Fast and Accurate Blind Flexible Docking

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial structural changes by assuming protein rigidity or suffer from low computational efficiency due to their reliance on generative models for structure sampling. To address these challenges, we propose FABFlex, a fast and accurate regression-based multi-task learning model designed for realistic blind flexible docking scenarios, where proteins exhibit flexibility and binding pocket sites are unknown (blind). Specifically, FABFlex's architecture comprises three specialized modules working in concert: (1) A pocket prediction module that identifies potential binding sites, addressing the challenges inherent in blind docking scenarios. (2) A ligand docking module that predicts the bound (holo) structures of ligands from their unbound (apo) states. (3) A pocket docking module that forecasts the holo structures of protein pockets from their apo conformations. Notably, FABFlex incorporates an iterative update mechanism that serves as a conduit between the ligand and pocket docking modules, enabling continuous structural refinements. This approach effectively integrates the three subtasks of blind flexible docking-pocket identification, ligand conformation prediction, and protein flexibility modeling-into a unified, coherent framework. Extensive experiments on public benchmark datasets demonstrate that FABFlex not only achieves superior effectiveness in predicting accurate binding modes but also exhibits a significant speed advantage (208 $\times$) compared to existing state-of-the-art methods. Our code is released at https://github.com/tmlr-group/FABFlex.

MetaNeRV: Meta Neural Representations for Videos with Spatial-Temporal Guidance

Neural Representations for Videos (NeRV) has emerged as a promising implicit neural representation (INR) approach for video analysis, which represents videos as neural networks with frame indexes as inputs. However, NeRV-based methods are time-consuming when adapting to a large number of diverse videos, as each video requires a separate NeRV model to be trained from scratch. In addition, NeRV-based methods spatially require generating a high-dimension signal (i.e., an entire image) from the input of a low-dimension timestamp, and a video typically consists of tens of frames temporally that have a minor change between adjacent frames. To improve the efficiency of video representation, we propose Meta Neural Representations for Videos, named MetaNeRV, a novel framework for fast NeRV representation for unseen videos. MetaNeRV leverages a meta-learning framework to learn an optimal parameter initialization, which serves as a good starting point for adapting to new videos. To address the unique spatial and temporal characteristics of video modality, we further introduce spatial-temporal guidance to improve the representation capabilities of MetaNeRV. Specifically, the spatial guidance with a multi-resolution loss aims to capture the information from different resolution stages, and the temporal guidance with an effective progressive learning strategy could gradually refine the number of fitted frames during the meta-learning process. Extensive experiments conducted on multiple datasets demonstrate the superiority of MetaNeRV for video representations and video compression.

LamRA: Large Multimodal Model as Your Advanced Retrieval Assistant

With the rapid advancement of multimodal information retrieval, increasingly complex retrieval tasks have emerged. Existing methods predominately rely on task-specific fine-tuning of vision-language models, often those trained with image-text contrastive learning. In this paper, we explore the possibility of re-purposing generative Large Multimodal Models (LMMs) for retrieval. This approach enables unifying all retrieval tasks under the same formulation and, more importantly, allows for extrapolation towards unseen retrieval tasks without additional training. Our contributions can be summarised in the following aspects: (i) We introduce LamRA, a versatile framework designed to empower LMMs with sophisticated retrieval and reranking capabilities. (ii) For retrieval, we adopt a two-stage training strategy comprising language-only pre-training and multimodal instruction tuning to progressively enhance LMM's retrieval performance. (iii) For reranking, we employ joint training for both pointwise and listwise reranking, offering two distinct ways to further boost the retrieval performance. (iv) Extensive experimental results underscore the efficacy of our method in handling more than ten retrieval tasks, demonstrating robust performance in both supervised and zero-shot settings, including scenarios involving previously unseen retrieval tasks.

Self-Calibrated Tuning of Vision-Language Models for Out-of-Distribution Detection

Out-of-distribution (OOD) detection is crucial for deploying reliable machine learning models in open-world applications. Recent advances in CLIP-based OOD detection have shown promising results via regularizing prompt tuning with OOD features extracted from ID data. However, the irrelevant context mined from ID data can be spurious due to the inaccurate foreground-background decomposition, thus limiting the OOD detection performance. In this work, we propose a novel framework, namely, Self-Calibrated Tuning (SCT), to mitigate this problem for effective OOD detection with only the given few-shot ID data. Specifically, SCT introduces modulating factors respectively on the two components of the original learning objective. It adaptively directs the optimization process between the two tasks during training on data with different prediction uncertainty to calibrate the influence of OOD regularization, which is compatible with many prompt tuning based OOD detection methods. Extensive experiments and analyses have been conducted to characterize and demonstrate the effectiveness of the proposed SCT. The code is publicly available.

LoRKD: Low-Rank Knowledge Decomposition for Medical Foundation Models

The widespread adoption of large-scale pre-training techniques has significantly advanced the development of medical foundation models, enabling them to serve as versatile tools across a broad range of medical tasks. However, despite their strong generalization capabilities, medical foundation models pre-trained on large-scale datasets tend to suffer from domain gaps between heterogeneous data, leading to suboptimal performance on specific tasks compared to specialist models, as evidenced by previous studies. In this paper, we explore a new perspective called "Knowledge Decomposition" to improve the performance on specific medical tasks, which deconstructs the foundation model into multiple lightweight expert models, each dedicated to a particular anatomical region, with the aim of enhancing specialization and simultaneously reducing resource consumption. To accomplish the above objective, we propose a novel framework named Low-Rank Knowledge Decomposition (LoRKD), which explicitly separates gradients from different tasks by incorporating low-rank expert modules and efficient knowledge separation convolution. The low-rank expert modules resolve gradient conflicts between heterogeneous data from different anatomical regions, providing strong specialization at lower costs. The efficient knowledge separation convolution significantly improves algorithm efficiency by achieving knowledge separation within a single forward propagation. Extensive experimental results on segmentation and classification tasks demonstrate that our decomposed models not only achieve state-of-the-art performance but also exhibit superior transferability on downstream tasks, even surpassing the original foundation models in task-specific evaluations. The code is available at here.

Knowledge-Enhanced Facial Expression Recognition with Emotional-to-Neutral Transformation

Existing facial expression recognition (FER) methods typically fine-tune a pre-trained visual encoder using discrete labels. However, this form of supervision limits to specify the emotional concept of different facial expressions. In this paper, we observe that the rich knowledge in text embeddings, generated by vision-language models, is a promising alternative for learning discriminative facial expression representations. Inspired by this, we propose a novel knowledge-enhanced FER method with an emotional-to-neutral transformation. Specifically, we formulate the FER problem as a process to match the similarity between a facial expression representation and text embeddings. Then, we transform the facial expression representation to a neutral representation by simulating the difference in text embeddings from textual facial expression to textual neutral. Finally, a self-contrast objective is introduced to pull the facial expression representation closer to the textual facial expression, while pushing it farther from the neutral representation. We conduct evaluation with diverse pre-trained visual encoders including ResNet-18 and Swin-T on four challenging facial expression datasets. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art FER methods. The code will be publicly available.

Reprogramming Distillation for Medical Foundation Models

Medical foundation models pre-trained on large-scale datasets have demonstrated powerful versatile capabilities for various tasks. However, due to the gap between pre-training tasks (or modalities) and downstream tasks (or modalities), the real-world computation and speed constraints, it might not be straightforward to apply medical foundation models in the downstream scenarios. Previous methods, such as parameter efficient fine-tuning (PEFT) methods and knowledge distillation (KD) methods, are unable to simultaneously address the task (or modality) inconsistency and achieve personalized lightweight deployment under diverse real-world demands. To address the above issues, we propose a novel framework called Reprogramming Distillation (RD). On one hand, RD reprograms the original feature space of the foundation model so that it is more relevant to downstream scenarios, aligning tasks and modalities. On the other hand, through a co-training mechanism and a shared classifier, connections are established between the reprogrammed knowledge and the knowledge of student models, ensuring that the reprogrammed feature space can be smoothly mimic by the student model of different structures. Further, to reduce the randomness under different training conditions, we design a Centered Kernel Alignment (CKA) distillation to promote robust knowledge transfer. Empirically, we show that on extensive datasets, RD consistently achieve superior performance compared with previous PEFT and KD methods.

Exploring Training on Heterogeneous Data with Mixture of Low-rank Adapters

Training a unified model to take multiple targets into account is a trend towards artificial general intelligence. However, how to efficiently mitigate the training conflicts among heterogeneous data collected from different domains or tasks remains under-explored. In this study, we explore to leverage Mixture of Low-rank Adapters (MoLA) to mitigate conflicts in heterogeneous data training, which requires to jointly train the multiple low-rank adapters and their shared backbone. Specifically, we introduce two variants of MoLA, namely, MoLA-Grad and MoLA-Router, to respectively handle the target-aware and target-agnostic scenarios during inference. The former uses task identifiers to assign personalized low-rank adapters to each task, disentangling task-specific knowledge towards their adapters, thereby mitigating heterogeneity conflicts. The latter uses a novel Task-wise Decorrelation (TwD) loss to intervene the router to learn oriented weight combinations of adapters to homogeneous tasks, achieving similar effects. We conduct comprehensive experiments to verify the superiority of MoLA over previous state-of-the-art methods and present in-depth analysis on its working mechanism. Source code is available at: https://github.com/MediaBrain-SJTU/MoLA

Decoupling the Class Label and the Target Concept in Machine Unlearning

Machine unlearning as an emerging research topic for data regulations, aims to adjust a trained model to approximate a retrained one that excludes a portion of training data. Previous studies showed that class-wise unlearning is successful in forgetting the knowledge of a target class, through gradient ascent on the forgetting data or fine-tuning with the remaining data. However, while these methods are useful, they are insufficient as the class label and the target concept are often considered to coincide. In this work, we decouple them by considering the label domain mismatch and investigate three problems beyond the conventional all matched forgetting, e.g., target mismatch, model mismatch, and data mismatch forgetting. We systematically analyze the new challenges in restrictively forgetting the target concept and also reveal crucial forgetting dynamics in the representation level to realize these tasks. Based on that, we propose a general framework, namely, TARget-aware Forgetting (TARF). It enables the additional tasks to actively forget the target concept while maintaining the rest part, by simultaneously conducting annealed gradient ascent on the forgetting data and selected gradient descent on the hard-to-affect remaining data. Empirically, various experiments under the newly introduced settings are conducted to demonstrate the effectiveness of our TARF.

Diversified Batch Selection for Training Acceleration

The remarkable success of modern machine learning models on large datasets often demands extensive training time and resource consumption. To save cost, a prevalent research line, known as online batch selection, explores selecting informative subsets during the training process. Although recent efforts achieve advancements by measuring the impact of each sample on generalization, their reliance on additional reference models inherently limits their practical applications, when there are no such ideal models available. On the other hand, the vanilla reference-model-free methods involve independently scoring and selecting data in a sample-wise manner, which sacrifices the diversity and induces the redundancy. To tackle this dilemma, we propose Diversified Batch Selection (DivBS), which is reference-model-free and can efficiently select diverse and representative samples. Specifically, we define a novel selection objective that measures the group-wise orthogonalized representativeness to combat the redundancy issue of previous sample-wise criteria, and provide a principled selection-efficient realization. Extensive experiments across various tasks demonstrate the significant superiority of DivBS in the performance-speedup trade-off. The code is publicly available.