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Publications
Towards AI-designed genomes using a variational autoencoder
Synthetic biology holds great promise for bioengineering applications such as environmental bioremediation, probiotic formulation, and produ… (see more)ction of renewable biofuels. Humans’ capacity to design biological systems from scratch is limited by their sheer size and complexity. We introduce a framework for training a machine learning model to learn the basic genetic principles underlying the gene composition of bacterial genomes. Our variational autoencoder model, DeepGenomeVector, was trained to take as input corrupted bacterial genetic blueprints (i.e. complete gene sets, henceforth ‘genome vectors’) in which most genes had been “removed”, and re-create the original. The resulting model effectively captures the complex dependencies in genomic networks, as evaluated by both qualitative and quantitative metrics. An in-depth functional analysis of a generated gene vector shows that its encoded pathways are interconnected and nearly complete. On the test set, where the model’s ability to re-generate the original, uncorrupted genome vector was evaluated, an AUC score of 0.98 and an F1 score of 0.82 provide support for the model’s ability to generate diverse, high-quality genome vectors. This work showcases the power of machine learning approaches for synthetic biology and highlights the possibility that just as humans can design an AI that animates a robot, AIs may one day be able to design a genomic blueprint that animates a carbon-based cell. SIGNIFICANCE STATEMENT Genomes serve as the blueprints for life, encoding complex networks of genes whose products must seamlessly interact to result in living organisms. In this work, we develop a framework for training a machine learning algorithm to learn the basic genetic principles that underlie genome composition. This innovation may eventually lead to improvements in the genome design process, increasing the speed and reliability of designs while decreasing cost. It further suggests that AI agents may one day have the potential to design blueprints for carbon-based life.
2024-12-11
Proceedings of the Royal Society B: Biological Sciences (published)
Imitation learning is a data-driven approach to learning policies from expert behavior, but it is prone to unreliable outcomes in out-of-sam… (see more)ple (OOS) regions. While previous research relying on stable dynamical systems guarantees convergence to a desired state, it often overlooks transient behavior. We propose a framework for learning policies using modeled by contractive dynamical systems, ensuring that all policy rollouts converge regardless of perturbations, and in turn, enable efficient OOS recovery. By leveraging recurrent equilibrium networks and coupling layers, the policy structure guarantees contractivity for any parameter choice, which facilitates unconstrained optimization. Furthermore, we provide theoretical upper bounds for worst-case and expected loss terms, rigorously establishing the reliability of our method in deployment. Empirically, we demonstrate substantial OOS performance improvements in robotics manipulation and navigation tasks in simulation.
While one commonly trains large diffusion models by collecting datasets on target downstream tasks, it is often desired to align and finetun… (see more)e pretrained diffusion models on some reward functions that are either designed by experts or learned from small-scale datasets. Existing methods for finetuning diffusion models typically suffer from lack of diversity in generated samples, lack of prior preservation, and/or slow convergence in finetuning. Inspired by recent successes in generative flow networks (GFlowNets), a class of probabilistic models that sample with the unnormalized density of a reward function, we propose a novel GFlowNet method dubbed Nabla-GFlowNet (abbreviated as
While one commonly trains large diffusion models by collecting datasets on target downstream tasks, it is often desired to align and finetun… (see more)e pretrained diffusion models on some reward functions that are either designed by experts or learned from small-scale datasets. Existing methods for finetuning diffusion models typically suffer from lack of diversity in generated samples, lack of prior preservation, and/or slow convergence in finetuning. Inspired by recent successes in generative flow networks (GFlowNets), a class of probabilistic models that sample with the unnormalized density of a reward function, we propose a novel GFlowNet method dubbed Nabla-GFlowNet (abbreviated as
Loss of plasticity, trainability loss, and primacy bias have been identified as issues arising when training deep neural networks on sequenc… (see more)es of tasks -- all referring to the increased difficulty in training on new tasks. We propose to use Parseval regularization, which maintains orthogonality of weight matrices, to preserve useful optimization properties and improve training in a continual reinforcement learning setting. We show that it provides significant benefits to RL agents on a suite of gridworld, CARL and MetaWorld tasks. We conduct comprehensive ablations to identify the source of its benefits and investigate the effect of certain metrics associated to network trainability including weight matrix rank, weight norms and policy entropy.
Loss of plasticity, trainability loss, and primacy bias have been identified as issues arising when training deep neural networks on sequenc… (see more)es of tasks -- all referring to the increased difficulty in training on new tasks. We propose to use Parseval regularization, which maintains orthogonality of weight matrices, to preserve useful optimization properties and improve training in a continual reinforcement learning setting. We show that it provides significant benefits to RL agents on a suite of gridworld, CARL and MetaWorld tasks. We conduct comprehensive ablations to identify the source of its benefits and investigate the effect of certain metrics associated to network trainability including weight matrix rank, weight norms and policy entropy.
Training and fine-tuning Large Language Models (LLMs) require significant memory due to the substantial growth in the size of weight paramet… (see more)ers and optimizer states. While methods like low-rank adaptation (LoRA), which introduce low-rank trainable modules in parallel to frozen pre-trained weights, effectively reduce memory usage, they often fail to preserve the optimization trajectory and are generally less effective for pre-training models. On the other hand, approaches, such as GaLore, that project gradients onto lower-dimensional spaces maintain the training trajectory and perform well in pre-training but suffer from high computational complexity, as they require repeated singular value decomposition on large matrices. In this work, we propose Randomized Gradient Projection (RGP), which outperforms GaLore, the current state-of-the-art in efficient fine-tuning, on the GLUE task suite, while being 74% faster on average and requiring similar memory.
2024-12-10
Proceedings of The 4th NeurIPS Efficient Natural Language and Speech Processing Workshop (published)
To endow models with greater understanding of physics and motion, it is useful to enable them to perceive how solid surfaces move and deform… (see more) in real scenes. This can be formalized as Tracking-Any-Point (TAP), which requires the algorithm to track any point on solid surfaces in a video, potentially densely in space and time. Large-scale groundtruth training data for TAP is only available in simulation, which currently has a limited variety of objects and motion. In this work, we demonstrate how large-scale, unlabeled, uncurated real-world data can improve a TAP model with minimal architectural changes, using a selfsupervised student-teacher setup. We demonstrate state-of-the-art performance on the TAP-Vid benchmark surpassing previous results by a wide margin: for example, TAP-Vid-DAVIS performance improves from 61.3% to 67.4%, and TAP-Vid-Kinetics from 57.2% to 62.5%. For visualizations, see our project webpage at https://bootstap.github.io/
Deep Learning (DL) is a class of machine learning algorithms that are used in a wide variety of applications. Like any software system, DL p… (see more)rograms can have bugs. To support bug localization in DL programs, several tools have been proposed in the past. As most of the bugs that occur due to improper model structure known as structural bugs lead to inadequate performance during training, it is challenging for developers to identify the root cause and address these bugs. To support bug detection and localization in DL programs, in this paper, we propose Theia, which detects and localizes structural bugs in DL programs. Unlike the previous works, Theia considers the training dataset characteristics to automatically detect bugs in DL programs developed using two deep learning libraries,
Keras
and
PyTorch
. Since training the DL models is a time-consuming process, Theia detects these bugs at the beginning of the training process and alerts the developer with informative messages containing the bug's location and actionable fixes which will help them to improve the structure of the model. We evaluated Theia on a benchmark of 40 real-world buggy DL programs obtained from
Stack Overflow
. Our results show that Theia successfully localizes 57/75 structural bugs in 40 buggy programs, whereas NeuraLint, a state-of-the-art approach capable of localizing structural bugs before training localizes 17/75 bugs.
Deep Learning (DL) is a class of machine learning algorithms that are used in a wide variety of applications. Like any software system, DL p… (see more)rograms can have bugs. To support bug localization in DL programs, several tools have been proposed in the past. As most of the bugs that occur due to improper model structure known as structural bugs lead to inadequate performance during training, it is challenging for developers to identify the root cause and address these bugs. To support bug detection and localization in DL programs, in this paper, we propose Theia, which detects and localizes structural bugs in DL programs. Unlike the previous works, Theia considers the training dataset characteristics to automatically detect bugs in DL programs developed using two deep learning libraries,
Keras
and
PyTorch
. Since training the DL models is a time-consuming process, Theia detects these bugs at the beginning of the training process and alerts the developer with informative messages containing the bug's location and actionable fixes which will help them to improve the structure of the model. We evaluated Theia on a benchmark of 40 real-world buggy DL programs obtained from
Stack Overflow
. Our results show that Theia successfully localizes 57/75 structural bugs in 40 buggy programs, whereas NeuraLint, a state-of-the-art approach capable of localizing structural bugs before training localizes 17/75 bugs.
Deep Learning (DL) is a class of machine learning algorithms that are used in a wide variety of applications. Like any software system, DL p… (see more)rograms can have bugs. To support bug localization in DL programs, several tools have been proposed in the past. As most of the bugs that occur due to improper model structure known as structural bugs lead to inadequate performance during training, it is challenging for developers to identify the root cause and address these bugs. To support bug detection and localization in DL programs, in this paper, we propose Theia, which detects and localizes structural bugs in DL programs. Unlike the previous works, Theia considers the training dataset characteristics to automatically detect bugs in DL programs developed using two deep learning libraries, Keras and PyTorch. Since training the DL models is a time-consuming process, Theia detects these bugs at the beginning of the training process and alerts the developer with informative messages containing the bug's location and actionable fixes which will help them to improve the structure of the model. We evaluated Theia on a benchmark of 40 real-world buggy DL programs obtained from Stack Overflow. Our results show that Theia successfully localizes 57/75 structural bugs in 40 buggy programs, whereas NeuraLint, a state-of-the-art approach capable of localizing structural bugs before training localizes 17/75 bugs.
