Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive framework for learning the complex topological and geometric features of drug-like molecules, cementing their role in modern molecular modeling. This review provides a comprehensive overview of the methodological foundations and representative applications of GNNs in drug discovery, spanning tasks such as molecular property prediction, virtual screening, molecular generation, biomedical knowledge graph construction, and synthesis planning. Particular attention is given to recent methodological advances, including geometric GNNs, interpretable models, uncertainty quantification, scalable graph architectures, and graph generative frameworks. We also discuss how these models integrate with modern deep learning approaches, such as self-supervised learning, multi-task learning, meta-learning and pre-training. Throughout this review, we highlight the practical challenges and methodological bottlenecks encountered when applying GNNs to real-world drug discovery pipelines, and conclude with a discussion on future directions.
Multi-task learning for dense prediction is limited by the need for extensive annotation for every task, though recent works have explored training with partial task labels. Leveraging the generalization power of diffusion models, we extend the partial learning setup to a zero-shot setting, training a multi-task model on multiple synthetic datasets, each labeled for only a subset of tasks. Our method, StableMTL, repurposes image generators for latent regression. Adapting a denoising framework with task encoding, per-task conditioning and a tailored training scheme. Instead of per-task losses requiring careful balancing, a unified latent loss is adopted, enabling seamless scaling to more tasks. To encourage inter-task synergy, we introduce a multi-stream model with a task-attention mechanism that converts N-to-N task interactions into efficient 1-to-N attention, promoting effective cross-task sharing. StableMTL outperforms baselines on 7 tasks across 8 benchmarks.
Single-image super-resolution refers to the reconstruction of a high-resolution image from a single low-resolution observation. Although recent deep learning-based methods have demonstrated notable success on simulated datasets -- with low-resolution images obtained by degrading and downsampling high-resolution ones -- they frequently fail to generalize to real-world settings, such as document scans, which are affected by complex degradations and semantic variability. In this study, we introduce a task-driven, multi-task learning framework for training a super-resolution network specifically optimized for optical character recognition tasks. We propose to incorporate auxiliary loss functions derived from high-level vision tasks, including text detection using the connectionist text proposal network, text recognition via a convolutional recurrent neural network, keypoints localization using Key.Net, and hue consistency. To balance these diverse objectives, we employ dynamic weight averaging mechanism, which adaptively adjusts the relative importance of each loss term based on its convergence behavior. We validate our approach upon the SRResNet architecture, which is a well-established technique for single-image super-resolution. Experimental evaluations on both simulated and real-world scanned document datasets demonstrate that the proposed approach improves text detection, measured with intersection over union, while preserving overall image fidelity. These findings underscore the value of multi-objective optimization in super-resolution models for bridging the gap between simulated training regimes and practical deployment in real-world scenarios.
Pareto Set Learning (PSL) is popular as an efficient approach to obtaining the complete optimal solution in Multi-objective Learning (MOL). A set of optimal solutions approximates the Pareto set, and its mapping is a set of dense points in the Pareto front in objective space. However, some current methods face a challenge: how to make the Pareto solution is diverse while maximizing the hypervolume value. In this paper, we propose a novel method to address this challenge, which employs Stein Variational Gradient Descent (SVGD) to approximate the entire Pareto set. SVGD pushes a set of particles towards the Pareto set by applying a form of functional gradient descent, which helps to converge and diversify optimal solutions. Additionally, we employ diverse gradient direction strategies to thoroughly investigate a unified framework for SVGD in multi-objective optimization and adapt this framework with an annealing schedule to promote stability. We introduce our method, SVH-MOL, and validate its effectiveness through extensive experiments on multi-objective problems and multi-task learning, demonstrating its superior performance.
Future 6G networks are envisioned to enhance the user experience in a multitude of different ways. The unification of existing terrestrial networks with non-terrestrial network (NTN) components will provide users with ubiquitous connectivity. Multi-access edge computing (MEC) will enable low-latency services, with computations performed closer to the end users, and distributed learning paradigms. Advanced multiple access schemes, such as sparse code multiple access (SCMA), can be employed to efficiently move data from edge nodes to spaceborne MEC servers. However, the non-orthogonal nature of SCMA results in interference, limiting the effectiveness of traditional SCMA receivers. Hence, NTN links should be protected with robust channel codes, significantly reducing the uplink throughput. Thus, we investigate the application of artificial intelligence (AI) to SCMA receivers for 6G NTNs. We train an AI model with multi-task learning to optimally separate and receive superimposed SCMA signals. Through link level simulations, we evaluate the block error rate (BLER) and the aggregated theoretical throughput achieved by the AI model as a function of the received energy per bit over noise power spectral density ratio (Eb/N0). We show that the proposed receiver achieves a target 10% BLER with 3.5dB lower Eb/N0 with respect to the benchmark algorithm. We conclude the assessment discussing the complexity-related challenges to the implementation of the AI model on board of a low earth orbit satellite.
Self-harm detection on social media is critical for early intervention and mental health support, yet remains challenging due to the subtle, context-dependent nature of such expressions. Identifying self-harm intent aids suicide prevention by enabling timely responses, but current large language models (LLMs) struggle to interpret implicit cues in casual language and emojis. This work enhances LLMs' comprehension of self-harm by distinguishing intent through nuanced language-emoji interplay. We present the Centennial Emoji Sensitivity Matrix (CESM-100), a curated set of 100 emojis with contextual self-harm interpretations and the Self-Harm Identification aNd intent Extraction with Supportive emoji sensitivity (SHINES) dataset, offering detailed annotations for self-harm labels, casual mentions (CMs), and serious intents (SIs). Our unified framework: a) enriches inputs using CESM-100; b) fine-tunes LLMs for multi-task learning: self-harm detection (primary) and CM/SI span detection (auxiliary); c) generates explainable rationales for self-harm predictions. We evaluate the framework on three state-of-the-art LLMs-Llama 3, Mental-Alpaca, and MentalLlama, across zero-shot, few-shot, and fine-tuned scenarios. By coupling intent differentiation with contextual cues, our approach commendably enhances LLM performance in both detection and explanation tasks, effectively addressing the inherent ambiguity in self-harm signals. The SHINES dataset, CESM-100 and codebase are publicly available at: https://www.iitp.ac.in/~ai-nlp-ml/resources.html#SHINES .
Gaussian Process (GP) regression is a popular and sample-efficient approach for many engineering applications, where observations are expensive to acquire, and is also a central ingredient of Bayesian optimization (BO), a highly prevailing method for the optimization of black-box functions. However, when all or some input variables are categorical, building a predictive and computationally efficient GP remains challenging. Starting from the naive target encoding idea, where the original categorical values are replaced with the mean of the target variable for that category, we propose a generalization based on distributional encoding (DE) which makes use of all samples of the target variable for a category. To handle this type of encoding inside the GP, we build upon recent results on characteristic kernels for probability distributions, based on the maximum mean discrepancy and the Wasserstein distance. We also discuss several extensions for classification, multi-task learning and incorporation or auxiliary information. Our approach is validated empirically, and we demonstrate state-of-the-art predictive performance on a variety of synthetic and real-world datasets. DE is naturally complementary to recent advances in BO over discrete and mixed-spaces.
Lakehouse systems enable the same data to be queried with multiple execution engines. However, selecting the engine best suited to run a SQL query still requires a priori knowledge of the query computational requirements and an engine capability, a complex and manual task that only becomes more difficult with the emergence of new engines and workloads. In this paper, we address this limitation by proposing a cross-engine optimizer that can automate engine selection for diverse SQL queries through a learned cost model. Optimized with hints, a query plan is used for query cost prediction and routing. Cost prediction is formulated as a multi-task learning problem, and multiple predictor heads, corresponding to different engines and provisionings, are used in the model architecture. This eliminates the need to train engine-specific models and allows the flexible addition of new engines at a minimal fine-tuning cost. Results on various databases and engines show that using a query optimized logical plan for cost estimation decreases the average Q-error by even 12.6% over using unoptimized plans as input. Moreover, the proposed cross-engine optimizer reduces the total workload runtime by up to 25.2% in a zero-shot setting and 30.4% in a few-shot setting when compared to random routing.
Large language models (LLMs) have recently shown tremendous promise in serving as the backbone to agentic systems, as demonstrated by their performance in multi-faceted, challenging benchmarks like SWE-Bench and Agent-Bench. However, to realize the true potential of LLMs as autonomous agents, they must learn to identify, call, and interact with external tools and application program interfaces (APIs) to complete complex tasks. These tasks together are termed function calling. Endowing LLMs with function calling abilities leads to a myriad of advantages, such as access to current and domain-specific information in databases and knowledge sources, and the ability to outsource tasks that can be reliably performed by tools, e.g., a Python interpreter or calculator. While there has been significant progress in function calling with LLMs, there is still a dearth of open models that perform on par with proprietary LLMs like GPT, Claude, and Gemini. Therefore, in this work, we introduce the GRANITE-20B-FUNCTIONCALLING model under an Apache 2.0 license. The model is trained using a multi-task training approach on seven fundamental tasks encompassed in function calling, those being Nested Function Calling, Function Chaining, Parallel Functions, Function Name Detection, Parameter-Value Pair Detection, Next-Best Function, and Response Generation. We present a comprehensive evaluation on multiple out-of-domain datasets comparing GRANITE-20B-FUNCTIONCALLING to more than 15 other best proprietary and open models. GRANITE-20B-FUNCTIONCALLING provides the best performance among all open models on the Berkeley Function Calling Leaderboard and fourth overall. As a result of the diverse tasks and datasets used for training our model, we show that GRANITE-20B-FUNCTIONCALLING has better generalizability on multiple tasks in seven different evaluation datasets.
Multi-task learning (MTL) has emerged as an imperative machine learning tool to solve multiple learning tasks simultaneously and has been successfully applied to healthcare, marketing, and biomedical fields. However, in order to borrow information across different tasks effectively, it is essential to utilize both homogeneous and heterogeneous information. Among the extensive literature on MTL, various forms of heterogeneity are presented in MTL problems, such as block-wise, distribution, and posterior heterogeneity. Existing methods, however, struggle to tackle these forms of heterogeneity simultaneously in a unified framework. In this paper, we propose a two-step learning strategy for MTL which addresses the aforementioned heterogeneity. First, we impute the missing blocks using shared representations extracted from homogeneous source across different tasks. Next, we disentangle the mappings between input features and responses into a shared component and a task-specific component, respectively, thereby enabling information borrowing through the shared component. Our numerical experiments and real-data analysis from the ADNI database demonstrate the superior MTL performance of the proposed method compared to other competing methods.
Multi-task learning (MTL) has become an essential machine learning tool for addressing multiple learning tasks simultaneously and has been effectively applied across fields such as healthcare, marketing, and biomedical research. However, to enable efficient information sharing across tasks, it is crucial to leverage both shared and heterogeneous information. Despite extensive research on MTL, various forms of heterogeneity, including distribution and posterior heterogeneity, present significant challenges. Existing methods often fail to address these forms of heterogeneity within a unified framework. In this paper, we propose a dual-encoder framework to construct a heterogeneous latent factor space for each task, incorporating a task-shared encoder to capture common information across tasks and a task-specific encoder to preserve unique task characteristics. Additionally, we explore the intrinsic similarity structure of the coefficients corresponding to learned latent factors, allowing for adaptive integration across tasks to manage posterior heterogeneity. We introduce a unified algorithm that alternately learns the task-specific and task-shared encoders and coefficients. In theory, we investigate the excess risk bound for the proposed MTL method using local Rademacher complexity and apply it to a new but related task. Through simulation studies, we demonstrate that the proposed method outperforms existing data integration methods across various settings. Furthermore, the proposed method achieves superior predictive performance for time to tumor doubling across five distinct cancer types in PDX data.
Multimodal large language models (MLLMs) require a nuanced interpretation of complex image information, typically leveraging a vision encoder to perceive various visual scenarios. However, relying solely on a single vision encoder to handle diverse task domains proves difficult and inevitably leads to conflicts. Recent work enhances data perception by directly integrating multiple domain-specific vision encoders, yet this structure adds complexity and limits the potential for joint optimization. In this paper, we introduce Mixpert, an efficient mixture-of-vision-experts architecture that inherits the joint learning advantages from a single vision encoder while being restructured into a multi-expert paradigm for task-specific fine-tuning across different visual tasks. Additionally, we design a dynamic routing mechanism that allocates input images to the most suitable visual expert. Mixpert effectively alleviates domain conflicts encountered by a single vision encoder in multi-task learning with minimal additional computational cost, making it more efficient than multiple encoders. Furthermore, Mixpert integrates seamlessly into any MLLM, with experimental results demonstrating substantial performance gains across various tasks.
Federated Multi-Task Learning (FMTL) enables multiple clients performing heterogeneous tasks without exchanging their local data, offering broad potential for privacy preserving multi-task collaboration. However, most existing methods focus on building personalized models for each client and unable to support the aggregation of multiple heterogeneous tasks into a unified model. As a result, in real-world scenarios where task objectives, label spaces, and optimization paths vary significantly, conventional FMTL methods struggle to achieve effective joint training. To address this challenge, we propose FedDEA (Federated Decoupled Aggregation), an update-structure-aware aggregation method specifically designed for multi-task model integration. Our method dynamically identifies task-relevant dimensions based on the response strength of local updates and enhances their optimization effectiveness through rescaling. This mechanism effectively suppresses cross-task interference and enables task-level decoupled aggregation within a unified global model. FedDEA does not rely on task labels or architectural modifications, making it broadly applicable and deployment-friendly. Experimental results demonstrate that it can be easily integrated into various mainstream federated optimization algorithms and consistently delivers significant overall performance improvements on widely used NYUD-V2 and PASCAL-Context. These results validate the robustness and generalization capabilities of FedDEA under highly heterogeneous task settings.
Speech is a noninvasive digital phenotype that can offer valuable insights into mental health conditions, but it is often treated as a single modality. In contrast, we propose the treatment of patient speech data as a trimodal multimedia data source for depression detection. This study explores the potential of large language model-based architectures for speech-based depression prediction in a multimodal regime that integrates speech-derived text, acoustic landmarks, and vocal biomarkers. Adolescent depression presents a significant challenge and is often comorbid with multiple disorders, such as suicidal ideation and sleep disturbances. This presents an additional opportunity to integrate multi-task learning (MTL) into our study by simultaneously predicting depression, suicidal ideation, and sleep disturbances using the multimodal formulation. We also propose a longitudinal analysis strategy that models temporal changes across multiple clinical interactions, allowing for a comprehensive understanding of the conditions' progression. Our proposed approach, featuring trimodal, longitudinal MTL is evaluated on the Depression Early Warning dataset. It achieves a balanced accuracy of 70.8%, which is higher than each of the unimodal, single-task, and non-longitudinal methods.
While Multi-Task Learning (MTL) offers inherent advantages in complex domains such as medical imaging by enabling shared representation learning, effectively balancing task contributions remains a significant challenge. This paper addresses this critical issue by introducing DeepChest, a novel, computationally efficient and effective dynamic task-weighting framework specifically designed for multi-label chest X-ray (CXR) classification. Unlike existing heuristic or gradient-based methods that often incur substantial overhead, DeepChest leverages a performance-driven weighting mechanism based on effective analysis of task-specific loss trends. Given a network architecture (e.g., ResNet18), our model-agnostic approach adaptively adjusts task importance without requiring gradient access, thereby significantly reducing memory usage and achieving a threefold increase in training speed. It can be easily applied to improve various state-of-the-art methods. Extensive experiments on a large-scale CXR dataset demonstrate that DeepChest not only outperforms state-of-the-art MTL methods by 7% in overall accuracy but also yields substantial reductions in individual task losses, indicating improved generalization and effective mitigation of negative transfer. The efficiency and performance gains of DeepChest pave the way for more practical and robust deployment of deep learning in critical medical diagnostic applications. The code is publicly available at https://github.com/youssefkhalil320/DeepChest-MTL
With the rapid development of Large Language Models (LLMs), Parameter-Efficient Fine-Tuning (PEFT) methods have gained significant attention, which aims to achieve efficient fine-tuning of LLMs with fewer parameters. As a representative PEFT method, Low-Rank Adaptation (LoRA) introduces low-rank matrices to approximate the incremental tuning parameters and achieves impressive performance over multiple scenarios. After that, plenty of improvements have been proposed for further improvement. However, these methods either focus on single-task scenarios or separately train multiple LoRA modules for multi-task scenarios, limiting the efficiency and effectiveness of LoRA in multi-task scenarios. To better adapt to multi-task fine-tuning, in this paper, we propose a novel Mixture of Low-Rank Experts (MoRE) for multi-task PEFT. Specifically, instead of using an individual LoRA for each task, we align different ranks of LoRA module with different tasks, which we named low-rank experts. Moreover, we design a novel adaptive rank selector to select the appropriate expert for each task. By jointly training low-rank experts, MoRE can enhance the adaptability and efficiency of LoRA in multi-task scenarios. Finally, we conduct extensive experiments over multiple multi-task benchmarks along with different LLMs to verify model performance. Experimental results demonstrate that compared to traditional LoRA and its variants, MoRE significantly improves the performance of LLMs in multi-task scenarios and incurs no additional inference cost. We also release the model and code to facilitate the community.
The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce Prot2Token, a unified framework that overcomes these challenges by converting a wide spectrum of protein-related predictions, from sequence-level properties and residue-specific attributes to complex inter-protein interactions, into a standardized next-token prediction format. At its core, Prot2Token employs an autoregressive decoder, conditioned on embeddings from pre-trained protein encoders and guided by learnable task tokens, to perform diverse predictions. This architecture uniquely facilitates multi-task learning, enabling a single model to master numerous tasks with improved efficiency. We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Tokens strong predictive power in different types of protein-prediction tasks. Key results include significant speedups (e.g., near 1000x over AlphaFold2 with MSA) and performance often matching or exceeding specialized approaches. Beyond that, we introduce an auxiliary self-supervised decoder pre-training approach to improve spatially sensitive task performance. Prot2Token thus offers a significant step towards a versatile, high-throughput paradigm for protein modeling, promising to accelerate biological discovery and the development of novel therapeutics. The code is available at https://github.com/mahdip72/prot2token .
Diffusion MRI (dMRI) tractography enables in vivo mapping of brain structural connections, but traditional connectome generation is time-consuming and requires gray matter parcellation, posing challenges for large-scale studies. We introduce DeepMultiConnectome, a deep-learning model that predicts structural connectomes directly from tractography, bypassing the need for gray matter parcellation while supporting multiple parcellation schemes. Using a point-cloud-based neural network with multi-task learning, the model classifies streamlines according to their connected regions across two parcellation schemes, sharing a learned representation. We train and validate DeepMultiConnectome on tractography from the Human Connectome Project Young Adult dataset ($n = 1000$), labeled with an 84 and 164 region gray matter parcellation scheme. DeepMultiConnectome predicts multiple structural connectomes from a whole-brain tractogram containing 3 million streamlines in approximately 40 seconds. DeepMultiConnectome is evaluated by comparing predicted connectomes with traditional connectomes generated using the conventional method of labeling streamlines using a gray matter parcellation. The predicted connectomes are highly correlated with traditionally generated connectomes ($r = 0.992$ for an 84-region scheme; $r = 0.986$ for a 164-region scheme) and largely preserve network properties. A test-retest analysis of DeepMultiConnectome demonstrates reproducibility comparable to traditionally generated connectomes. The predicted connectomes perform similarly to traditionally generated connectomes in predicting age and cognitive function. Overall, DeepMultiConnectome provides a scalable, fast model for generating subject-specific connectomes across multiple parcellation schemes.
This paper presents a novel approach to catheter and line position detection in chest X-rays, combining multi-task learning with risk-sensitive conformal prediction to address critical clinical requirements. Our model simultaneously performs classification, segmentation, and landmark detection, leveraging the synergistic relationship between these tasks to improve overall performance. We further enhance clinical reliability through risk-sensitive conformal prediction, which provides statistically guaranteed prediction sets with higher reliability for clinically critical findings. Experimental results demonstrate excellent performance with 90.68\% overall empirical coverage and 99.29\% coverage for critical conditions, while maintaining remarkable precision in prediction sets. Most importantly, our risk-sensitive approach achieves zero high-risk mispredictions (cases where the system dangerously declares problematic tubes as confidently normal), making the system particularly suitable for clinical deployment. This work offers both accurate predictions and reliably quantified uncertainty -- essential features for life-critical medical applications.
In the era of Industry 4.0 and smart manufacturing, process systems engineering must adapt to digital transformation. While reinforcement learning offers a model-free approach to process control, its applications are limited by the dependence on accurate digital twins and well-designed reward functions. To address these limitations, this paper introduces a novel framework that integrates inverse reinforcement learning (IRL) with multi-task learning for data-driven, multi-mode control design. Using historical closed-loop data as expert demonstrations, IRL extracts optimal reward functions and control policies. A latent-context variable is incorporated to distinguish modes, enabling the training of mode-specific controllers. Case studies on a continuous stirred tank reactor and a fed-batch bioreactor validate the effectiveness of this framework in handling multi-mode data and training adaptable controllers.