method based on split conformal.

Conformal prediction has emerged as a popular technique for facilitating valid predictive inference across a spectrum of machine learning models, under minimal assumption of exchangeability. Recently, Hoff (2023) showed that full conformal Bayes provides the most efficient prediction sets (smallest by expected volume) among all prediction sets that are valid at the $(1 - \alpha)$ level if the model is correctly specified. However, a critical issue arises when the Bayesian model itself may be mis-specified, resulting in prediction interval that might be suboptimal, even though it still enjoys the frequentist coverage guarantee. To address this limitation, we propose an innovative solution that combines Bayesian model averaging (BMA) with conformal prediction. This hybrid not only leverages the strengths of Bayesian conformal prediction but also introduces a layer of robustness through model averaging. Theoretically, we prove that the resulting prediction interval will converge to the optimal level of efficiency, if the true model is included among the candidate models. This assurance of optimality, even under potential model uncertainty, provides a significant improvement over existing methods, ensuring more reliable and precise uncertainty quantification.

Conformal prediction has recently emerged as a promising strategy for quantifying the uncertainty of a predictive model; these algorithms modify the model to output sets of labels that are guaranteed to contain the true label with high probability. However, existing conformal prediction algorithms have largely targeted classification and regression settings, where the structure of the prediction set has a simple form as a level set of the scoring function. However, for complex structured outputs such as text generation, these prediction sets might include a large number of labels and therefore be hard for users to interpret. In this paper, we propose a general framework for conformal prediction in the structured prediction setting, that modifies existing conformal prediction algorithms to output structured prediction sets that implicitly represent sets of labels. In addition, we demonstrate how our approach can be applied in domains where the prediction sets can be represented as a set of nodes in a directed acyclic graph; for instance, for hierarchical labels such as image classification, a prediction set might be a small subset of coarse labels implicitly representing the prediction set of all their more fine-descendants. We demonstrate how our algorithm can be used to construct prediction sets that satisfy a desired coverage guarantee in several domains.