It is challenging to deal with censored data, where we only have access to the incomplete information of survival time instead of its exact value. Fortunately, under linear predictor assumption, people can obtain guaranteed coverage for the confidence interval of survival time using methods like Cox Regression. However, when relaxing the linear assumption with neural networks (e.g., Cox-MLP \citep{katzman2018deepsurv,kvamme2019time}), we lose the guaranteed coverage. To recover the guaranteed coverage without linear assumption, we propose two algorithms based on conformal inference. In the first algorithm \emph{WCCI}, we revisit weighted conformal inference and introduce a new non-conformity score based on partial likelihood. We then propose a two-stage algorithm \emph{T-SCI}, where we run WCCI in the first stage and apply quantile conformal inference to calibrate the results in the second stage. Theoretical analysis shows that T-SCI returns guaranteed coverage under milder assumptions than WCCI. We conduct extensive experiments on synthetic data and real data using different methods, which validate our analysis.

Retrosynthetic planning is a fundamental problem in chemistry for finding a pathway of reactions to synthesize a target molecule. Recently, search algorithms have shown promising results for solving this problem by using deep neural networks (DNNs) to expand their candidate solutions, i.e., adding new reactions to reaction pathways. However, the existing works on this line are suboptimal; the retrosynthetic planning problem requires the reaction pathways to be (a) represented by real-world reactions and (b) executable using “building block” molecules, yet the DNNs expand reaction pathways without fully incorporating such requirements. Motivated by this, we propose an end-to-end framework for directly training the DNNs towards generating reaction pathways with the desirable properties. Our main idea is based on a self-improving procedure that trains the model to imitate successful trajectories found by itself. We also propose a novel reaction augmentation scheme based on a forward reaction model. Our experiments demonstrate that our scheme significantly improves the success rate of solving the retrosynthetic problem from 86.84% to 96.32% while maintaining the performance of DNN for predicting valid reactions.

Generative probabilistic modeling of biological sequences has widespread existing and potential application across biology and biomedicine, from evolutionary biology to epidemiology to protein design. Many standard sequence analysis methods preprocess data using a multiple sequence alignment (MSA) algorithm, one of the most widely used computational methods in all of science. However, as we show in this article, training generative probabilistic models with MSA preprocessing leads to statistical pathologies in the context of sequence prediction and forecasting. To address these problems, we propose a principled drop-in alternative to MSA preprocessing in the form of a structured observation distribution (the "MuE" distribution). We prove theoretically that the MuE distribution comprehensively generalizes popular methods for inferring biological sequence alignments, and provide a precise characterization of how such biological models have differed from natural language latent alignment models. We show empirically that models that use the MuE as an observation distribution outperform comparable methods across a variety of datasets, and apply MuE models to a novel problem for generative probabilistic sequence models: forecasting pathogen evolution.

Humans can learn and reason under substantial uncertainty in a space of infinitely many compositional, productive concepts. For example, if a scene with two blue spheres qualifies as “daxy,” one can reason that the underlying concept may require scenes to have “only blue spheres” or “only spheres” or “only two objects.” In contrast, standard benchmarks for compositional reasoning do not explicitly capture a notion of reasoning under uncertainty or evaluate compositional concept acquisition. We introduce a new benchmark, Compositional Reasoning Under Uncertainty (CURI) that instantiates a series of few-shot, meta-learning tasks in a productive concept space to evaluate different aspects of systematic generalization under uncertainty, including splits that test abstract understandings of disentangling, productive generalization, learning boolean operations, variable binding, etc. Importantly, we also contribute a model-independent “compositionality gap” to evaluate the difficulty of generalizing out-of-distribution along each of these axes, allowing objective comparison of the difficulty of each compositional split. Evaluations across a range of modeling choices and splits reveal substantial room for improvement on the proposed benchmark.

We investigate the adversarial robustness of CNNs from the perspective of channel-wise activations. By comparing normally trained and adversarially trained models, we observe that adversarial training (AT) robustifies CNNs by aligning the channel-wise activations of adversarial data with those of their natural counterparts. However, the channels that are \textit{negatively-relevant} (NR) to predictions are still over-activated when processing adversarial data. Besides, we also observe that AT does not result in similar robustness for all classes. For the robust classes, channels with larger activation magnitudes are usually more \textit{positively-relevant} (PR) to predictions, but this alignment does not hold for the non-robust classes. Given these observations, we hypothesize that suppressing NR channels and aligning PR ones with their relevances further enhances the robustness of CNNs under AT. To examine this hypothesis, we introduce a novel mechanism, \textit{i.e.}, \underline{C}hannel-wise \underline{I}mportance-based \underline{F}eature \underline{S}election (CIFS). The CIFS manipulates channels' activations of certain layers by generating non-negative multipliers to these channels based on their relevances to predictions. Extensive experiments on benchmark datasets including CIFAR10 and SVHN clearly verify the hypothesis and CIFS's effectiveness of robustifying CNNs.