Technology
ProtGO: Function-Guided Protein Modeling for Unified Representation Learning
Protein representation learning is indispensable for various downstream applications of artificial intelligence for bio-medicine research, such as drug design and function prediction. However, achieving effective representation learning for proteins poses challenges due to the diversity of data modalities involved, including sequence, structure, and function annotations. Despite the impressive capabilities of large language models in biomedical text modelling, there remains a pressing need for a framework that seamlessly integrates these diverse modalities, particularly focusing on the three critical aspects of protein information: sequence, structure, and function. Moreover, addressing the inherent data scale differences among these modalities is essential. To tackle these challenges, we introduce ProtGO, a unified model that harnesses a teacher network equipped with a customized graph neural network (GNN) and a Gene Ontology (GO) encoder to learn hybrid embeddings. Notably, our approach eliminates the need for additional functions as input for the student network, which shares the same GNN module. Importantly, we utilize a domain adaptation method to facilitate distribution approximation for guiding the training of the teacher-student framework. This approach leverages distributions learned from latent representations to avoid the alignment of individual samples. Benchmark experiments highlight that ProtGO significantly outperforms state-of-the-art baselines, clearly demonstrating the advantages of the proposed unified framework.
IDGen: Item Discrimination Induced Prompt Generation for LLM Evaluation
As Large Language Models (LLMs) become more capable of handling increasingly complex tasks, the evaluation set must keep pace with these advancements to ensure it remains sufficiently discriminative. Item Discrimination (ID) theory, which is widely used in educational assessment, measures the ability of individual test items to differentiate between high and low performers. Inspired by this theory, we propose an ID-induced prompt synthesis framework for evaluating LLMs so that the evaluation set continually updates and refines according to model abilities.
Hidden in Plain Sight: Evaluating Abstract Shape Recognition in Vision-Language Models
Despite the importance of shape perception in human vision, early neural image classifiers relied less on shape information for object recognition than other (often spurious) features. While recent research suggests that current large Vision-Language Models (VLMs) exhibit more reliance on shape, we find them to still be seriously limited in this regard. To quantify such limitations, we introduce IllusionBench, a dataset that challenges current cutting-edge VLMs to decipher shape information when the shape is represented by an arrangement of visual elements in a scene. Our extensive evaluations reveal that, while these shapes are easily detectable by human annotators, current VLMs struggle to recognize them, indicating important avenues for future work in developing more robust visual perception systems.
Trap-MID: Trapdoor-based Defense against Model Inversion Attacks
Model Inversion (MI) attacks pose a significant threat to the privacy of Deep Neural Networks by recovering training data distribution from well-trained models. While existing defenses often rely on regularization techniques to reduce information leakage, they remain vulnerable to recent attacks. In this paper, we propose the Trapdoor-based Model Inversion Defense (Trap-MID) to mislead MI attacks. A trapdoor is integrated into the model to predict a specific label when the input is injected with the corresponding trigger. Consequently, this trapdoor information serves as the shortcut for MI attacks, leading them to extract trapdoor triggers rather than private data. We provide theoretical insights into the impacts of trapdoor's effectiveness and naturalness on deceiving MI attacks. In addition, empirical experiments demonstrate the state-of-the-art defense performance of Trap-MID against various MI attacks without the requirements for extra data or large computational overhead.
bit2bit: 1-bit quanta video reconstruction via self-supervised photon prediction
Quanta image sensors, such as SPAD arrays, are an emerging sensor technology, producing 1-bit arrays representing photon detection events over exposures as short as a few nanoseconds. In practice, raw data are post-processed using heavy spatiotemporal binning to create more useful and interpretable images at the cost of degrading spatiotemporal resolution. In this work, we propose bit2bit, a new method for reconstructing high-quality image stacks at the original spatiotemporal resolution from sparse binary quanta image data. Inspired by recent work on Poisson denoising, we developed an algorithm that creates a dense image sequence from sparse binary photon data by predicting the photon arrival location probability distribution. However, due to the binary nature of the data, we show that the assumption of a Poisson distribution is inadequate.
Renovating Names in Open-Vocabulary Segmentation Benchmarks
Names are essential to both human cognition and vision-language models. Open-vocabulary models utilize class names as text prompts to generalize to categories unseen during training. However, the precision of these names is often overlooked in existing datasets. In this paper, we address this underexplored problem by presenting a framework for renovating names in open-vocabulary segmentation benchmarks (RENOVATE). Our framework features a renaming model that enhances the quality of names for each visual segment. Through experiments, we demonstrate that our renovated names help train stronger open-vocabulary models with up to 15% relative improvement and significantly enhance training efficiency with improved data quality. We also show that our renovated names improve evaluation by better measuring misclassification and enabling fine-grained model analysis.
On the Optimality of Dilated Entropy and Lower Bounds for Online Learning in Extensive-Form Games
First-order methods (FOMs) are arguably the most scalable algorithms for equilibrium computation in large extensive-form games. To operationalize these methods, a distance-generating function, acting as a regularizer for the strategy space, must be chosen. The ratio between the strong convexity modulus and the diameter of the regularizer is a key parameter in the analysis of FOMs.A natural question is then: what is the optimal distance-generating function for extensive-form decision spaces? In this paper, we make a number of contributions, ultimately establishing that the weight-one dilated entropy (DilEnt) distance-generating function is optimal up to logarithmic factors. The DilEnt regularizer is notable due to its iterate-equivalence with Kernelized OMWU (KOMWU)---the algorithm with state-of-the-art dependence on the game tree size in extensive-form games---when used in conjunction with the online mirror descent (OMD) algorithm. However, the standard analysis for OMD is unable to establish such a result; the only current analysis is by appealing to the iterate equivalence to KOMWU. We close this gap by introducing a pair of primal-dual treeplex norms, which we contend form the natural analytic viewpoint for studying the strong convexity of DilEnt. Using these norm pairs, we recover the diameter-to-strong-convexity ratio that predicts the same performance as KOMWU. Along with a new regret lower bound for online learning in sequence-form strategy spaces, we show that this ratio is nearly optimal.Finally, we showcase our analytic techniques by refining the analysis of Clairvoyant OMD when paired with DilEnt, establishing an $\mathcal{O}(n \log |\mathcal{V}| \log T/T)$ approximation rate to coarse correlated equilibrium in $n$-player games, where $|\mathcal{V}|$ is the number of reduced normal-form strategies of the players, establishing the new state of the art.
Taming Cross-Domain Representation Variance in Federated Prototype Learning with Heterogeneous Data Domains
Federated learning (FL) allows collaborative machine learning training without sharing private data. While most FL methods assume identical data domains across clients, real-world scenarios often involve heterogeneous data domains. Federated Prototype Learning (FedPL) addresses this issue, using mean feature vectors as prototypes to enhance model generalization. However, existing FedPL methods create the same number of prototypes for each client, leading to cross-domain performance gaps and disparities for clients with varied data distributions. To mitigate cross-domain feature representation variance, we introduce FedPLVM, which establishes variance-aware dual-level prototypes clustering and employs a novel $\alpha$-sparsity prototype loss. The dual-level prototypes clustering strategy creates local clustered prototypes based on private data features, then performs global prototypes clustering to reduce communication complexity and preserve local data privacy.
DeTeCtive: Detecting AI-generated Text via Multi-Level Contrastive Learning
Current techniques for detecting AI-generated text are largely confined to manual feature crafting and supervised binary classification paradigms. These methodologies typically lead to performance bottlenecks and unsatisfactory generalizability. Consequently, these methods are often inapplicable for out-of-distribution (OOD) data and newly emerged large language models (LLMs). In this paper, we revisit the task of AI-generated text detection. We argue that the key to accomplishing this task lies in distinguishing writing styles of different authors, rather than simply classifying the text into human-written or AI-generated text.