Optimizing Deep Neural Networks (DNNs) to obtain high-quality models for efficient real-world deployment has posed multi-faceted challenges to machine learning engineers. Existing methods either search for neural architectures in heuristic design spaces or apply low-level adjustments to computation primitives to improve inference efficiency on hardware. We present Automated Graph Optimization (AutoGO), a framework to evolve neural networks in a low-level Computation Graph (CG) of primitive operations to improve both its performance and hardware friendliness. Through a tokenization scheme, AutoGO performs variable-sized segment mutations, making both primitive changes and larger-grained changes to CGs. We introduce our segmentation and mutation algorithms, efficient frequent segment mining technique, as well as a pretrained context-aware predictor to estimate the impact of segment replacements. Extensive experimental results show that AutoGO can automatically evolve several typical large convolutional networks to achieve significant task performance improvement and FLOPs reduction on a range of CV tasks, ranging from Classification, Semantic Segmentation, Human Pose Estimation, to Super Resolution, yet without introducing any newer primitive operations. We also demonstrate the lightweight deployment results of AutoGOoptimized super-resolution and denoising U-Nets on a cycle simulator for a Neural Processing Unit (NPU), achieving PSNR improvement and latency/power reduction simultaneously.

Antibody lead optimization is inherently a multi-objective challenge in drug discovery. Achieving a balance between different drug-like properties is crucial for the development of viable candidates, and this search becomes exponentially challenging as desired properties grow. The ever-growing zoo of sophisticated in silico tools for predicting antibody properties calls for an efficient joint optimization procedure to overcome resource-intensive sequential filtering pipelines. We present BOAT, a versatile Bayesian optimization framework for multi-property antibody engineering. Our `plug-and-play' framework couples uncertainty-aware surrogate modeling with a genetic algorithm to jointly optimize various predicted antibody traits while enabling efficient exploration of sequence space. Through systematic benchmarking against genetic algorithms and newer generative learning approaches, we demonstrate competitive performance with state-of-the-art methods for multi-objective protein optimization. We identify clear regimes where surrogate-driven optimization outperforms expensive generative approaches and establish practical limits imposed by sequence dimensionality and oracle costs.

Antibodies have become an important class of therapeutic agents to treat human diseases.To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria.However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences.To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens.By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences.All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method.Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein.This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations.We report experimental benchmark results on AVIDa-hIL6 by using machine learning models.The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants.The dataset is available at https://avida-hil6.cognanous.com.

Exploiting the short-sighted gradients should be balanced with adequate explorations.

Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases.

Automatically generating novel and interesting games is a complex task.

Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets.

In this work, we propose an innovative test-time poisoned sample detection framework that hinges on the in-terpretability of model predictions, grounded in the semantic meaning of inputs. We contend that triggers (e.g., infrequent words) are not supposed to fundamentally alter the underlying semantic meanings of poisoned samples as they want to