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The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about their true capabilities. In this work, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands CodeAct, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. In addition, we evaluate OpenAI o1 with direct prompting and self-debug, which demonstrates the effectiveness of increasing inference-time compute. Still, our results underscore the limitations of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research., Comment: 57 pages

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/)

Unraveling the relation between structural information and the dynamic properties of supercooled liquids is one of the grand challenges of physics. Dynamic heterogeneity, characterized by the propensity of particles, is often used as a proxy for the dynamic slowing down. In this work, we introduce an unsupervised machine learning approach based on a time-lagged autoencoder (TAE) to elucidate the effect of structural features on the long-time dynamic heterogeneity of supercooled liquids. The TAE uses an autoencoder to reconstruct features at time $t + \Delta t$ from input features at time $t$ for individual particles, and the resulting latent space variables are considered as order parameters. In the Kob-Andersen system, with a $\Delta t$ about a thousand times smaller than the relaxation time, the TAE order parameter exhibits a remarkable correlation with the long-time propensity. We find that radial features on all length-scales are required to capture the long-time dynamics, consistent with recent simulations. This shows that fluctuations of structural features contain sufficient information about the long-time dynamic heterogeneity.

Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the complex configuration space is coarse-grained into conformational states, with the dynamics modeled by a series of Markovian transitions among these states at discrete lag times. Constructing the Markovian model at a specific lag time requires state defined without significant internal energy barriers, enabling internal dynamics relaxation within the lag time. This process coarse grains time and space, integrating out rapid motions within metastable states. This work introduces a continuous embedding approach for molecular conformations using the state predictive information bottleneck (SPIB), which unifies dimensionality reduction and state space partitioning via a continuous, machine learned basis set. Without explicit optimization of VAMP-based scores, SPIB demonstrates state-of-the-art performance in identifying slow dynamical processes and constructing predictive multi-resolution Markovian models. When applied to mini-proteins trajectories, SPIB showcases unique advantages compared to competing methods. It automatically adjusts the number of metastable states based on a specified minimal time resolution, eliminating the need for manual tuning. While maintaining efficacy in dynamical properties, SPIB excels in accurately distinguishing metastable states and capturing numerous well-populated macrostates. Furthermore, SPIB's ability to learn a low-dimensional continuous embedding of the underlying MSMs enhances the interpretation of dynamic pathways. Accordingly, we propose SPIB as an easy-to-implement methodology for end-to-end MSM construction., Comment: 19 pages, 7 figures

The Spiking Neural Network (SNN), as one of the biologically inspired neural network infrastructures, has drawn increasing attention recently. It adopts binary spike activations to transmit information, thus the multiplications of activations and weights can be substituted by additions, which brings high energy efficiency. However, in the paper, we theoretically and experimentally prove that the binary spike activation map cannot carry enough information, thus causing information loss and resulting in accuracy decreasing. To handle the problem, we propose a ternary spike neuron to transmit information. The ternary spike neuron can also enjoy the event-driven and multiplication-free operation advantages of the binary spike neuron but will boost the information capacity. Furthermore, we also embed a trainable factor in the ternary spike neuron to learn the suitable spike amplitude, thus our SNN will adopt different spike amplitudes along layers, which can better suit the phenomenon that the membrane potential distributions are different along layers. To retain the efficiency of the vanilla ternary spike, the trainable ternary spike SNN will be converted to a standard one again via a re-parameterization technique in the inference. Extensive experiments with several popular network structures over static and dynamic datasets show that the ternary spike can consistently outperform state-of-the-art methods. Our code is open-sourced at https://github.com/yfguo91/Ternary-Spike., Comment: Accepted by AAAI2024

As one of the energy-efficient alternatives of conventional neural networks (CNNs), spiking neural networks (SNNs) have gained more and more interest recently. To train the deep models, some effective batch normalization (BN) techniques are proposed in SNNs. All these BNs are suggested to be used after the convolution layer as usually doing in CNNs. However, the spiking neuron is much more complex with the spatio-temporal dynamics. The regulated data flow after the BN layer will be disturbed again by the membrane potential updating operation before the firing function, i.e., the nonlinear activation. Therefore, we advocate adding another BN layer before the firing function to normalize the membrane potential again, called MPBN. To eliminate the induced time cost of MPBN, we also propose a training-inference-decoupled re-parameterization technique to fold the trained MPBN into the firing threshold. With the re-parameterization technique, the MPBN will not introduce any extra time burden in the inference. Furthermore, the MPBN can also adopt the element-wised form, while these BNs after the convolution layer can only use the channel-wised form. Experimental results show that the proposed MPBN performs well on both popular non-spiking static and neuromorphic datasets. Our code is open-sourced at \href{https://github.com/yfguo91/MPBN}{MPBN}., Comment: Accepted by ICCV2023

Spiking Neural Networks (SNNs) as one of the biology-inspired models have received much attention recently. It can significantly reduce energy consumption since they quantize the real-valued membrane potentials to 0/1 spikes to transmit information thus the multiplications of activations and weights can be replaced by additions when implemented on hardware. However, this quantization mechanism will inevitably introduce quantization error, thus causing catastrophic information loss. To address the quantization error problem, we propose a regularizing membrane potential loss (RMP-Loss) to adjust the distribution which is directly related to quantization error to a range close to the spikes. Our method is extremely simple to implement and straightforward to train an SNN. Furthermore, it is shown to consistently outperform previous state-of-the-art methods over different network architectures and datasets., Comment: Accepted by ICCV2023

The Spiking Neural Network (SNN) has attracted more and more attention recently. It adopts binary spike signals to transmit information. Benefitting from the information passing paradigm of SNNs, the multiplications of activations and weights can be replaced by additions, which are more energy-efficient. However, its "Hard Reset" mechanism for the firing activity would ignore the difference among membrane potentials when the membrane potential is above the firing threshold, causing information loss. Meanwhile, quantifying the membrane potential to 0/1 spikes at the firing instants will inevitably introduce the quantization error thus bringing about information loss too. To address these problems, we propose to use the "Soft Reset" mechanism for the supervised training-based SNNs, which will drive the membrane potential to a dynamic reset potential according to its magnitude, and Membrane Potential Rectifier (MPR) to reduce the quantization error via redistributing the membrane potential to a range close to the spikes. Results show that the SNNs with the "Soft Reset" mechanism and MPR outperform their vanilla counterparts on both static and dynamic datasets., Comment: Accepted by ECCV2022

The spiking neural network (SNN), as a promising brain-inspired computational model with binary spike information transmission mechanism, rich spatially-temporal dynamics, and event-driven characteristics, has received extensive attention. However, its intricately discontinuous spike mechanism brings difficulty to the optimization of the deep SNN. Since the surrogate gradient method can greatly mitigate the optimization difficulty and shows great potential in directly training deep SNNs, a variety of direct learning-based deep SNN works have been proposed and achieved satisfying progress in recent years. In this paper, we present a comprehensive survey of these direct learning-based deep SNN works, mainly categorized into accuracy improvement methods, efficiency improvement methods, and temporal dynamics utilization methods. In addition, we also divide these categorizations into finer granularities further to better organize and introduce them. Finally, the challenges and trends that may be faced in future research are prospected., Comment: Accepted by Frontiers in Neuroscience. If your relevant work is omitted, feel free to email me at yfguo@pku.edu.cn

Emerged as a biology-inspired method, Spiking Neural Networks (SNNs) mimic the spiking nature of brain neurons and have received lots of research attention. SNNs deal with binary spikes as their activation and therefore derive extreme energy efficiency on hardware. However, it also leads to an intrinsic obstacle that training SNNs from scratch requires a re-definition of the firing function for computing gradient. Artificial Neural Networks (ANNs), however, are fully differentiable to be trained with gradient descent. In this paper, we propose a joint training framework of ANN and SNN, in which the ANN can guide the SNN's optimization. This joint framework contains two parts: First, the knowledge inside ANN is distilled to SNN by using multiple branches from the networks. Second, we restrict the parameters of ANN and SNN, where they share partial parameters and learn different singular weights. Extensive experiments over several widely used network structures show that our method consistently outperforms many other state-of-the-art training methods. For example, on the CIFAR100 classification task, the spiking ResNet-18 model trained by our method can reach to 77.39% top-1 accuracy with only 4 time steps., Comment: Accepted by Pattern Recognition

Brain-inspired spiking neural networks (SNNs) have recently drawn more and more attention due to their event-driven and energy-efficient characteristics. The integration of storage and computation paradigm on neuromorphic hardwares makes SNNs much different from Deep Neural Networks (DNNs). In this paper, we argue that SNNs may not benefit from the weight-sharing mechanism, which can effectively reduce parameters and improve inference efficiency in DNNs, in some hardwares, and assume that an SNN with unshared convolution kernels could perform better. Motivated by this assumption, a training-inference decoupling method for SNNs named as Real Spike is proposed, which not only enjoys both unshared convolution kernels and binary spikes in inference-time but also maintains both shared convolution kernels and Real-valued Spikes during training. This decoupling mechanism of SNN is realized by a re-parameterization technique. Furthermore, based on the training-inference-decoupled idea, a series of different forms for implementing Real Spike on different levels are presented, which also enjoy shared convolutions in the inference and are friendly to both neuromorphic and non-neuromorphic hardware platforms. A theoretical proof is given to clarify that the Real Spike-based SNN network is superior to its vanilla counterpart. Experimental results show that all different Real Spike versions can consistently improve the SNN performance. Moreover, the proposed method outperforms the state-of-the-art models on both non-spiking static and neuromorphic datasets., Comment: Accepted by ECCV2022

Recurrent neural networks for language models like long short-term memory (LSTM) have been utilized as a tool for modeling and predicting long term dynamics of complex stochastic molecular systems. Recently successful examples on learning slow dynamics by LSTM are given with simulation data of low dimensional reaction coordinate. However, in this report we show that the following three key factors significantly affect the performance of language model learning, namely dimensionality of reaction coordinates, temporal resolution and state partition. When applying recurrent neural networks to molecular dynamics simulation trajectories of high dimensionality, we find that rare events corresponding to the slow dynamics might be obscured by other faster dynamics of the system, and cannot be efficiently learned. Under such conditions, we find that coarse graining the conformational space into metastable states and removing recrossing events when estimating transition probabilities between states could greatly help improve the accuracy of slow dynamics learning in molecular dynamics. Moreover, we also explore other models like Transformer, which do not show superior performance than LSTM in overcoming these issues. Therefore, to learn rare events of slow molecular dynamics by LSTM and Transformer, it is critical to choose proper temporal resolution (i.e., saving intervals of MD simulation trajectories) and state partition in high resolution data, since deep neural network models might not automatically disentangle slow dynamics from fast dynamics when both are present in data influencing each other.

Recently, the transductive graph-based methods have achieved great success in the few-shot classification task. However, most existing methods ignore exploring the class-level knowledge that can be easily learned by humans from just a handful of samples. In this paper, we propose an Explicit Class Knowledge Propagation Network (ECKPN), which is composed of the comparison, squeeze and calibration modules, to address this problem. Specifically, we first employ the comparison module to explore the pairwise sample relations to learn rich sample representations in the instance-level graph. Then, we squeeze the instance-level graph to generate the class-level graph, which can help obtain the class-level visual knowledge and facilitate modeling the relations of different classes. Next, the calibration module is adopted to characterize the relations of the classes explicitly to obtain the more discriminative class-level knowledge representations. Finally, we combine the class-level knowledge with the instance-level sample representations to guide the inference of the query samples. We conduct extensive experiments on four few-shot classification benchmarks, and the experimental results show that the proposed ECKPN significantly outperforms the state-of-the-art methods., Comment: Accepted by CVPR2021

Spiking neural networks (SNNs) possess energy-efficient potential due to event-based computation. However, supervised training of SNNs remains a challenge as spike activities are non-differentiable. Previous SNNs training methods can be generally categorized into two basic classes, i.e., backpropagation-like training methods and plasticity-based learning methods. The former methods are dependent on energy-inefficient real-valued computation and non-local transmission, as also required in artificial neural networks (ANNs), whereas the latter are either considered to be biologically implausible or exhibit poor performance. Hence, biologically plausible (bio-plausible) high-performance supervised learning (SL) methods for SNNs remain deficient. In this paper, we proposed a novel bio-plausible SNN model for SL based on the symmetric spike-timing dependent plasticity (sym-STDP) rule found in neuroscience. By combining the sym-STDP rule with bio-plausible synaptic scaling and intrinsic plasticity of the dynamic threshold, our SNN model implemented SL well and achieved good performance in the benchmark recognition task (MNIST dataset). To reveal the underlying mechanism of our SL model, we visualized both layer-based activities and synaptic weights using the t-distributed stochastic neighbor embedding (t-SNE) method after training and found that they were well clustered, thereby demonstrating excellent classification ability. Furthermore, to verify the robustness of our model, we trained it on another more realistic dataset (Fashion-MNIST), which also showed good performance. As the learning rules were bio-plausible and based purely on local spike events, our model could be easily applied to neuromorphic hardware for online training and may be helpful for understanding SL information processing at the synaptic level in biological neural systems., Comment: 29 pages, 6 figures