Automating reward function configuration for drug design

Designing reward functions that guide generative molecular design (GMD) algorithms to desirable areas of chemical space is of critical importance in AI-driven drug discovery. Traditionally, this has been a manual and error-prone task; the selection of appropriate computational methods to approximate biological assays is challenging and the aggregation of computed values into a single score even more so, leading to potential reliance on trial-and-error approaches. We propose a novel approach for automated reward configuration that relies solely on experimental data, mitigating the challenges of manual reward adjustment on drug discovery projects. Our method achieves this by constructing a ranking over experimental data based on Pareto dominance over the multi-objective space, then training a neural network to approximate the reward function such that rankings determined by the predicted reward correlate with those determined by the Pareto dominance relation. We validate our method using two case studies. In the first study we simulate Design-Make-Test-Analyse (DMTA) cycles by alternating reward function updates and generative runs guided by that function. We show that the learned function adapts over time to yield compounds that score highly with respect to evaluation functions taken from the literature. In the second study we apply our algorithm to historical data from four real drug discovery projects. We show that our algorithm yields reward functions that outperform the predictive accuracy of human-defined functions, achieving an improvement of up to 0.4 in Spearman's correlation against a ground truth evaluation function that encodes the target drug profile for that project. Our method provides an efficient data-driven way to configure reward functions for GMD, and serves as a strong baseline for future research into transformative approaches for the automation of drug discovery.

Plasticine3D: Non-rigid 3D editting with text guidance

With the help of Score Distillation Sampling(SDS) and the rapid development of various trainable 3D representations, Text-to-Image(T2I) diffusion models have been applied to 3D generation tasks and achieved considerable results. There are also some attempts toward the task of editing 3D objects leveraging this Text-to-3D pipeline. However, most methods currently focus on adding additional geometries, overwriting textures or both. But few of them can perform non-rigid transformation of 3D objects. For those who can perform non-rigid editing, on the other hand, suffer from low-resolution, lack of fidelity and poor flexibility. In order to address these issues, we present: Plasticine3D, a general, high-fidelity, photo-realistic and controllable non-rigid editing pipeline. Firstly, our work divides the editing process into a geometry editing stage and a texture editing stage to achieve more detailed and photo-realistic results ; Secondly, in order to perform non-rigid transformation with controllable results while maintain the fidelity towards original 3D models in the same time, we propose a multi-view-embedding(MVE) optimization strategy to ensure that the diffusion model learns the overall features of the original object and an embedding-fusion(EF) to control the degree of editing by adjusting the value of the fusing rate. We also design a geometry processing step before optimizing on the base geometry to cope with different needs of various editing tasks. Further more, to fully leverage the geometric prior from the original 3D object, we provide an optional replacement of score distillation sampling named score projection sampling(SPS) which enables us to directly perform optimization from the origin 3D mesh in most common median non-rigid editing scenarios. We demonstrate the effectiveness of our method on both the non-rigid 3D editing task and general 3D editing task.

ClusT3: Information Invariant Test-Time Training

Deep Learning models have shown remarkable performance in a broad range of vision tasks. However, they are often vulnerable against domain shifts at test-time. Test-time training (TTT) methods have been developed in an attempt to mitigate these vulnerabilities, where a secondary task is solved at training time simultaneously with the main task, to be later used as an self-supervised proxy task at test-time. In this work, we propose a novel unsupervised TTT technique based on the maximization of Mutual Information between multi-scale feature maps and a discrete latent representation, which can be integrated to the standard training as an auxiliary clustering task. Experimental results demonstrate competitive classification performance on different popular test-time adaptation benchmarks.

Online Decision Making with History-Average Dependent Costs (Extended)

In many online sequential decision-making scenarios, a learner's choices affect not just their current costs but also the future ones. In this work, we look at one particular case of such a situation where the costs depend on the time average of past decisions over a history horizon. We first recast this problem with history dependent costs as a problem of decision making under stage-wise constraints. To tackle this, we then propose the novel Follow-The-Adaptively-Regularized-Leader (FTARL) algorithm. Our innovative algorithm incorporates adaptive regularizers that depend explicitly on past decisions, allowing us to enforce stage-wise constraints while simultaneously enabling us to establish tight regret bounds. We also discuss the implications of the length of history horizon on design of no-regret algorithms for our problem and present impossibility results when it is the full learning horizon.

Neural Autoencoder-Based Structure-Preserving Model Order Reduction and Control Design for High-Dimensional Physical Systems

This work concerns control-oriented and structure-preserving learning of low-dimensional approximations of high-dimensional physical systems, with a focus on mechanical systems. We investigate the integration of neural autoencoders in model order reduction, while at the same time preserving Hamiltonian or Lagrangian structures. We focus on extensively evaluating the considered methodology by performing simulation and control experiments on large mass-spring-damper networks, with hundreds of states. The empirical findings reveal that compressed latent dynamics with less than 5 degrees of freedom can accurately reconstruct the original systems' transient and steady-state behavior with a relative total error of around 4\%, while simultaneously accurately reconstructing the total energy. Leveraging this system compression technique, we introduce a model-based controller that exploits the mathematical structure of the compressed model to regulate the configuration of heavily underactuated mechanical systems.

Comparative Study of ZF, LMS and RLS Adaptive Equalization for alpha-mu Fading Channels

Wireless communication systems generally endure severe fading and interference caused by the time-dispersive channel. Major transmission distortion is produced by channel multipath propagation and overlap of subsequent symbols. To counteract channel response, equalization techniques are employed to operate on channel output and recover transmitted signal at the receiver. This work investigates equalization of channels undergoing alpha-mu fading distribution, which models multipath propagation in millimeter Wave (mmWave) and sub-Terahertz (sub-THz) frequencies bands. Three equalization algorithms, which are non-adaptive Zero-Forcing (ZF), adaptive Least-Mean-Square (LMS) and adaptive Recursive-Least-Square (RLS) are implemented and addressed in terms of Bit Error Rate (BER), Convergence speed and implementation complexity. Monte Carlo simulations are then carried out to compare algorithms and assess performance by varying multiple parameters such as training lengths, channel order, equalization taps and diverse fading conditions.

Towards Model-Based Data Acquisition for Subjective Multi-Task NLP Problems

Data annotated by humans is a source of knowledge by describing the peculiarities of the problem and therefore fueling the decision process of the trained model. Unfortunately, the annotation process for subjective natural language processing (NLP) problems like offensiveness or emotion detection is often very expensive and time-consuming. One of the inevitable risks is to spend some of the funds and annotator effort on annotations that do not provide any additional knowledge about the specific task. To minimize these costs, we propose a new model-based approach that allows the selection of tasks annotated individually for each text in a multi-task scenario. The experiments carried out on three datasets, dozens of NLP tasks, and thousands of annotations show that our method allows up to 40% reduction in the number of annotations with negligible loss of knowledge. The results also emphasize the need to collect a diverse amount of data required to efficiently train a model, depending on the subjectivity of the annotation task. We also focused on measuring the relation between subjective tasks by evaluating the model in single-task and multi-task scenarios. Moreover, for some datasets, training only on the labels predicted by our model improved the efficiency of task selection as a self-supervised learning regularization technique.

Projective Parallel Single-Pixel Imaging: 3D Structured Light Scanning Under Global Illumination

We present projective parallel single-pixel imaging (pPSI), a 3D photography method that provides a robust and efficient way to analyze the light transport behavior and enables separation of light effect due to global illumination, thereby achieving 3D structured light scanning under global illumination. The light transport behavior is described by the light transport coefficients (LTC), which contain complete information for a projector camera pair, and is a 4D data set. However, the capture of LTC is generally time consuming. The 4D LTC in pPSI are reduced to projection functions, thereby enabling a highly efficient data capture process. We introduce the local maximum constraint, which provides constraint for the location of candidate correspondence matching points when projections are captured. Local slice extension (LSE) method is introduced to accelerate the capture of projection functions. Optimization is conducted for pPSI under several situations. The number of projection functions required for pPSI is optimized and the influence of capture ratio in LSE on the accuracy of the correspondence matching points is investigated. Discussions and experiments include two typical kinds of global illuminations: inter-reflections and subsurface scattering. The proposed method is validated with several challenging scenarios, and outperforms the state-of-the-art methods.

AutoNumerics-Zero: Automated Discovery of State-of-the-Art Mathematical Functions

Computers calculate transcendental functions by approximating them through the composition of a few limited-precision instructions. For example, an exponential can be calculated with a Taylor series. These approximation methods were developed over the centuries by mathematicians, who emphasized the attainability of arbitrary precision. Computers, however, operate on few limited precision types, such as the popular float32. In this study, we show that when aiming for limited precision, existing approximation methods can be outperformed by programs automatically discovered from scratch by a simple evolutionary algorithm. In particular, over real numbers, our method can approximate the exponential function reaching orders of magnitude more precision for a given number of operations when compared to previous approaches. More practically, over float32 numbers and constrained to less than 1 ULP of error, the same method attains a speedup over baselines by generating code that triggers better XLA/LLVM compilation paths. In other words, in both cases, evolution searched a vast space of possible programs, without knowledge of mathematics, to discover previously unknown optimized approximations to high precision, for the first time. We also give evidence that these results extend beyond the exponential. The ubiquity of transcendental functions suggests that our method has the potential to reduce the cost of scientific computing applications.

SplaTAM: Splat, Track & Map 3D Gaussians for Dense RGB-D SLAM

Dense simultaneous localization and mapping (SLAM) is pivotal for embodied scene understanding. Recent work has shown that 3D Gaussians enable high-quality reconstruction and real-time rendering of scenes using multiple posed cameras. In this light, we show for the first time that representing a scene by 3D Gaussians can enable dense SLAM using a single unposed monocular RGB-D camera. Our method, SplaTAM, addresses the limitations of prior radiance field-based representations, including fast rendering and optimization, the ability to determine if areas have been previously mapped, and structured map expansion by adding more Gaussians. We employ an online tracking and mapping pipeline while tailoring it to specifically use an underlying Gaussian representation and silhouette-guided optimization via differentiable rendering. Extensive experiments show that SplaTAM achieves up to 2X state-of-the-art performance in camera pose estimation, map construction, and novel-view synthesis, demonstrating its superiority over existing approaches, while allowing real-time rendering of a high-resolution dense 3D map.