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Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

The Stochastic Gradient Descent method (SGD) and its stochastic variants have become methods of choice for solving finite-sum optimization problems arising from machine learning and data science thanks to their ability to handle large-scale applications and big datasets. In the last decades, researchers have made substantial effort to study the theoretical performance of SGD and its shuffling variants. However, only limited work has investigated its shuffling momentum variants, including shuffling heavy-ball momentum schemes for non-convex problems and Nesterov's momentum for convex settings. In this work, we extend the analysis of the shuffling momentum gradient method developed in [Tran et al (2021)] to both finite-sum convex and strongly convex optimization problems. We provide the first analysis of shuffling momentum-based methods for the strongly convex setting, attaining a convergence rate of $O(1/nT^2)$, where $n$ is the number of samples and $T$ is the number of training epochs. Our analysis is a state-of-the-art, matching the best rates of existing shuffling stochastic gradient algorithms in the literature.

Purpose: The treatment of cardiovascular diseases requires complex and challenging navigation of a guidewire and catheter. This often leads to lengthy interventions during which the patient and clinician are exposed to X-ray radiation. Deep Reinforcement Learning approaches have shown promise in learning this task and may be the key to automating catheter navigation during robotized interventions. Yet, existing training methods show limited capabilities at generalizing to unseen vascular anatomies, requiring to be retrained each time the geometry changes. Methods: In this paper, we propose a zero-shot learning strategy for three-dimensional autonomous endovascular navigation. Using a very small training set of branching patterns, our reinforcement learning algorithm is able to learn a control that can then be applied to unseen vascular anatomies without retraining. Results: We demonstrate our method on 4 different vascular systems, with an average success rate of 95% at reaching random targets on these anatomies. Our strategy is also computationally efficient, allowing the training of our controller to be performed in only 2 hours. Conclusion: Our training method proved its ability to navigate unseen geometries with different characteristics, thanks to a nearly shape-invariant observation space.

Safety of Large Language Models (LLMs) has become a central issue given their rapid progress and wide applications. Greedy Coordinate Gradient (GCG) is shown to be effective in constructing prompts containing adversarial suffixes to break the presumingly safe LLMs, but the optimization of GCG is time-consuming and limits its practicality. To reduce the time cost of GCG and enable more comprehensive studies of LLM safety, in this work, we study a new algorithm called $\texttt{Probe sampling}$ to accelerate the GCG algorithm. At the core of the algorithm is a mechanism that dynamically determines how similar a smaller draft model's predictions are to the target model's predictions for prompt candidates. When the target model is similar to the draft model, we rely heavily on the draft model to filter out a large number of potential prompt candidates to reduce the computation time. Probe sampling achieves up to $5.6$ times speedup using Llama2-7b and leads to equal or improved attack success rate (ASR) on the AdvBench.

Phase I clinical trials are essential to bringing novel therapies from chemical development to widespread use. Traditional approaches to dose-finding in Phase I trials, such as the '3+3' method and the Continual Reassessment Method (CRM), provide a principled approach for escalating across dose levels. However, these methods lack the ability to incorporate uncertainty regarding the dose-toxicity ordering as found in combination drug trials. Under this setting, dose-levels vary across multiple drugs simultaneously, leading to multiple possible dose-toxicity orderings. The Partial Ordering CRM (POCRM) extends to these settings by allowing for multiple dose-toxicity orderings. In this work, it is shown that the POCRM is vulnerable to 'estimation incoherency' whereby toxicity estimates shift in an illogical way, threatening patient safety and undermining clinician trust in dose-finding models. To this end, the Bayesian model averaged POCRM (BMA-POCRM) is proposed. BMA-POCRM uses Bayesian model averaging to take into account all possible orderings simultaneously, reducing the frequency of estimation incoherencies. The effectiveness of BMA-POCRM in drug combination settings is demonstrated through a specific instance of estimate incoherency of POCRM and simulation studies. The results highlight the improved safety, accuracy and reduced occurrence of estimate incoherency in trials applying the BMA-POCRM relative to the POCRM model.

Spiking Neural Networks (SNN). SNNs are based on a more biologically inspired approach than usual artificial neural networks. Such models are characterized by complex dynamics between neurons and spikes. These are very sensitive to the hyperparameters, making their optimization challenging. To tackle hyperparameter optimization of SNNs, we initially extended the signal loss issue of SNNs to what we call silent networks. These networks fail to emit enough spikes at their outputs due to mistuned hyperparameters or architecture. Generally, search spaces are heavily restrained, sometimes even discretized, to prevent the sampling of such networks. By defining an early stopping criterion detecting silent networks and by designing specific constraints, we were able to instantiate larger and more flexible search spaces. We applied a constrained Bayesian optimization technique, which was asynchronously parallelized, as the evaluation time of a SNN is highly stochastic. Large-scale experiments were carried-out on a multi-GPU Petascale architecture. By leveraging silent networks, results show an acceleration of the search, while maintaining good performances of both the optimization algorithm and the best solution obtained. We were able to apply our methodology to two popular training algorithms, known as spike timing dependent plasticity and surrogate gradient. Early detection allowed us to prevent worthless and costly computation, directing the search toward promising hyperparameter combinations. Our methodology could be applied to multi-objective problems, where the spiking activity is often minimized to reduce the energy consumption. In this scenario, it becomes essential to find the delicate frontier between low-spiking and silent networks. Finally, our approach may have implications for neural architecture search, particularly in defining suitable spiking architectures.

Multimodal Large Language Model (MLLM) recently has been a new rising research hotspot, which uses powerful Large Language Models (LLMs) as a brain to perform multimodal tasks. The surprising emergent capabilities of MLLM, such as writing stories based on images and OCR-free math reasoning, are rare in traditional methods, suggesting a potential path to artificial general intelligence. In this paper, we aim to trace and summarize the recent progress of MLLM. First of all, we present the formulation of MLLM and delineate its related concepts. Then, we discuss the key techniques and applications, including Multimodal Instruction Tuning (M-IT), Multimodal In-Context Learning (M-ICL), Multimodal Chain of Thought (M-CoT), and LLM-Aided Visual Reasoning (LAVR). Finally, we discuss existing challenges and point out promising research directions. In light of the fact that the era of MLLM has only just begun, we will keep updating this survey and hope it can inspire more research. An associated GitHub link collecting the latest papers is available at //github.com/BradyFU/Awesome-Multimodal-Large-Language-Models.

Medical Visual Question Answering (VQA) is a combination of medical artificial intelligence and popular VQA challenges. Given a medical image and a clinically relevant question in natural language, the medical VQA system is expected to predict a plausible and convincing answer. Although the general-domain VQA has been extensively studied, the medical VQA still needs specific investigation and exploration due to its task features. In the first part of this survey, we cover and discuss the publicly available medical VQA datasets up to date about the data source, data quantity, and task feature. In the second part, we review the approaches used in medical VQA tasks. In the last part, we analyze some medical-specific challenges for the field and discuss future research directions.

Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.