Occupancy Prediction

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation https://github.com/WillHua127/ReactZyme.

Accurately predicting the future fluid is vital to extensive areas such as meteorology, oceanology, and aerodynamics. However, since the fluid is usually observed from the Eulerian perspective, its moving and intricate dynamics are seriously obscured and confounded in static grids, bringing thorny challenges to the prediction. This paper introduces a new Lagrangian-Eulerian combined paradigm to tackle the tanglesome fluid dynamics. Instead of solely predicting the future based on Eulerian observations, we propose DeepLag to discover hidden Lagrangian dynamics within the fluid by tracking the movements of adaptively sampled key particles. Further, DeepLag presents a new paradigm for fluid prediction, where the Lagrangian movement of the tracked particles is inferred from Eulerian observations, and their accumulated Lagrangian dynamics information is incorporated into global Eulerian evolving features to guide future prediction respectively. Tracking key particles not only provides a transparent and interpretable clue for fluid dynamics but also makes our model free from modeling complex correlations among massive grids for better efficiency. Experimentally, DeepLag excels in three challenging fluid prediction tasks covering 2D and 3D, simulated and real-world fluids. Code is available at this repository: https://github.com/thuml/DeepLag.

Occupancy prediction has increasingly garnered attention in recent years for its fine-grained understanding of 3D scenes. Traditional approaches typically rely on dense, regular grid representations, which often leads to excessive computational demands and a loss of spatial details for small objects. This paper introduces OctreeOcc, an innovative 3D occupancy prediction framework that leverages the octree representation to adaptively capture valuable information in 3D, offering variable granularity to accommodate object shapes and semantic regions of varying sizes and complexities. In particular, we incorporate image semantic information to improve the accuracy of initial octree structures and design an effective rectification mechanism to refine the octree structure iteratively. Our extensive evaluations show that OctreeOcc not only surpasses state-of-the-art methods in occupancy prediction, but also achieves a 15%-24% reduction in computational overhead compared to dense-grid-based methods.

Survival prediction often involves estimating the time-to-event distribution from censored datasets. Previous approaches have focused on enhancing discrimination and marginal calibration. In this paper, we highlight the significance of *conditional calibration* for real-world applications – especially its role in individual decision-making. We propose a method based on conformal prediction that uses the model’s predicted individual survival probability at that instance’s observed time. This method effectively improves the model’s marginal and conditional calibration, without compromising discrimination. We provide asymptotic theoretical guarantees for both marginal and conditional calibration and test it extensively across 15 diverse real-world datasets, demonstrating the method’s practical effectiveness and versatility in various settings.

Top-down Bird's Eye View (BEV) maps are a popular perception representation for ground robot navigation due to their richness and flexibility for downstream tasks. While recent methods have shown promise for predicting BEV maps from First-Person View (FPV) images, their generalizability is limited to small regions captured by current autonomous vehicle-based datasets. In this context, we show that a more scalable approach towards generalizable map prediction can be enabled by using two large-scale crowd-sourced mapping platforms, Mapillary for FPV images and OpenStreetMap for BEV semantic maps. We introduce Map It Anywhere (MIA), a data engine that enables seamless curation and modeling of labeled map prediction data from existing open-source map platforms. Using our MIA data engine, we display the ease of automatically collecting a 1.2 million FPV & BEV pair dataset encompassing diverse geographies, landscapes, environmental factors, camera models & capture scenarios. We further train a simple camera model-agnostic model on this data for BEV map prediction. Extensive evaluations using established benchmarks and our dataset show that the data curated by MIA enables effective pretraining for generalizable BEV map prediction, with zero-shot performance far exceeding baselines trained on existing datasets by 35%. Our analysis highlights the promise of using large-scale public maps for developing & testing generalizable BEV perception, paving the way for more robust autonomous navigation. Website: mapitanywhere.github.io

We study the fractal structure of language, aiming to provide a precise formalism for quantifying properties that may have been previously suspected but not formally shown. We establish that language is: (1) self-similar, exhibiting complexities at all levels of granularity, with no particular characteristic context length, and (2) long-range dependent (LRD), with a Hurst parameter of approximately 0.7. Based on these findings, we argue that short-term patterns/dependencies in language, such as in paragraphs, mirror the patterns/dependencies over larger scopes, like entire documents. This may shed some light on how next-token prediction can capture the structure of text across multiple levels of granularity, from words and clauses to broader contexts and intents. In addition, we carry out an extensive analysis across different domains and architectures, showing that fractal parameters are robust. Finally, we demonstrate that the tiny variations in fractal parameters seen across LLMs improve upon perplexity-based bits-per-byte (BPB) in predicting their downstream performance. We hope these findings offer a fresh perspective on language and the mechanisms underlying the success of LLMs.

Occupancy prediction, aiming at predicting the occupancy status within voxelized 3D environment, is quickly gaining momentum within the autonomous driving community. Mainstream occupancy prediction works first discretize the 3D environment into voxels, then perform classification on such dense grids. However, inspection on sample data reveals that the vast majority of voxels is unoccupied. Performing classification on these empty voxels demands suboptimal computation resource allocation, and reducing such empty voxels necessitates complex algorithm designs. To this end, we present a novel perspective on the occupancy prediction task: formulating it as a streamlined set prediction paradigm without the need for explicit space modeling or complex sparsification procedures. Our proposed framework, called OPUS, utilizes a transformer encoder-decoder architecture to simultaneously predict occupied locations and classes using a set of learnable queries. Firstly, we employ the Chamfer distance loss to scale the set-to-set comparison problem to unprecedented magnitudes, making training such model end-to-end a reality. Subsequently, semantic classes are adaptively assigned using nearest neighbor search based on the learned locations. In addition, OPUS incorporates a suite of non-trivial strategies to enhance model performance, including coarse-to-fine learning, consistent point sampling, and adaptive re-weighting, etc. Finally, compared with current state-of-the-art methods, our lightest model achieves superior RayIoU on the Occ3D-nuScenes dataset at near 2x FPS, while our heaviest model surpasses previous best results by 6.1 RayIoU.

Message Passing Neural Networks (MPNNs) have emerged as the {\em de facto} standard in graph representation learning. However, when it comes to link prediction, they are not always superior to simple heuristics such as Common Neighbor (CN). This discrepancy stems from a fundamental limitation: while MPNNs excel in node-level representation, they stumble with encoding the joint structural features essential to link prediction, like CN. To bridge this gap, we posit that, by harnessing the orthogonality of input vectors, pure message-passing can indeed capture joint structural features. Specifically, we study the proficiency of MPNNs in approximating CN heuristics. Based on our findings, we introduce the Message Passing Link Predictor (MPLP), a novel link prediction model. MPLP taps into quasi-orthogonal vectors to estimate link-level structural features, all while preserving the node-level complexities. We conduct experiments on benchmark datasets from various domains, where our method consistently outperforms the baseline methods, establishing new state-of-the-arts.

This paper introduces a boosted conformal procedure designed to tailor conformalized prediction intervals toward specific desired properties, such as enhanced conditional coverage or reduced interval length. We employ machine learning techniques, notably gradient boosting, to systematically improve upon a predefined conformity score function. This process is guided by carefully constructed loss functions that measure the deviation of prediction intervals from the targeted properties. The procedure operates post-training, relying solely on model predictions and without modifying the trained model (e.g., the deep network). Systematic experiments demonstrate that starting from conventional conformal methods, our boosted procedure achieves substantial improvements in reducing interval length and decreasing deviation from target conditional coverage.

Temporal link prediction, aiming at predicting future interactions among entities based on historical interactions, is crucial for a series of real-world applications. Although previous methods have demonstrated the importance of relative encodings for effective temporal link prediction, computational efficiency remains a major concern in constructing these encodings. Moreover, existing relative encodings are usually constructed based on structural connectivity, where temporal information is seldom considered. To address the aforementioned issues, we first analyze existing relative encodings and unify them as a function of temporal walk matrices. This unification establishes a connection between relative encodings and temporal walk matrices, providing a more principled way for analyzing and designing relative encodings. Based on this analysis, we propose a new temporal graph neural network called TPNet, which introduces a temporal walk matrix that incorporates the time decay effect to simultaneously consider both temporal and structural information. Moreover, TPNet designs a random feature propagation mechanism with theoretical guarantees to implicitly maintain the temporal walk matrices, which improves the computation and storage efficiency. Experimental results on 13 benchmark datasets verify the effectiveness and efficiency of TPNet, where TPNet outperforms other baselines on most datasets and achieves a maximum speedup of $33.3 \times$ compared to the SOTA baseline.

We quantify the efficiency of temporal difference (TD) learning over the direct, or Monte Carlo (MC), estimator for policy evaluation in reinforcement learning, with an emphasis on estimation of quantities related to rare events. Policy evaluation is complicated in the rare event setting by the long timescale of the event and by the need for \emph{relative accuracy} in estimates of very small values. Specifically, we focus on least-squares TD (LSTD) prediction for finite state Markov chains, and show that LSTD can achieve relative accuracy far more efficiently than MC. We prove a central limit theorem for the LSTD estimator and upper bound the \emph{relative asymptotic variance} by simple quantities characterizing the connectivity of states relative to the transition probabilities between them. Using this bound, we show that, even when both the timescale of the rare event and the relative accuracy of the MC estimator are exponentially large in the number of states, LSTD maintains a fixed level of relative accuracy with a total number of observed transitions of the Markov chain that is only \emph{polynomially} large in the number of states.

Epitope identification is vital for antibody design yet challenging due to the inherent variability in antibodies. While many deep learning methods have been developed for general protein binding site prediction tasks, whether they work for epitope prediction remains an understudied research question. The challenge is also heightened by the lack of a consistent evaluation pipeline with sufficient dataset size and epitope diversity. We introduce a filtered antibody-antigen complex structure dataset, AsEP (Antibody-specific Epitope Prediction). AsEP is the largest of its kind and provides clustered epitope groups, allowing the community to develop and test novel epitope prediction methods and evaluate their generalisability. AsEP comes with an easy-to-use interface in Python and pre-built graph representations of each antibody-antigen complex while also supporting customizable embedding methods. Using this new dataset, we benchmark several representative general protein-binding site prediction methods and find that their performances fall short of expectations for epitope prediction. To address this, we propose a novel method, WALLE, which leverages both unstructured modeling from protein language models and structural modeling from graph neural networks. WALLE demonstrate up to 3-10X performance improvement over the baseline methods. Our empirical findings suggest that epitope prediction benefits from combining sequential features provided by language models with geometrical information from graph representations. This provides a guideline for future epitope prediction method design. In addition, we reformulate the task as bipartite link prediction, allowing convenient model performance attribution and interpretability. We open source our data and code at https://github.com/biochunan/AsEP-dataset.

Transformers have achieved extraordinary success in modern machine learning due to their excellent ability to handle sequential data, especially in next-token prediction (NTP) tasks. However, the theoretical understanding of their performance in NTP is limited, with existing studies focusing mainly on asymptotic performance. This paper provides a fine-grained non-asymptotic analysis of the training dynamics of a one-layer transformer consisting of a self-attention module followed by a feed-forward layer. We first characterize the essential structural properties of training datasets for NTP using a mathematical framework based on partial orders. Then, we design a two-stage training algorithm, where the pre-processing stage for training the feed-forward layer and the main stage for training the attention layer exhibit fast convergence performance. Specifically, both layers converge sub-linearly to the direction of their corresponding max-margin solutions. We also show that the cross-entropy loss enjoys a linear convergence rate. Furthermore, we show that the trained transformer presents non-trivial prediction ability with dataset shift, which sheds light on the remarkable generalization performance of transformers. Our analysis technique involves the development of novel properties on the attention gradient and further in-depth analysis of how these properties contribute to the convergence of the training process. Our experiments further validate our theoretical findings.

Distribution variations in machine learning, driven by the dynamic nature of deployment environments, significantly impact the performance of learning models. This paper explores endogenous distribution shifts in learning systems, where deployed models influence environments and subsequently alter data distributions. This phenomenon is formulated by a decision-dependent distribution mapping within the recently proposed framework of performative prediction (PP) Perdomo et al. (2020). We investigate the performative effect in a decentralized noncooperative game, where players aim to minimize private cost functions while simultaneously managing coupled inequality constraints. Under performativity, we examine two equilibrium concepts for the studied game: performative stable equilibrium (PSE) and Nash equilibrium (NE), and establish sufficient conditions for their existence and uniqueness. Notably, we provide the first upper bound on the distance between the PSE and NE in the literature, which is challenging to evaluate due to the absence of strong convexity on the joint cost function. Furthermore, we develop a decentralized stochastic primal-dual algorithm for efficiently computing the PSE point. By carefully bounding the performative effect in theoretical analysis, we prove that the proposed algorithm achieves sublinear convergence rates for both performative regrets and constraint violation and maintains the same order of convergence rate as the case without performativity. Numerical experiments validate the effectiveness of our algorithm and theoretical results.

We develop new conformal inference methods for obtaining validity guarantees on the output of large language models (LLMs). Prior work in conformal language modeling identifies a subset of the text that satisfies a high-probability guarantee of correctness. These methods work by filtering claims from the LLM's original response if a scoring function evaluated on the claim fails to exceed a threshold calibrated via split conformal prediction. Existing methods in this area suffer from two deficiencies. First, the guarantee stated is not conditionally valid. The trustworthiness of the filtering step may vary based on the topic of the response. Second, because the scoring function is imperfect, the filtering step can remove many valuable and accurate claims. We address both of these challenges via two new conformal methods. First, we generalize the conditional conformal procedure of Gibbs et al. (2023) in order to adaptively issue weaker guarantees when they are required to preserve the utility of the output. Second, we show how to systematically improve the quality of the scoring function via a novel algorithm for differentiating through the conditional conformal procedure. We demonstrate the efficacy of our approach on biography and medical question-answering datasets.

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10--50m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time series of climatic variables, and satellite time series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

Models for student reading performance can empower educators and institutions to proactively identify at-risk students, thereby enabling early and tailored instructional interventions. However, there are no suitable publicly available educational datasets for modeling and predicting future reading performance. In this work, we introduce the Enhanced Core Reading Instruction (ECRI) dataset, a novel large-scale longitudinal tabular dataset collected across 44 schools with 6,916 students and 172 teachers. We leverage the dataset to empirically evaluate the ability of state-of-the-art machine learning models to recognize early childhood educational patterns in multivariate and partial measurements. Specifically, we demonstrate a simple self-supervised strategy in which a Multi-Layer Perception (MLP) network is pre-trained over masked inputs to outperform several strong baselines while generalizing over diverse educational settings. To facilitate future developments in precise modeling and responsible use of models for individualized and early intervention strategies, our data and code are available at https://ecri-data.github.io/.

Performative prediction aims to model scenarios where predictive outcomes subsequently influence the very systems they target. The pursuit of a performative optimum (PO)—minimizing performative risk—is generally reliant on modeling of the distribution map, which characterizes how a deployed ML model alters the data distribution. Unfortunately, inevitable misspecification of the distribution map can lead to a poor approximation of the true PO. To address this issue, we introduce a novel framework of distributionally robust performative prediction and study a new solution concept termed as distributionally robust performative optimum (DRPO). We show provable guarantees for DRPO as a robust approximation to the true PO when the nominal distribution map is different from the actual one. Moreover, distributionally robust performative prediction can be reformulated as an augmented performative prediction problem, enabling efficient optimization. The experimental results demonstrate that DRPO offers potential advantages over traditional PO approach when the distribution map is misspecified at either micro- or macro-level.

Vision-based Semantic Scene Completion (SSC) has gained much attention due to its widespread applications in various 3D perception tasks. Existing sparse-to-dense approaches typically employ shared context-independent queries across various input images, which fails to capture distinctions among them as the focal regions of different inputs vary and may result in undirected feature aggregation of cross-attention. Additionally, the absence of depth information may lead to points projected onto the image plane sharing the same 2D position or similar sampling points in the feature map, resulting in depth ambiguity. In this paper, we present a novel context and geometry aware voxel transformer. It utilizes a context aware query generator to initialize context-dependent queries tailored to individual input images, effectively capturing their unique characteristics and aggregating information within the region of interest. Furthermore, it extend deformable cross-attention from 2D to 3D pixel space, enabling the differentiation of points with similar image coordinates based on their depth coordinates. Building upon this module, we introduce a neural network named CGFormer to achieve semantic scene completion. Simultaneously, CGFormer leverages multiple 3D representations (i.e., voxel and TPV) to boost the semantic and geometric representation abilities of the transformed 3D volume from both local and global perspectives. Experimental results demonstrate that CGFormer achieves state-of-the-art performance on the SemanticKITTI and SSCBench-KITTI-360 benchmarks, attaining a mIoU of 16.87 and 20.05, as well as an IoU of 45.99 and 48.07, respectively. Remarkably, CGFormer even outperforms approaches employing temporal images as inputs or much larger image backbone networks.

3D occupancy-based perception pipeline has significantly advanced autonomous driving by capturing detailed scene descriptions and demonstrating strong generalizability across various object categories and shapes. Current methods predominantly rely on LiDAR or camera inputs for 3D occupancy prediction. These methods are susceptible to adverse weather conditions, limiting the all-weather deployment of self-driving cars. To improve perception robustness, we leverage the recent advances in automotive radars and introduce a novel approach that utilizes 4D imaging radar sensors for 3D occupancy prediction. Our method, RadarOcc, circumvents the limitations of sparse radar point clouds by directly processing the 4D radar tensor, thus preserving essential scene details. RadarOcc innovatively addresses the challenges associated with the voluminous and noisy 4D radar data by employing Doppler bins descriptors, sidelobe-aware spatial sparsification, and range-wise self-attention mechanisms. To minimize the interpolation errors associated with direct coordinate transformations, we also devise a spherical-based feature encoding followed by spherical-to-Cartesian feature aggregation. We benchmark various baseline methods based on distinct modalities on the public K-Radar dataset. The results demonstrate RadarOcc's state-of-the-art performance in radar-based 3D occupancy prediction and promising results even when compared with LiDAR- or camera-based methods. Additionally, we present qualitative evidence of the superior performance of 4D radar in adverse weather conditions and explore the impact of key pipeline components through ablation studies.