Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at \url{//github.com/ChnQ/LLM4Mol}.
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Variational regularization is commonly used to solve linear inverse problems, and involves augmenting a data fidelity by a regularizer. The regularizer is used to promote a priori information and is weighted by a regularization parameter. Selection of an appropriate regularization parameter is critical, with various choices leading to very different reconstructions. Classical strategies used to determine a suitable parameter value include the discrepancy principle and the L-curve criterion, and in recent years a supervised machine learning approach called bilevel learning has been employed. Bilevel learning is a powerful framework to determine optimal parameters and involves solving a nested optimization problem. While previous strategies enjoy various theoretical results, the well-posedness of bilevel learning in this setting is still an open question. In particular, a necessary property is positivity of the determined regularization parameter. In this work, we provide a new condition that better characterizes positivity of optimal regularization parameters than the existing theory. Numerical results verify and explore this new condition for both small and high-dimensional problems.
Bayesian predictive inference provides a coherent description of entire predictive uncertainty through predictive distributions. We examine several widely used sparsity priors from the predictive (as opposed to estimation) inference viewpoint. Our context is estimating a predictive distribution of a high-dimensional Gaussian observation with a known variance but an unknown sparse mean under the Kullback-Leibler loss. First, we show that LASSO (Laplace) priors are incapable of achieving rate-optimal performance. This new result contributes to the literature on negative findings about Bayesian LASSO posteriors. However, deploying the Laplace prior inside the Spike-and-Slab framework (for example with the Spike-and-Slab LASSO prior), rate-minimax performance can be attained with properly tuned parameters (depending on the sparsity level sn). We highlight the discrepancy between prior calibration for the purpose of prediction and estimation. Going further, we investigate popular hierarchical priors which are known to attain adaptive rate-minimax performance for estimation. Whether or not they are rate-minimax also for predictive inference has, until now, been unclear. We answer affirmatively by showing that hierarchical Spike-and-Slab priors are adaptive and attain the minimax rate without the knowledge of sn. This is the first rate-adaptive result in the literature on predictive density estimation in sparse setups. This finding celebrates benefits of fully Bayesian inference.
Large language models have exhibited emergent abilities, demonstrating exceptional performance across diverse tasks for which they were not explicitly trained, including those that require complex reasoning abilities. The emergence of such abilities carries profound implications for the future direction of research in NLP, especially as the deployment of such models becomes more prevalent. However, one key challenge is that the evaluation of these abilities is often confounded by competencies that arise in models through alternative prompting techniques, such as in-context learning and instruction following, which also emerge as the models are scaled up. In this study, we provide the first comprehensive examination of these emergent abilities while accounting for various potentially biasing factors that can influence the evaluation of models. We conduct rigorous tests on a set of 18 models, encompassing a parameter range from 60 million to 175 billion parameters, across a comprehensive set of 22 tasks. Through an extensive series of over 1,000 experiments, we provide compelling evidence that emergent abilities can primarily be ascribed to in-context learning. We find no evidence for the emergence of reasoning abilities, thus providing valuable insights into the underlying mechanisms driving the observed abilities and thus alleviating safety concerns regarding their use.
We consider the problem of inferring the underlying graph topology from smooth graph signals in a novel but practical scenario where data are located in distributed clients and are privacy-sensitive. The main difficulty of this task lies in how to utilize the potentially heterogeneous data of all isolated clients under privacy constraints. Towards this end, we propose a framework where personalized graphs for local clients as well as a consensus graph are jointly learned. The personalized graphs match local data distributions, thereby mitigating data heterogeneity, while the consensus graph captures the global information. We next devise a tailored algorithm to solve the induced problem without violating privacy constraints, i.e., all private data are processed locally. To further enhance privacy protection, we introduce differential privacy (DP) into the proposed algorithm to resist privacy attacks when transmitting model updates. Theoretically, we establish provable convergence analyses for the proposed algorithms, including that with DP. Finally, extensive experiments on both synthetic and real-world data are carried out to validate the proposed framework. Experimental results illustrate that our approach can learn graphs effectively in the target scenario.
Cellwise outliers are widespread in data and traditional robust methods may fail when applied to datasets under such contamination. We propose a variable selection procedure, that uses a pairwise robust estimator to obtain an initial empirical covariance matrix among the response and potentially many predictors. Then we replace the primary design matrix and the response vector with their robust counterparts based on the estimated covariance matrix. Finally, we adopt the adaptive Lasso to obtain variable selection results. The proposed approach is robust to cellwise outliers in regular and high dimensional settings and empirical results show good performance in comparison with recently proposed alternative robust approaches, particularly in the challenging setting when contamination rates are high but the magnitude of outliers is moderate. Real data applications demonstrate the practical utility of the proposed method.
The capabilities and use cases of automatic natural language processing (NLP) have grown significantly over the last few years. While much work has been devoted to understanding how humans deal with discourse connectives, this phenomenon is understudied in computational systems. Therefore, it is important to put NLP models under the microscope and examine whether they can adequately comprehend, process, and reason within the complexity of natural language. In this chapter, we introduce the main mechanisms behind automatic sentence processing systems step by step and then focus on evaluating discourse connective processing. We assess nine popular systems in their ability to understand English discourse connectives and analyze how context and language understanding tasks affect their connective comprehension. The results show that NLP systems do not process all discourse connectives equally well and that the computational processing complexity of different connective kinds is not always consistently in line with the presumed complexity order found in human processing. In addition, while humans are more inclined to be influenced during the reading procedure but not necessarily in the final comprehension performance, discourse connectives have a significant impact on the final accuracy of NLP systems. The richer knowledge of connectives a system learns, the more negative effect inappropriate connectives have on it. This suggests that the correct explicitation of discourse connectives is important for computational natural language processing.
Feature attribution methods are popular in interpretable machine learning. These methods compute the attribution of each input feature to represent its importance, but there is no consensus on the definition of "attribution", leading to many competing methods with little systematic evaluation, complicated in particular by the lack of ground truth attribution. To address this, we propose a dataset modification procedure to induce such ground truth. Using this procedure, we evaluate three common methods: saliency maps, rationales, and attentions. We identify several deficiencies and add new perspectives to the growing body of evidence questioning the correctness and reliability of these methods applied on datasets in the wild. We further discuss possible avenues for remedy and recommend new attribution methods to be tested against ground truth before deployment. The code is available at \url{//github.com/YilunZhou/feature-attribution-evaluation}.
Non-convex optimization is ubiquitous in modern machine learning. Researchers devise non-convex objective functions and optimize them using off-the-shelf optimizers such as stochastic gradient descent and its variants, which leverage the local geometry and update iteratively. Even though solving non-convex functions is NP-hard in the worst case, the optimization quality in practice is often not an issue -- optimizers are largely believed to find approximate global minima. Researchers hypothesize a unified explanation for this intriguing phenomenon: most of the local minima of the practically-used objectives are approximately global minima. We rigorously formalize it for concrete instances of machine learning problems.
Compared with cheap addition operation, multiplication operation is of much higher computation complexity. The widely-used convolutions in deep neural networks are exactly cross-correlation to measure the similarity between input feature and convolution filters, which involves massive multiplications between float values. In this paper, we present adder networks (AdderNets) to trade these massive multiplications in deep neural networks, especially convolutional neural networks (CNNs), for much cheaper additions to reduce computation costs. In AdderNets, we take the $\ell_1$-norm distance between filters and input feature as the output response. The influence of this new similarity measure on the optimization of neural network have been thoroughly analyzed. To achieve a better performance, we develop a special back-propagation approach for AdderNets by investigating the full-precision gradient. We then propose an adaptive learning rate strategy to enhance the training procedure of AdderNets according to the magnitude of each neuron's gradient. As a result, the proposed AdderNets can achieve 74.9% Top-1 accuracy 91.7% Top-5 accuracy using ResNet-50 on the ImageNet dataset without any multiplication in convolution layer.
The dominant sequence transduction models are based on complex recurrent or convolutional neural networks in an encoder-decoder configuration. The best performing models also connect the encoder and decoder through an attention mechanism. We propose a new simple network architecture, the Transformer, based solely on attention mechanisms, dispensing with recurrence and convolutions entirely. Experiments on two machine translation tasks show these models to be superior in quality while being more parallelizable and requiring significantly less time to train. Our model achieves 28.4 BLEU on the WMT 2014 English-to-German translation task, improving over the existing best results, including ensembles by over 2 BLEU. On the WMT 2014 English-to-French translation task, our model establishes a new single-model state-of-the-art BLEU score of 41.8 after training for 3.5 days on eight GPUs, a small fraction of the training costs of the best models from the literature. We show that the Transformer generalizes well to other tasks by applying it successfully to English constituency parsing both with large and limited training data.
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