Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization

Molecular optimization is a crucial yet complex and time-intensive process that often acts as a bottleneck for drug development. Traditional methods rely heavily on trial and error, making multi-objective optimization both time-consuming and resource-intensive. Current AI-based methods have shown limited success in handling multi-objective optimization tasks, hampering their practical utilization. To address this challenge, we present MultiMol, a collaborative large language model (LLM) system designed to guide multi-objective molecular optimization. MultiMol comprises two agents, including a data-driven worker agent and a literature-guided research agent. The data-driven worker agent is a large language model being fine-tuned to learn how to generate optimized molecules considering multiple objectives, while the literature-guided research agent is responsible for searching task-related literature to find useful prior knowledge that facilitates identifying the most promising optimized candidates. In evaluations across six multi-objective optimization tasks, MultiMol significantly outperforms existing methods, achieving a 82.30% success rate, in sharp contrast to the 27.50% success rate of current strongest methods. To further validate its practical impact, we tested MultiMol on two real-world challenges. First, we enhanced the selectivity of Xanthine Amine Congener (XAC), a promiscuous ligand that binds both A1R and A2AR, successfully biasing it towards A1R. Second, we improved the bioavailability of Saquinavir, an HIV-1 protease inhibitor with known bioavailability limitations. Overall, these results indicate that MultiMol represents a highly promising approach for multi-objective molecular optimization, holding great potential to accelerate the drug development process and contribute to the advancement of pharmaceutical research.

One Head Eight Arms: Block Matrix based Low Rank Adaptation for CLIP-based Few-Shot Learning

Recent advancements in fine-tuning Vision-Language Foundation Models (VLMs) have garnered significant attention for their effectiveness in downstream few-shot learning tasks.While these recent approaches exhibits some performance improvements, they often suffer from excessive training parameters and high computational costs. To address these challenges, we propose a novel Block matrix-based low-rank adaptation framework, called Block-LoRA, for fine-tuning VLMs on downstream few-shot tasks. Inspired by recent work on Low-Rank Adaptation (LoRA), Block-LoRA partitions the original low-rank decomposition matrix of LoRA into a series of sub-matrices while sharing all down-projection sub-matrices. This structure not only reduces the number of training parameters, but also transforms certain complex matrix multiplication operations into simpler matrix addition, significantly lowering the computational cost of fine-tuning. Notably, Block-LoRA enables fine-tuning CLIP on the ImageNet few-shot benchmark using a single 24GB GPU. We also show that Block-LoRA has the more tighter bound of generalization error than vanilla LoRA. Without bells and whistles, extensive experiments demonstrate that Block-LoRA achieves competitive performance compared to state-of-the-art CLIP-based few-shot methods, while maintaining a low training parameters count and reduced computational overhead.

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.

TSINR: Capturing Temporal Continuity via Implicit Neural Representations for Time Series Anomaly Detection

Time series anomaly detection aims to identify unusual patterns in data or deviations from systems' expected behavior. The reconstruction-based methods are the mainstream in this task, which learn point-wise representation via unsupervised learning. However, the unlabeled anomaly points in training data may cause these reconstruction-based methods to learn and reconstruct anomalous data, resulting in the challenge of capturing normal patterns. In this paper, we propose a time series anomaly detection method based on implicit neural representation (INR) reconstruction, named TSINR, to address this challenge. Due to the property of spectral bias, TSINR enables prioritizing low-frequency signals and exhibiting poorer performance on high-frequency abnormal data. Specifically, we adopt INR to parameterize time series data as a continuous function and employ a transformer-based architecture to predict the INR of given data. As a result, the proposed TSINR method achieves the advantage of capturing the temporal continuity and thus is more sensitive to discontinuous anomaly data. In addition, we further design a novel form of INR continuous function to learn inter- and intra-channel information, and leverage a pre-trained large language model to amplify the intense fluctuations in anomalies. Extensive experiments demonstrate that TSINR achieves superior overall performance on both univariate and multivariate time series anomaly detection benchmarks compared to other state-of-the-art reconstruction-based methods. Our codes are available.

Repurposing Foundation Model for Generalizable Medical Time Series Classification

Medical time series (MedTS) classification is critical for a wide range of healthcare applications such as Alzheimer's Disease diagnosis. However, its real-world deployment is severely challenged by poor generalizability due to inter- and intra-dataset heterogeneity in MedTS, including variations in channel configurations, time series lengths, and diagnostic tasks. Here, we propose FORMED, a foundation classification model that leverages a pre-trained backbone and tackles these challenges through re-purposing. FORMED integrates the general representation learning enabled by the backbone foundation model and the medical domain knowledge gained on a curated cohort of MedTS datasets. FORMED can adapt seamlessly to unseen MedTS datasets, regardless of the number of channels, sample lengths, or medical tasks. Experimental results show that, without any task-specific adaptation, the repurposed FORMED achieves performance that is competitive with, and often superior to, 11 baseline models trained specifically for each dataset. Furthermore, FORMED can effectively adapt to entirely new, unseen datasets, with lightweight parameter updates, consistently outperforming baselines. Our results highlight FORMED as a versatile and scalable model for a wide range of MedTS classification tasks, positioning it as a strong foundation model for future research in MedTS analysis.

SAM-SP: Self-Prompting Makes SAM Great Again

The recently introduced Segment Anything Model (SAM), a Visual Foundation Model (VFM), has demonstrated impressive capabilities in zero-shot segmentation tasks across diverse natural image datasets. Despite its success, SAM encounters noticeably performance degradation when applied to specific domains, such as medical images. Current efforts to address this issue have involved fine-tuning strategies, intended to bolster the generalizability of the vanilla SAM. However, these approaches still predominantly necessitate the utilization of domain specific expert-level prompts during the evaluation phase, which severely constrains the model's practicality. To overcome this limitation, we introduce a novel self-prompting based fine-tuning approach, called SAM-SP, tailored for extending the vanilla SAM model. Specifically, SAM-SP leverages the output from the previous iteration of the model itself as prompts to guide subsequent iteration of the model. This self-prompting module endeavors to learn how to generate useful prompts autonomously and alleviates the dependence on expert prompts during the evaluation phase, significantly broadening SAM's applicability. Additionally, we integrate a self-distillation module to enhance the self-prompting process further. Extensive experiments across various domain specific datasets validate the effectiveness of the proposed SAM-SP. Our SAM-SP not only alleviates the reliance on expert prompts but also exhibits superior segmentation performance comparing to the state-of-the-art task-specific segmentation approaches, the vanilla SAM, and SAM-based approaches.

Attention Beats Linear for Fast Implicit Neural Representation Generation

Implicit Neural Representation (INR) has gained increasing popularity as a data representation method, serving as a prerequisite for innovative generation models. Unlike gradient-based methods, which exhibit lower efficiency in inference, the adoption of hyper-network for generating parameters in Multi-Layer Perceptrons (MLP), responsible for executing INR functions, has surfaced as a promising and efficient alternative. However, as a global continuous function, MLP is challenging in modeling highly discontinuous signals, resulting in slow convergence during the training phase and inaccurate reconstruction performance. Moreover, MLP requires massive representation parameters, which implies inefficiencies in data representation. In this paper, we propose a novel Attention-based Localized INR (ANR) composed of a localized attention layer (LAL) and a global MLP that integrates coordinate features with data features and converts them to meaningful outputs. Subsequently, we design an instance representation framework that delivers a transformer-like hyper-network to represent data instances as a compact representation vector. With instance-specific representation vector and instance-agnostic ANR parameters, the target signals are well reconstructed as a continuous function. We further address aliasing artifacts with variational coordinates when obtaining the super-resolution inference results. Extensive experimentation across four datasets showcases the notable efficacy of our ANR method, e.g. enhancing the PSNR value from 37.95dB to 47.25dB on the CelebA dataset. Code is released at https://github.com/Roninton/ANR.

Towards a Unified Framework of Clustering-based Anomaly Detection

Unsupervised Anomaly Detection (UAD) plays a crucial role in identifying abnormal patterns within data without labeled examples, holding significant practical implications across various domains. Although the individual contributions of representation learning and clustering to anomaly detection are well-established, their interdependencies remain under-explored due to the absence of a unified theoretical framework. Consequently, their collective potential to enhance anomaly detection performance remains largely untapped. To bridge this gap, in this paper, we propose a novel probabilistic mixture model for anomaly detection to establish a theoretical connection among representation learning, clustering, and anomaly detection. By maximizing a novel anomaly-aware data likelihood, representation learning and clustering can effectively reduce the adverse impact of anomalous data and collaboratively benefit anomaly detection. Meanwhile, a theoretically substantiated anomaly score is naturally derived from this framework. Lastly, drawing inspiration from gravitational analysis in physics, we have devised an improved anomaly score that more effectively harnesses the combined power of representation learning and clustering. Extensive experiments, involving 17 baseline methods across 30 diverse datasets, validate the effectiveness and generalization capability of the proposed method, surpassing state-of-the-art methods.

Guarding Graph Neural Networks for Unsupervised Graph Anomaly Detection

Unsupervised graph anomaly detection aims at identifying rare patterns that deviate from the majority in a graph without the aid of labels, which is important for a variety of real-world applications. Recent advances have utilized Graph Neural Networks (GNNs) to learn effective node representations by aggregating information from neighborhoods. This is motivated by the hypothesis that nodes in the graph tend to exhibit consistent behaviors with their neighborhoods. However, such consistency can be disrupted by graph anomalies in multiple ways. Most existing methods directly employ GNNs to learn representations, disregarding the negative impact of graph anomalies on GNNs, resulting in sub-optimal node representations and anomaly detection performance. While a few recent approaches have redesigned GNNs for graph anomaly detection under semi-supervised label guidance, how to address the adverse effects of graph anomalies on GNNs in unsupervised scenarios and learn effective representations for anomaly detection are still under-explored. To bridge this gap, in this paper, we propose a simple yet effective framework for Guarding Graph Neural Networks for Unsupervised Graph Anomaly Detection (G3AD). Specifically, G3AD introduces two auxiliary networks along with correlation constraints to guard the GNNs from inconsistent information encoding. Furthermore, G3AD introduces an adaptive caching module to guard the GNNs from solely reconstructing the observed data that contains anomalies. Extensive experiments demonstrate that our proposed G3AD can outperform seventeen state-of-the-art methods on both synthetic and real-world datasets.

Graph Spatiotemporal Process for Multivariate Time Series Anomaly Detection with Missing Values

The detection of anomalies in multivariate time series data is crucial for various practical applications, including smart power grids, traffic flow forecasting, and industrial process control. However, real-world time series data is usually not well-structured, posting significant challenges to existing approaches: (1) The existence of missing values in multivariate time series data along variable and time dimensions hinders the effective modeling of interwoven spatial and temporal dependencies, resulting in important patterns being overlooked during model training; (2) Anomaly scoring with irregularly-sampled observations is less explored, making it difficult to use existing detectors for multivariate series without fully-observed values. In this work, we introduce a novel framework called GST-Pro, which utilizes a graph spatiotemporal process and anomaly scorer to tackle the aforementioned challenges in detecting anomalies on irregularly-sampled multivariate time series. Our approach comprises two main components. First, we propose a graph spatiotemporal process based on neural controlled differential equations. This process enables effective modeling of multivariate time series from both spatial and temporal perspectives, even when the data contains missing values. Second, we present a novel distribution-based anomaly scoring mechanism that alleviates the reliance on complete uniform observations. By analyzing the predictions of the graph spatiotemporal process, our approach allows anomalies to be easily detected. Our experimental results show that the GST-Pro method can effectively detect anomalies in time series data and outperforms state-of-the-art methods, regardless of whether there are missing values present in the data. Our code is available: https://github.com/huankoh/GST-Pro.