ICML 2024 论文列表

The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexity. In this work, we reformulate the RNA secondary structure prediction as a K-Rook problem, thereby simplifying the prediction process into probabilistic matching within a finite solution space. Building on this innovative perspective, we introduce RFold, a simple yet effective method that learns to predict the most matching K-Rook solution from the given sequence. RFold employs a bi-dimensional optimization strategy that decomposes the probabilistic matching problem into row-wise and column-wise components to reduce the matching complexity, simplifying the solving process while guaranteeing the validity of the output. Extensive experiments demonstrate that RFold achieves competitive performance and about eight times faster inference efficiency than the state-of-the-art approaches. The code is available at https://github.com/A4Bio/RFold.

Can a mere next-token predictor faithfully model human thinking? Our work is aimed at crystallizing this intuitive concern, which is currently fragmented in the literature. First, we emphasize isolating the two phases of next-token prediction that are often conflated: autoregression during inference vs. teacher-forcing during training. We argue that the previously-identified problem of "exponential error accumulation" is a symptom of autoregressive inference. But more concerningly, we identify that teacher-forcing can let the model fit the training data by cheating, causing total in-distribution failure. We design a minimal planning task where empirically both the Transformer and the Mamba architecture fail in this manner - remarkably, despite the task being easy to learn. Overall, our work consolidates these and other essential arguments surrounding next-token prediction. We hope this effort can ground future discussions and inspire explorations beyond the next-token prediction paradigm.

Creation of nanomaterials with specific morphology remains a complex experimental process, even though there is a growing demand for these materials in various industry sectors. This study explores the potential of AI to predict the morphology of nanoparticles within the data availability constraints. For that, we first generated a new multi-modal dataset that is double the size of analogous studies. Then, we systematically evaluated performance of classical machine learning and large language models in prediction of nanomaterial shapes and sizes. Finally, we prototyped a text-to-image system, discussed the obtained empirical results, as well as the limitations and promises of existing approaches.

Conformal prediction has shown impressive capacity in constructing statistically rigorous prediction sets for machine learning models with exchangeable data samples. The siloed datasets, coupled with the escalating privacy concerns related to local data sharing, have inspired recent innovations extending conformal prediction into federated environments with distributed data samples. However, this framework for distributed uncertainty quantification is susceptible to Byzantine failures. A minor subset of malicious clients can significantly compromise the practicality of coverage guarantees. To address this vulnerability, we introduce a novel framework Rob-FCP, which executes robust federated conformal prediction, effectively countering malicious clients capable of reporting arbitrary statistics with the conformal calibration process. We theoretically provide the conformal coverage bound of Rob-FCP in the Byzantine setting and show that the coverage of Rob-FCP is asymptotically close to the desired coverage level. We also propose a malicious client number estimator to tackle a more challenging setting where the number of malicious clients is unknown to the defender and theoretically shows its effectiveness. We empirically demonstrate the robustness of Rob-FCP against diverse proportions of malicious clients under a variety of Byzantine attacks on five standard benchmark and real-world healthcare datasets.

In real-world scenarios, arbitrary interactions with the environment can often be costly, and actions of expert demonstrations are not always available. To reduce the need for both, offline Learning from Observations (LfO) is extensively studied: the agent learns to solve a task given only expert states and task-agnostic non-expert state-action pairs. The state-of-the-art DIstribution Correction Estimation (DICE) methods, as exemplified by SMODICE, minimize the state occupancy divergence between the learner's and empirical expert policies. However, such methods are limited to either $f$-divergences (KL and $\chi^2$) or Wasserstein distance with Rubinstein duality, the latter of which constrains the underlying distance metric crucial to the performance of Wasserstein-based solutions. To enable more flexible distance metrics, we propose Primal Wasserstein DICE (PW-DICE). It minimizes the primal Wasserstein distance between the learner and expert state occupancies and leverages a contrastively learned distance metric. Theoretically, our framework is a generalization of SMODICE, and is the first work that unifies $f$-divergence and Wasserstein minimization. Empirically, we find that PW-DICE improves upon several state-of-the-art methods. The code is available at https://github.com/KaiYan289/PW-DICE.

Multimodal survival methods combining gigapixel histology whole-slide images (WSIs) and transcriptomic profiles are particularly promising for patient prognostication and stratification. Current approaches involve tokenizing the WSIs into smaller patches ($>10^4$ patches) and transcriptomics into gene groups, which are then integrated using a Transformer for predicting outcomes. However, this process generates many tokens, which leads to high memory requirements for computing attention and complicates post-hoc interpretability analyses. Instead, we hypothesize that we can: (1) effectively summarize the morphological content of a WSI by condensing its constituting tokens using morphological prototypes, achieving more than $300\times$ compression; and (2) accurately characterize cellular functions by encoding the transcriptomic profile with biological pathway prototypes, all in an unsupervised fashion. The resulting multimodal tokens are then processed by a fusion network, either with a Transformer or an optimal transport cross-alignment, which now operates with a small and fixed number of tokens without approximations. Extensive evaluation on six cancer types shows that our framework outperforms state-of-the-art methods with much less computation while unlocking new interpretability analyses. The code is available at https://github.com/mahmoodlab/MMP.