As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current methods often make assumptions about the relations between data that may not be valid in practice. In response, we introduce SAVAE (Survival Analysis Variational Autoencoder), a novel approach based on Variational Autoencoders. SAVAE contributes significantly to the field by introducing a tailored ELBO formulation for survival analysis, supporting various parametric distributions for covariates and survival time (as long as the log-likelihood is differentiable). It offers a general method that consistently performs well on various metrics, demonstrating robustness and stability through different experiments. Our proposal effectively estimates time-to-event, accounting for censoring, covariate interactions, and time-varying risk associations. We validate our model in diverse datasets, including genomic, clinical, and demographic data, with varying levels of censoring. This approach demonstrates competitive performance compared to state-of-the-art techniques, as assessed by the Concordance Index and the Integrated Brier Score. SAVAE also offers an interpretable model that parametrically models covariates and time. Moreover, its generative architecture facilitates further applications such as clustering, data imputation, and the generation of synthetic patient data through latent space inference from survival data.
Evaluating the average causal effect (ACE) of a treatment on an outcome often involves overcoming the challenges posed by confounding factors in observational studies. A traditional approach uses the back-door criterion, seeking adjustment sets to block confounding paths between treatment and outcome. However, this method struggles with unmeasured confounders. As an alternative, the front-door criterion offers a solution, even in the presence of unmeasured confounders between treatment and outcome. This method relies on identifying mediators that are not directly affected by these confounders and that completely mediate the treatment's effect. Here, we introduce novel estimation strategies for the front-door criterion based on the targeted minimum loss-based estimation theory. Our estimators work across diverse scenarios, handling binary, continuous, and multivariate mediators. They leverage data-adaptive machine learning algorithms, minimizing assumptions and ensuring key statistical properties like asymptotic linearity, double-robustness, efficiency, and valid estimates within the target parameter space. We establish conditions under which the nuisance functional estimations ensure the root n-consistency of ACE estimators. Our numerical experiments show the favorable finite sample performance of the proposed estimators. We demonstrate the applicability of these estimators to analyze the effect of early stage academic performance on future yearly income using data from the Finnish Social Science Data Archive.
Support vector machines (SVMs) are well-studied supervised learning models for binary classification. In many applications, large amounts of samples can be cheaply and easily obtained. What is often a costly and error-prone process is to manually label these instances. Semi-supervised support vector machines (S3VMs) extend the well-known SVM classifiers to the semi-supervised approach, aiming at maximizing the margin between samples in the presence of unlabeled data. By leveraging both labeled and unlabeled data, S3VMs attempt to achieve better accuracy and robustness compared to traditional SVMs. Unfortunately, the resulting optimization problem is non-convex and hence difficult to solve exactly. In this paper, we present a new branch-and-cut approach for S3VMs using semidefinite programming (SDP) relaxations. We apply optimality-based bound tightening to bound the feasible set. Box constraints allow us to include valid inequalities, strengthening the lower bound. The resulting SDP relaxation provides bounds significantly stronger than the ones available in the literature. For the upper bound, instead, we define a local search exploiting the solution of the SDP relaxation. Computational results highlight the efficiency of the algorithm, showing its capability to solve instances with a number of data points 10 times larger than the ones solved in the literature.
Segment anything model (SAM) addresses two practical yet challenging segmentation tasks: \textbf{segment anything (SegAny)}, which utilizes a certain point to predict the mask for a single object of interest, and \textbf{segment everything (SegEvery)}, which predicts the masks for all objects on the image. What makes SegAny slow for SAM is its heavyweight image encoder, which has been addressed by MobileSAM via decoupled knowledge distillation. The efficiency bottleneck of SegEvery with SAM, however, lies in its mask decoder because it needs to first generate numerous masks with redundant grid-search prompts and then perform filtering to obtain the final valid masks. We propose to improve its efficiency by directly generating the final masks with only valid prompts, which can be obtained through object discovery. Our proposed approach not only helps reduce the total time on the mask decoder by at least 16 times but also achieves superior performance. Specifically, our approach yields an average performance boost of 3.6\% (42.5\% \textit{v.s.} 38.9\%) for zero-shot object proposal on the LVIS dataset with the mask AR@$K$ metric. Qualitative results show that our approach generates fine-grained masks while avoiding over-segmenting things. This project targeting faster SegEvery than the original SAM is termed MobileSAMv2 to differentiate from MobileSAM which targets faster SegAny. Moreover, we demonstrate that our new prompt sampling is also compatible with the distilled image encoders in MobileSAM, contributing to a unified framework for efficient SegAny and SegEvery. The code is available at the same link as MobileSAM Project \href{https://github.com/ChaoningZhang/MobileSAM}{\textcolor{red}{https://github.com/ChaoningZhang/MobileSAM}}. \end{abstract}
In this paper, we propose a novel approach for solving linear numeric planning problems, called Symbolic Pattern Planning. Given a planning problem $\Pi$, a bound $n$ and a pattern -- defined as an arbitrary sequence of actions -- we encode the problem of finding a plan for $\Pi$ with bound $n$ as a formula with fewer variables and/or clauses than the state-of-the-art rolled-up and relaxed-relaxed-$\exists$ encodings. More importantly, we prove that for any given bound, it is never the case that the latter two encodings allow finding a valid plan while ours does not. On the experimental side, we consider 6 other planning systems -- including the ones which participated in this year's International Planning Competition (IPC) -- and we show that our planner Patty has remarkably good comparative performances on this year's IPC problems.
Many problems in Reinforcement Learning (RL) seek an optimal policy with large discrete multidimensional yet unordered action spaces; these include problems in randomized allocation of resources such as placements of multiple security resources and emergency response units, etc. A challenge in this setting is that the underlying action space is categorical (discrete and unordered) and large, for which existing RL methods do not perform well. Moreover, these problems require validity of the realized action (allocation); this validity constraint is often difficult to express compactly in a closed mathematical form. The allocation nature of the problem also prefers stochastic optimal policies, if one exists. In this work, we address these challenges by (1) applying a (state) conditional normalizing flow to compactly represent the stochastic policy -- the compactness arises due to the network only producing one sampled action and the corresponding log probability of the action, which is then used by an actor-critic method; and (2) employing an invalid action rejection method (via a valid action oracle) to update the base policy. The action rejection is enabled by a modified policy gradient that we derive. Finally, we conduct extensive experiments to show the scalability of our approach compared to prior methods and the ability to enforce arbitrary state-conditional constraints on the support of the distribution of actions in any state.
Conformal prediction is a statistical tool for producing prediction regions for machine learning models that are valid with high probability. A key component of conformal prediction algorithms is a \emph{non-conformity score function} that quantifies how different a model's prediction is from the unknown ground truth value. Essentially, these functions determine the shape and the size of the conformal prediction regions. While prior work has gone into creating score functions that produce multi-model prediction regions, such regions are generally too complex for use in downstream planning and control problems. We propose a method that optimizes parameterized \emph{shape template functions} over calibration data, which results in non-conformity score functions that produce prediction regions with minimum volume. Our approach results in prediction regions that are \emph{multi-modal}, so they can properly capture residuals of distributions that have multiple modes, and \emph{practical}, so each region is convex and can be easily incorporated into downstream tasks, such as a motion planner using conformal prediction regions. Our method applies to general supervised learning tasks, while we illustrate its use in time-series prediction. We provide a toolbox and present illustrative case studies of F16 fighter jets and autonomous vehicles, showing an up to $68\%$ reduction in prediction region area compared to a circular baseline region.
Shape modeling of volumetric medical images is crucial for quantitative analysis and surgical planning in computer-aided diagnosis. To alleviate the burden of expert clinicians, reconstructed shapes are typically obtained from deep learning models, such as Convolutional Neural Networks (CNNs) or transformer-based architectures, followed by the marching cube algorithm. However, automatic shape reconstruction often falls short of perfection due to the limited resolution of images and the absence of shape prior constraints. To overcome these limitations, we propose the Reliable Shape Interaction with Implicit Template (ReShapeIT) network, which models anatomical structures in continuous space rather than discrete voxel grids. ReShapeIT represents an anatomical structure with an implicit template field shared within the same category, complemented by a deformation field. It ensures the implicit template field generates valid templates by strengthening the constraint of the correspondence between the instance shape and the template shape. The valid template shape can then be utilized for implicit generalization. A Template Interaction Module (TIM) is introduced to reconstruct unseen shapes by interacting the valid template shapes with the instance-wise latent codes. Experimental results on three datasets demonstrate the superiority of our approach in anatomical structure reconstruction. The Chamfer Distance/Earth Mover's Distance achieved by ReShapeIT are 0.225/0.318 on Liver, 0.125/0.067 on Pancreas, and 0.414/0.098 on Lung Lobe.
Estimating the relative camera pose from $n \geq 5$ correspondences between two calibrated views is a fundamental task in computer vision. This process typically involves two stages: 1) estimating the essential matrix between the views, and 2) disambiguating among the four candidate relative poses that satisfy the epipolar geometry. In this paper, we demonstrate a novel approach that, for the first time, bypasses the second stage. Specifically, we show that it is possible to directly estimate the correct relative camera pose from correspondences without needing a post-processing step to enforce the cheirality constraint on the correspondences. Building on recent advances in certifiable non-minimal optimization, we frame the relative pose estimation as a Quadratically Constrained Quadratic Program (QCQP). By applying the appropriate constraints, we ensure the estimation of a camera pose that corresponds to a valid 3D geometry and that is globally optimal when certified. We validate our method through exhaustive synthetic and real-world experiments, confirming the efficacy, efficiency and accuracy of the proposed approach. Code is available at https://github.com/javrtg/C2P.
The control of dynamical systems under temporal logic specifications among uncontrollable dynamic agents is challenging due to the agents' a-priori unknown behavior. Existing works have considered the problem where either all agents are controllable, the agent models are deterministic and known, or no safety guarantees are provided. We propose a predictive control synthesis framework that guarantees, with high probability, the satisfaction of signal temporal logic (STL) tasks that are defined over a controllable system in the presence of uncontrollable stochastic agents. We use trajectory predictors and conformal prediction to construct probabilistic prediction regions for each uncontrollable agent that are valid over multiple future time steps. Specifically, we construct a normalized prediction region over all agents and time steps to reduce conservatism and increase data efficiency. We then formulate a worst-case bilevel mixed integer program (MIP) that accounts for all agent realizations within the prediction region to obtain an open-loop controller that provably guarantee task satisfaction with high probability. To efficiently solve this bilevel MIP, we propose an equivalent MIP program based on KKT conditions of the original bilevel formulation. Building upon this, we design a closed-loop controller, where both recursive feasibility and task satisfaction can be guaranteed with high probability. We illustrate our control synthesis framework on two case studies.
In the era of fast-paced precision medicine, observational studies play a major role in properly evaluating new treatments in clinical practice. Yet, unobserved confounding can significantly compromise causal conclusions drawn from non-randomized data. We propose a novel strategy that leverages randomized trials to quantify unobserved confounding. First, we design a statistical test to detect unobserved confounding with strength above a given threshold. Then, we use the test to estimate an asymptotically valid lower bound on the unobserved confounding strength. We evaluate the power and validity of our statistical test on several synthetic and semi-synthetic datasets. Further, we show how our lower bound can correctly identify the absence and presence of unobserved confounding in a real-world setting.
Transformer models underpin many recent advances in practical machine learning applications, yet understanding their internal behavior continues to elude researchers. Given the size and complexity of these models, forming a comprehensive picture of their inner workings remains a significant challenge. To this end, we set out to understand small transformer models in a more tractable setting: that of solving mazes. In this work, we focus on the abstractions formed by these models and find evidence for the consistent emergence of structured internal representations of maze topology and valid paths. We demonstrate this by showing that the residual stream of only a single token can be linearly decoded to faithfully reconstruct the entire maze. We also find that the learned embeddings of individual tokens have spatial structure. Furthermore, we take steps towards deciphering the circuity of path-following by identifying attention heads (dubbed $\textit{adjacency heads}$), which are implicated in finding valid subsequent tokens.
Graph Neural Networks (GNNs) are powerful machine learning prediction models on graph-structured data. However, GNNs lack rigorous uncertainty estimates, limiting their reliable deployment in settings where the cost of errors is significant. We propose conformalized GNN (CF-GNN), extending conformal prediction (CP) to graph-based models for guaranteed uncertainty estimates. Given an entity in the graph, CF-GNN produces a prediction set/interval that provably contains the true label with pre-defined coverage probability (e.g. 90%). We establish a permutation invariance condition that enables the validity of CP on graph data and provide an exact characterization of the test-time coverage. Moreover, besides valid coverage, it is crucial to reduce the prediction set size/interval length for practical use. We observe a key connection between non-conformity scores and network structures, which motivates us to develop a topology-aware output correction model that learns to update the prediction and produces more efficient prediction sets/intervals. Extensive experiments show that CF-GNN achieves any pre-defined target marginal coverage while significantly reducing the prediction set/interval size by up to 74% over the baselines. It also empirically achieves satisfactory conditional coverage over various raw and network features.
We provide practical, efficient, and nonparametric methods for auditing the fairness of deployed classification and regression models. Whereas previous work relies on a fixed-sample size, our methods are sequential and allow for the continuous monitoring of incoming data, making them highly amenable to tracking the fairness of real-world systems. We also allow the data to be collected by a probabilistic policy as opposed to sampled uniformly from the population. This enables auditing to be conducted on data gathered for another purpose. Moreover, this policy may change over time and different policies may be used on different subpopulations. Finally, our methods can handle distribution shift resulting from either changes to the model or changes in the underlying population. Our approach is based on recent progress in anytime-valid inference and game-theoretic statistics-the "testing by betting" framework in particular. These connections ensure that our methods are interpretable, fast, and easy to implement. We demonstrate the efficacy of our approach on three benchmark fairness datasets.
Multi-modal human action segmentation is a critical and challenging task with a wide range of applications. Nowadays, the majority of approaches concentrate on the fusion of dense signals (i.e., RGB, optical flow, and depth maps). However, the potential contributions of sparse IoT sensor signals, which can be crucial for achieving accurate recognition, have not been fully explored. To make up for this, we introduce a Sparse signalguided Transformer (SigFormer) to combine both dense and sparse signals. We employ mask attention to fuse localized features by constraining cross-attention within the regions where sparse signals are valid. However, since sparse signals are discrete, they lack sufficient information about the temporal action boundaries. Therefore, in SigFormer, we propose to emphasize the boundary information at two stages to alleviate this problem. In the first feature extraction stage, we introduce an intermediate bottleneck module to jointly learn both category and boundary features of each dense modality through the inner loss functions. After the fusion of dense modalities and sparse signals, we then devise a two-branch architecture that explicitly models the interrelationship between action category and temporal boundary. Experimental results demonstrate that SigFormer outperforms the state-of-the-art approaches on a multi-modal action segmentation dataset from real industrial environments, reaching an outstanding F1 score of 0.958. The codes and pre-trained models have been available at https://github.com/LIUQI-creat/SigFormer.
In this study, we investigate the quantification of the statistical reliability of detected change points (CPs) in time series using a Recurrent Neural Network (RNN). Thanks to its flexibility, RNN holds the potential to effectively identify CPs in time series characterized by complex dynamics. However, there is an increased risk of erroneously detecting random noise fluctuations as CPs. The primary goal of this study is to rigorously control the risk of false detections by providing theoretically valid p-values to the CPs detected by RNN. To achieve this, we introduce a novel method based on the framework of Selective Inference (SI). SI enables valid inferences by conditioning on the event of hypothesis selection, thus mitigating selection bias. In this study, we apply SI framework to RNN-based CP detection, where characterizing the complex process of RNN selecting CPs is our main technical challenge. We demonstrate the validity and effectiveness of the proposed method through artificial and real data experiments.
Unobserved confounding is common in many applications, making causal inference from observational data challenging. As a remedy, causal sensitivity analysis is an important tool to draw causal conclusions under unobserved confounding with mathematical guarantees. In this paper, we propose NeuralCSA, a neural framework for generalized causal sensitivity analysis. Unlike previous work, our framework is compatible with (i) a large class of sensitivity models, including the marginal sensitivity model, f-sensitivity models, and Rosenbaum's sensitivity model; (ii) different treatment types (i.e., binary and continuous); and (iii) different causal queries, including (conditional) average treatment effects and simultaneous effects on multiple outcomes. The generality of NeuralCSA is achieved by learning a latent distribution shift that corresponds to a treatment intervention using two conditional normalizing flows. We provide theoretical guarantees that NeuralCSA is able to infer valid bounds on the causal query of interest and also demonstrate this empirically using both simulated and real-world data.
Zero-shot 6D object pose estimation involves the detection of novel objects with their 6D poses in cluttered scenes, presenting significant challenges for model generalizability. Fortunately, the recent Segment Anything Model (SAM) has showcased remarkable zero-shot transfer performance, which provides a promising solution to tackle this task. Motivated by this, we introduce SAM-6D, a novel framework designed to realize the task through two steps, including instance segmentation and pose estimation. Given the target objects, SAM-6D employs two dedicated sub-networks, namely Instance Segmentation Model (ISM) and Pose Estimation Model (PEM), to perform these steps on cluttered RGB-D images. ISM takes SAM as an advanced starting point to generate all possible object proposals and selectively preserves valid ones through meticulously crafted object matching scores in terms of semantics, appearance and geometry. By treating pose estimation as a partial-to-partial point matching problem, PEM performs a two-stage point matching process featuring a novel design of background tokens to construct dense 3D-3D correspondence, ultimately yielding the pose estimates. Without bells and whistles, SAM-6D outperforms the existing methods on the seven core datasets of the BOP Benchmark for both instance segmentation and pose estimation of novel objects.
A primary challenge facing modern scientific research is the limited availability of gold-standard data which can be costly, labor-intensive, or invasive to obtain. With the rapid development of machine learning (ML), scientists can now employ ML algorithms to predict gold-standard outcomes with variables that are easier to obtain. However, these predicted outcomes are often used directly in subsequent statistical analyses, ignoring imprecision and heterogeneity introduced by the prediction procedure. This will likely result in false positive findings and invalid scientific conclusions. In this work, we introduce PoSt-Prediction Adaptive inference (PSPA) that allows valid and powerful inference based on ML-predicted data. Its "assumption-lean" property guarantees reliable statistical inference without assumptions on the ML prediction. Its "data-adaptive" feature guarantees an efficiency gain over existing methods, regardless of the accuracy of ML prediction. We demonstrate the statistical superiority and broad applicability of our method through simulations and real-data applications.
Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.