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Supplementary Information: TARTARUS: Practical and Realistic Benchmarks for Inverse Molecular Design

Neural Information Processing Systems

S1. INTRODUCTION Traditionally, property-guided optimization has relied on expert intuition [1] and several rounds of trial, error, and human-inspired optimization, occasionally supported by computer simulations. Alternatively, computer-assisted approaches have employed virtual screening [2] or optimization algorithms such as genetic algorithms (GAs) [3-5]. More recently, with the surge of deep learning, deep generative models have emerged, specifically designed to operate in chemical space and tackle inverse molecular design [6-8]. This has led to the development of numerous algorithmic approaches for this purpose, with the most popular including variational autoencoders (VAEs) [9, 10], generative adversarial networks (GANs) [11, 12], and reinforcement learning (RL) [13, 14]. METHODSOVERVIEW In this section, we provide an overview of the molecular generative models employed throughout this work and summarize the associated design choices we needed to make during their implementation. The molecular design algorithms we considered are VAEs, long short-term memory hill climbing (LSTM-HC) models [15-17], REINVENT [18], JANUS [19], and a graph-based genetic algorithm (GB-GA) [20]. At the core of the majority of these approaches are molecular string representations, the most commonly used of which is the Simplified Molecular Input Line Entry System (SMILES) [21]. Accordingly, many of the algorithms tested rely on predicting subsequent characters from partial strings to propose structures. However, algorithms based on SMILES can regularly produce invalid strings that do not represent molecules, which is problematic both in terms of robustness and interpretability of the corresponding methodologies [22, 23]. Consequently, this issue was addressed systematically by introducing Self-Referencing Embedded Strings (SELFIES) [22], a molecular string representation that guarantees validity. Thus, unlike for SMILES, every arbitrary combination of SELFIES characters represents a molecule. Nevertheless, its impact on structure optimization has not yet been evaluated systematically [23]. To address this issue, we modify some of the existing generative models relying on SMILES to be also compatible with SELFIES and test their performance depending on representation, similar to how it has been done recently [24]. Among the models tested, REINVENT, the VAEs, and the LSTM-HC models use recurrent neural networks (RNNs) [25] to learn the conditional probability distributions of the characters that represent molecules. RNNs are a class of artificial neural networks (ANNs) that utilize sequential information from their previous predictions and states.



Towards Understanding the Condensation of Neural Networks at Initial Training

Neural Information Processing Systems

Empirical works show that for ReLU neural networks (NNs) with small initialization, input weights of hidden neurons (the input weight of a hidden neuron consists of the weight from its input layer to the hidden neuron and its bias term) condense onto isolated orientations. The condensation dynamics implies that the training implicitly regularizes a NN towards one with much smaller effective size. In this work, we illustrate the formation of the condensation in multi-layer fully connected NNs and show that the maximal number of condensed orientations in the initial training stage is twice the multiplicity of the activation function, where "multiplicity" indicates the multiple roots of activation function at origin. Our theoretical analysis confirms experiments for two cases, one is for the activation function of multiplicity one with arbitrary dimension input, which contains many common activation functions, and the other is for the layer with one-dimensional input and arbitrary multiplicity. This work makes a step towards understanding how small initialization leads NNs to condensation at the initial training stage.


What You See is What You Get: Principled Deep Learning via Distributional Generalization

Neural Information Processing Systems

Having similar behavior at training time and test time--what we call a "What You See Is What You Get" (WYSIWYG) property--is desirable in machine learning. Models trained with standard stochastic gradient descent (SGD), however, do not necessarily have this property, as their complex behaviors such as robustness or subgroup performance can differ drastically between training and test time. In contrast, we show that Differentially-Private (DP) training provably ensures the high-level WYSIWYG property, which we quantify using a notion of distributional generalization. Applying this connection, we introduce new conceptual tools for designing deep-learning methods by reducing generalization concerns to optimization ones: to mitigate unwanted behavior at test time, it is provably sufficient to mitigate this behavior on the training data. By applying this novel design principle, which bypasses "pathologies" of SGD, we construct simple algorithms that are competitive with SOTA in several distributional-robustness applications, significantly improve the privacy vs. disparate impact trade-off of DP-SGD, and mitigate robust overfitting in adversarial training. Finally, we also improve on theoretical bounds relating DP, stability, and distributional generalization.


Reusing Models by Multi linear Operators for Efficient Training

Neural Information Processing Systems

Training large models from scratch usually costs a substantial amount of resources. Towards this problem, recent studies such as bert2BERT and LiGO have reused small pretrained models to initialize a large model (termed the "target model"), leading to a considerable acceleration in training. Despite the successes of these previous studies, they grew pretrained models by mapping partial weights only, ignoring potential correlations across the entire model. As we show in this paper, there are inter-and intra-interactions among the weights of both the pretrained and the target models. As a result, the partial mapping may not capture the complete information and lead to inadequate growth. In this paper, we propose a method that linearly correlates each weight of the target model to all the weights of the pretrained model to further enhance acceleration ability. We utilize multi-linear operators to reduce computational and spacial complexity, enabling acceptable resource requirements. Experiments demonstrate that our method can save 76% computational costs on DeiT-base transferred from DeiT-small, which outperforms bert2BERT by +12.0% and LiGO by +20.7%, respectively.


Type-to-Track: Retrieve Any Object via Prompt-based Tracking

Neural Information Processing Systems

One of the recent trends in vision problems is to use natural language captions to describe the objects of interest. This approach can overcome some limitations of traditional methods that rely on bounding boxes or category annotations. This paper introduces a novel paradigm for Multiple Object Tracking called Type-toTrack, which allows users to track objects in videos by typing natural language descriptions. We present a new dataset for that Grounded Multiple Object Tracking task, called GroOT, that contains videos with various types of objects and their corresponding textual captions describing their appearance and action in detail. Additionally, we introduce two new evaluation protocols and formulate evaluation metrics specifically for this task. We develop a new efficient method that models a transformer-based eMbed-ENcoDE-extRact framework (MENDER) using the third-order tensor decomposition. The experiments in five scenarios show that our MENDER approach outperforms another two-stage design in terms of accuracy and efficiency, up to 14.7% accuracy and 4 speed faster.