Searching for novel and diverse molecular candidates is a critical undertaking in drug and material discovery. Existing approaches have successfully adapted the diffusion model, the most effective generative model in image generation, to create 1D SMILES strings, 2D chemical graphs, or 3D molecular conformers. However, these methods are not efficient and flexible enough to generate 3D molecules with multiple desired properties, as they require additional training for the models for each new property or even a new combination of existing properties. Moreover, some properties may potentially conflict, making it impossible to find a molecule that satisfies all of them simultaneously. To address these challenges, we present a training-free conditional 3D molecular generation algorithm based on off-the-shelf unconditional diffusion models and property prediction models. The key techniques include modeling the loss of property prediction models as energy functions, considering the property relation between multiple conditions as a probabilistic graph, and developing a stable posterior estimation for computing the conditional score function. We conducted experiments on both single-objective and multi-objective 3D molecule generation, focusing on quantum properties, and compared our approach with the trained or fine-tuned diffusion models. Our proposed model achieves superior performance in generating molecules that meet the conditions, without any additional training cost.
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Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however, fail to rigorously assess generalizability. Therefore, we develop DockGen, a new benchmark based on the ligand-binding domains of proteins, and we show that existing machine learning-based docking models have very weak generalization abilities. We carefully analyze the scaling laws of ML-based docking and show that, by scaling data and model size, as well as integrating synthetic data strategies, we are able to significantly increase the generalization capacity and set new state-of-the-art performance across benchmarks. Further, we propose Confidence Bootstrapping, a new training paradigm that solely relies on the interaction between diffusion and confidence models and exploits the multi-resolution generation process of diffusion models. We demonstrate that Confidence Bootstrapping significantly improves the ability of ML-based docking methods to dock to unseen protein classes, edging closer to accurate and generalizable blind docking methods.
Theory · Deep Learning
This work introduces the first toolkit around path-norms that fully encompasses general DAG ReLU networks with biases, skip connections and any operation based on the extraction of order statistics: max pooling, GroupSort etc.This toolkit notably allows us to establish generalization bounds for modern neural networks that are not only the most widely applicable path-norm based ones, but also recover or beat the sharpest known bounds of this type. These extended path-norms further enjoy the usual benefits of path-norms: ease of computation, invariance under the symmetries of the network, and improved sharpness on layered fully-connected networks compared to the product of operator norms, another complexity measure most commonly used.The versatility of the toolkit and its ease of implementation allow us to challenge the concrete promises of path-norm-based generalization bounds, by numerically evaluating the sharpest known bounds for ResNets on ImageNet.
Deep Learning · Sequential Models, Time series
Air quality prediction and modelling plays a pivotal role in public health and environment management, for individuals and authorities to make informed decisions. Although traditional data-driven models have shown promise in this domain, their long-term prediction accuracy can be limited, especially in scenarios with sparse or incomplete data and they often rely on black-box deep learning structures that lack solid physical foundation leading to reduced transparency and interpretability in predictions. To address these limitations, this paper presents a novel approach named Physics guided Neural Network for Air Quality Prediction (AirPhyNet). Specifically, we leverage two well-established physics principles of air particle movement (diffusion and advection) by representing them as differential equation networks. Then, we utilize a graph structure to integrate physics knowledge into a neural network architecture and exploit latent representations to capture spatio-temporal relationships within the air quality data. Experiments on two real-world benchmark datasets demonstrate that AirPhyNet outperforms state-of-the-art models for different testing scenarios including different lead time (24h, 48h, 72h), sparse data and sudden change prediction, achieving reduction in prediction errors up to 10\%. Moreover, a case study further validates that our model captures underlying physical processes of particle movement and generates accurate predictions with real physical meaning. The code is available at: https://github.com/kethmih/AirPhyNet
Applications · Computer Vision
Modeling and analyzing object and shape has been well studied in the past. However, manipulation of these complex tools and articulated objects remains difficult for autonomous agents. Our human hands, however, are dexterous and adaptive. We can easily adapt a manipulation skill on one object to all objects in the class and to other similar classes. Our intuition comes from that there is a close connection between manipulations and topology and articulation of objects. The possible articulation of objects indicates the types of manipulation necessary to operate the object. In this work, we aim to take a manipulation perspective to understand everyday objects and tools. We collect a multi-modal visual-tactile dataset that contains paired full-hand force pressure maps and manipulation videos. We also propose a novel method to learn a cross-modal latent manifold that allow for cross-modal prediction and discovery of latent structure in different data modalities. We conduct extensive experiments to demonstrate the effectiveness of our method.
Deep Learning · Generative Models and Autoencoders
Text-to-image generative models have garnered immense attention for their ability to produce high-fidelity images from text prompts. Among these, Stable Diffusion distinguishes itself as a leading open-source model in this fast-growing field. However, the intricacies of fine-tuning these models pose multiple challenges from new methodology integration to systematic evaluation. Addressing these issues, this paper introduces LyCORIS (Lora beYond Conventional methods, Other Rank adaptation Implementations for Stable diffusion), an open-source library that offers a wide selection of fine-tuning methodologies for Stable Diffusion. Furthermore, we present a thorough framework for the systematic assessment of varied fine-tuning techniques. This framework employs a diverse suite of metrics and delves into multiple facets of fine-tuning, including hyperparameter adjustments and the evaluation with different prompt types across various concept categories. Through this comprehensive approach, our work provides essential insights into the nuanced effects of fine-tuning parameters, bridging the gap between state-of-the-art research and practical application.
Deep Learning · Generative Models and Autoencoders
Text-to-video editing aims to edit the visual appearance of a source video conditional on textual prompts.A major challenge in this task is to ensure that all frames in the edited video are visually consistent. Most recent works apply advanced text-to-image diffusion models to this task by inflating 2D spatial attention in the U-Net into spatio-temporal attention.Although temporal context can be added through spatio-temporal attention, it may introduce some irrelevant information for each patch and therefore cause inconsistency in the edited video. In this paper, for the first time, we introduce optical flow into the attention module in diffusion model's U-Net to address the inconsistency issue for text-to-video editing.Our method, FLATTEN, enforces the patches on the same flow path across different frames to attend to each other in the attention module, thus improving the visual consistency in the edited videos. Additionally, our method is training-free and can be seamlessly integrated into any diffusion based text-to-video editing methods and improve their visual consistency.Experiment results on existing text-to-video editing benchmarks show that our proposed method achieves the new state-of-the-art performance. In particular, our method excels in maintaining the visual consistency in the edited videos.
Social Aspects · Privacy-preserving Statistics and Machine Learning
Label differentially private (label DP) algorithms seek to preserve the privacy of the labels in a training dataset in settings where the features are known to the adversary. In this work, we study a new family of label DP training algorithms. Unlike most prior label DP algorithms that have been based on label randomization, our algorithm naturally leverages the power of the central model of DP. It interleaves gradient projection operations with private stochastic gradient descent steps in order to improve the utility of the trained model while guaranteeing the privacy of the labels. We show that such projection-based algorithms can be made practical and that they improve on the state-of-the art for label DP training in the high-privacy regime. We complement our empirical evaluation with theoretical results shedding light on the efficacy of our method through the lens of bias-variance trade-offs.
Deep Learning · Large Language Models
Large Language Models (LLMs) have recently demonstrated a remarkable success across various tasks. However, efficiently serving LLMs has been a challenge due to its large memory bottleneck, specifically in small batch inference settings (e.g. mobile devices). Weight-only quantization can be a promising approach, but sub-4 bit quantization remains a challenge due to large-magnitude activation outliers. To mitigate the undesirable outlier effect, we first propose per-IC quantization, a simple yet effective method that creates quantization groups within each input channel (IC) rather than the conventional per-output channel (OC). Our method is motivated by the observation that activation outliers affect the input dimension of the weight matrix, so similarly grouping the weights in the IC direction can $\textit{isolate outliers to be within a group}$. We also find that activation outliers do not dictate quantization difficulty, and inherent weight sensitivities also exist. With per-IC quantization as a new outlier-friendly scheme, we then propose Adaptive Dimensions ($\textbf{AdaDim}$), a versatile quantization framework that can adapt to various weight sensitivity patterns. We demonstrate the effectiveness of AdaDim by augmenting prior methods such as Round-To-Nearest and GPTQ, showing significant improvements across various language modeling benchmarks for both base (up to $+4.7\%$ on MMLU) and instruction-tuned (up to $+10\%$ on HumanEval) LLMs.
With the rapid growth of large language models (LLMs), there is increasing demand for memory and computation in LLMs. Recent efforts on post-training pruning of LLMs aim to reduce the model size and computation requirements, yet the performance is still sub-optimal. In this paper, we present a plug-and-play solution for post-training pruning of LLMs.The proposed solution has two innovative components: 1) **Relative Importance and Activations (RIA)**, a new pruning metric that jointly considers the weight and activations efficiently on LLMs, and 2) **Channel Permutation**, a new approach to maximally preserves important weights under N:M sparsity.The two proposed components can be readily combined to further enhance the N:M semi-structured pruning of LLMs.Our empirical experiments show that RIA alone can already surpass all existing post-training pruning methods on prevalent LLMs, e.g., LLaMA ranging from 7B to 65B. Furthermore, N:M semi-structured pruning with channel permutation can even outperform the original LLaMA2-70B on zero-shot tasks, together with practical speed-up on specific hardware.Our code is available at: https://github.com/biomedical-cybernetics/Relative-importance-and-activation-pruning
Recent works have shown that Large Language Models (LLMs) could empower traditional neuro-symbolic models via programming capabilities to translate languages into module descriptions, thus achieving strong visual reasoning results while maintaining the model’s transparency and efficiency. However, these models usually exhaustively generate the entire code snippet given each new instance of a task, which is extremely ineffective. On the contrary, human beings gradually acquire knowledge that can be reused and grow into more profound skills for fast generalization to new tasks since we are an infant. Inspired by this, we propose generative neuro-symbolic visual reasoning by growing and reusing modules. Specifically, our model consists of three unique stages, module initialization, module generation, and module execution. First, given a vision-language task, we adopt LLMs to examine whether we could reuse and grow over established modules to handle this new task. If not, we initialize a new module needed by the task and specify the inputs and outputs of this new module. After that, the new module is created by querying LLMs to generate corresponding code snippets that match the requirements. In order to get a better sense of the new module’s ability, we treat few-shot training examples as test cases to see if our new module could pass these cases. If yes, the new module is added to the module library for future reuse. Finally, we evaluate the performance of our model on the testing set by executing the parsed programs with the newly made visual modules to get the results. We find the proposed GENOME model possesses several advantages. First, it performs competitively on standard tasks like visual question answering and referring expression comprehension; Second, the visual modules learned from one task can be seamlessly transferred to new tasks; Last but not least, it is able to adapt to new visual reasoning tasks by observing a few training examples and reusing modules.
Deep Learning · Sequential Models, Time series
*Not all positive pairs are beneficial to time series contrastive learning*. In this paper, we study two types of bad positive pairs that can impair the quality of time series representation learned through contrastive learning: the noisy positive pair and the faulty positive pair. We observe that, with the presence of noisy positive pairs, the model tends to simply learn the pattern of noise (Noisy Alignment). Meanwhile, when faulty positive pairs arise, the model wastes considerable amount of effort aligning non-representative patterns (Faulty Alignment). To address this problem, we propose a Dynamic Bad Pair Mining (DBPM) algorithm, which reliably identifies and suppresses bad positive pairs in time series contrastive learning. Specifically, DBPM utilizes a memory module to dynamically track the training behavior of each positive pair along training process. This allows us to identify potential bad positive pairs at each epoch based on their historical training behaviors. The identified bad pairs are subsequently down-weighted through a transformation module, thereby mitigating their negative impact on the representation learning process. DBPM is a simple algorithm designed as a lightweight **plug-in** without learnable parameters to enhance the performance of existing state-of-the-art methods. Through extensive experiments conducted on four large-scale, real-world time series datasets, we demonstrate DBPM's efficacy in mitigating the adverse effects of bad positive pairs.
Deep Learning · Other Representation Learning
Recognition problems in long-tailed data, in which the sample size per class is heavily skewed, have gained importance because the distribution of the sample size per class in a dataset is generally exponential unless the sample size is intentionally adjusted. Various methods have been devised to address these problems.Recently, weight balancing, which combines well-known classical regularization techniques with two-stage training, has been proposed. Despite its simplicity, it is known for its high performance compared with existing methods devised in various ways.However, there is a lack of understanding as to why this method is effective for long-tailed data. In this study, we analyze weight balancing by focusing on neural collapse and the cone effect at each training stage and found that it can be decomposed into an increase in Fisher's discriminant ratio of the feature extractor caused by weight decay and cross entropy loss and implicit logit adjustment caused by weight decay and class-balanced loss. Our analysis enables the training method to be further simplified by reducing the number of training stages to one while increasing accuracy. Code is available at https://github.com/HN410/Exploring-Weight-Balancing-on-Long-Tailed-Recognition-Problem.
Deep Learning · Other Representation Learning
Similarity-based representation learning has shown impressive capabilities in both supervised (e.g., metric learning) and unsupervised (e.g., contrastive learning) scenarios. Existing approaches effectively constrained the representation difference (i.e., the disagreement between the embeddings of two instances) to fit the corresponding (pseudo) similarity supervision. However, most of them can hardly restrict the variation of representation difference, sometimes leading to overfitting results where the clusters are disordered by drastically changed differences. In this paper, we thus propose a novel difference alignment regularization (DAR) to encourage all representation differences between inter-class instances to be as close as possible, so that the learning algorithm can produce consistent differences to distinguish data points from each other. To this end, we construct a new cross-total-variation (CTV) norm to measure the divergence among representation differences, and we convert it into an equivalent stochastic form for easy optimization. Then, we integrate the proposed regularizer into the empirical loss for difference-aligned similarity learning (DASL), shrinking the hypothesis space and alleviating overfitting. Theoretically, we prove that our regularizer tightens the error bound of the traditional similarity learning. Experiments on multi-domain data demonstrate the superiority of DASL over existing approaches in both supervised metric learning and unsupervised contrastive learning tasks.
Applications · Computer Vision
More distinguishable and consistent pixel features for each category will benefit the semantic segmentation under various settings.Existing efforts to mine better pixel-level features attempt to explicitly model the categorical distribution, which fails to achieve optimal due to the significant pixel feature variance.Moreover, prior research endeavors have scarcely delved into the thorough analysis and meticulous handling of pixel-level variance, leaving semantic segmentation at a coarse granularity.In this work, we analyze the causes of pixel-level variance and introduce the concept of $\textbf{pixel learning}$ to concentrate on the tailored learning process of pixels to handle the pixel-level variance, enhancing the per-pixel recognition capability of segmentation models.Under the context of the pixel learning scheme, each image is viewed as a distribution of pixels, and pixel learning aims to pursue consistent pixel representation inside an image, continuously align pixels from different images (distributions), and eventually achieve consistent pixel representation for each category, even cross-domains.We proposed a pure pixel-level learning framework, namely PiXL, which consists of a pixel partition module to divide pixels into sub-domains, a prototype generation, a selection module to prepare targets for subsequent alignment, and a pixel alignment module to guarantee pixel feature consistency intra-/inter-images, and inter-domains.Extensive evaluations of multiple learning paradigms, including unsupervised domain adaptation and semi-/fully-supervised segmentation, show that PiXL outperforms state-of-the-art performances, especially when annotated images are scarce.Visualization of the embedding space further demonstrates that pixel learning attains a superior representation of pixel features.The code is available at https://github.com/ChenGan-JS/PiXL.
Applications · Neuroscience, Cognitive Science
Motivated by a recent neuroscientific hypothesis, some theoretical studies have accounted for neural cognitive maps in the rodent hippocampal formation as a representation of the general relational structure across task environments. However, despite their remarkable results, it is unclear whether their account can be extended to more general settings beyond spatial random-walk tasks in 2D environments. To address this question, we construct a novel cognitive model that performs memory-based relational decision-making tasks, inspired by previous human studies, for learning abstract structures in non-spatial relations. Building on previous approaches of modular architecture, we develop a learning algorithm that performs reward-guided search for representation of abstract relations, while dynamically maintaining their binding to concrete entities using our specific memory mechanism enabling content replacement. Our experiments show (i) the capability of our model to capture relational structures that can generalize over new domains with unseen entities, (ii) the difficulty of our task that leads previous models, including Neural Turing Machine and vanilla Transformer, to complete failure, and (iii) the similarity of performance and internal representations of our model to recent human behavioral and fMRI experimental data in the human hippocampal formation.
Deep Learning · Other Representation Learning
We present ReMasker, a new method of imputing missing values in tabular data by extending the masked autoencoding framework. Compared with prior work, ReMasker is extremely simple -- besides the missing values (i.e., naturally masked), we randomly "re-mask" another set of values, optimize the autoencoder by reconstructing this re-masked set, and apply the trained model to predict the missing values; and yet highly effective -- with extensive evaluation on benchmark datasets, we show that ReMasker performs on par with or outperforms state-of-the-art methods in terms of both imputation fidelity and utility under various missingness settings, while its performance advantage often increases with the ratio of missing data. We further explore theoretical justification for its effectiveness, showing that ReMasker tends to learn missingness-invariant representations of tabular data. Our findings indicate that masked modeling represents a promising direction for further research on tabular data imputation. The code is publicly available.
Deep Learning · Large Language Models
Quantization is an indispensable technique for serving Large Language Models (LLMs) and has recently found its way into LoRA fine-tuning (Dettmers et al., 2023). In this work we focus on the scenario where quantization and LoRA fine- tuning are applied together on a pre-trained model. In such cases it is common to observe a consistent gap in the performance on downstream tasks between full fine-tuning and quantization plus LoRA fine-tuning approach. In response, we propose LoftQ (LoRA-Fine-Tuning-aware Quantization), a novel quantization framework that simultaneously quantizes an LLM and finds a proper low-rank initialization for LoRA fine-tuning. Such an initialization alleviates the discrep- ancy between the quantized and full-precision model and significantly improves the generalization in downstream tasks. We evaluate our method on natural lan- guage understanding, question answering, summarization, and natural language generation tasks. Experiments show that our method is highly effective and out- performs existing quantization methods, especially in the challenging 2-bit and 2/4-bit mixed precision regimes. We will release our code.
Deep Learning · Generative Models and Autoencoders
Learning disentangled representations for time series is a promising path to facilitate reliable generalization to in- and out-of distribution (OOD), offering benefits like feature derivation and improved interpretability and fairness, thereby enhancing downstream tasks. We focus on disentangled representation learning for home appliance electricity usage, enabling users to understand and optimize their consumption for a reduced carbon footprint. Our approach frames the problem as disentangling each attribute's role in total consumption. Unlike existing methods assuming attribute independence which leads to non-identiability, we acknowledge real-world time series attribute correlations, learned up to a smooth bijection using contrastive learning and a single autoencoder. To address this, we propose a Disentanglement under Independence-Of-Support via Contrastive Learning (DIOSC), facilitating representation generalization across diverse correlated scenarios. Our method utilizes innovative \textit{l}-variational inference layers with self-attention, effectively addressing temporal dependencies across bottom-up and top-down networks. We find that DIOSC can enhance the task of representation of time series electricity consumption. We introduce TDS (Time Disentangling Score) to gauge disentanglement quality. TDS reliably reflects disentanglement performance, making it a valuable metric for evaluating time series representations disentanglement. Code available at https://institut-polytechnique-de-paris.github.io/time-disentanglement-lib.
We investigate learning the equilibria in non-stationary multi-agent systems and address the challenges that differentiate multi-agent learning from single-agent learning. Specifically, we focus on games with bandit feedback, where testing an equilibrium can result in substantial regret even when the gap to be tested is small, and the existence of multiple optimal solutions (equilibria) in stationary games poses extra challenges. To overcome these obstacles, we propose a versatile black-box approach applicable to a broad spectrum of problems, such as general-sum games, potential games, and Markov games, when equipped with appropriate learning and testing oracles for stationary environments. Our algorithms can achieve $\widetilde{O}\left(\Delta^{1/4}T^{3/4}\right)$ regret when the degree of nonstationarity, as measured by total variation $\Delta$, is known, and $\widetilde{O}\left(\Delta^{1/5}T^{4/5}\right)$ regret when $\Delta$ is unknown, where $T$ is the number of rounds. Meanwhile, our algorithm inherits the favorable dependence on number of agents from the oracles. As a side contribution that may be independent of interest, we show how to test for various types of equilibria by a black-box reduction to single-agent learning, which includes Nash equilibria, correlated equilibria, and coarse correlated equilibria.