Predicting cellular responses to various perturbations is a critical focus in drug discovery and personalized therapeutics, with deep learning models playing a significant role in this endeavor. Single-cell datasets contain technical artifacts that may hinder the predictability of such models, which poses quality control issues highly regarded in this area. To address this, we propose Cradle-VAE, a causal generative framework tailored for single-cell gene perturbation modeling, enhanced with counterfactual reasoning-based artifact disentanglement. Throughout training, Cradle-VAE models the underlying latent distribution of technical artifacts and perturbation effects present in single-cell datasets. It employs counterfactual reasoning to effectively disentangle such artifacts by modulating the latent basal spaces and learns robust features for generating cellular response data with improved quality. Experimental results demonstrate that this approach improves not only treatment effect estimation performance but also generative quality as well.

Despite the great success of large language models (LLMs), efficiently controlling the length of the output sequence still remains a challenge. In this paper, we propose Hansel, an efficient framework for length control in LLMs without affecting its generation ability. Hansel utilizes periodically outputted hidden special tokens to keep track of the remaining target length of the output sequence. Together with techniques to avoid abrupt termination of the output, this seemingly simple method proved to be efficient and versatile, while not harming the coherency and fluency of the generated text. The framework can be applied to any pre-trained LLMs during the finetuning stage of the model, regardless of its original positional encoding method. We demonstrate this by finetuning four different LLMs with Hansel and show that the mean absolute error of the output sequence decreases significantly in every model and dataset compared to the prompt-based length control finetuning. Moreover, the framework showed a substantially improved ability to extrapolate to target lengths unseen during finetuning, such as long dialog responses or extremely short summaries. This indicates that the model learns the general means of length control, rather than learning to match output lengths to those seen during training.

Large language models (LLMs) are increasingly deployed with task-specific adapters catering to multiple downstream applications.In such a scenario, the additional compute associated with these apparently insignificant number of adapter parameters (typically less than 1% of the base model) turns out to be disproportionately significant during inference time (upto 2.5x times that of the base model).In this paper, we propose a new zero-latency fused low-rank adapter (zFLoRA) that introduces zero or negligible latency overhead on top of the base model.Experimental results on LLMs of size 1B, 3B and 7B show that zFLoRA compares favorably against the popular supervised fine-tuning benchmarks including lowrank adapters (LoRA) as well as full fine-tuning (FFT).Experiments are conducted on 18 different tasks across three different categories namely commonsense reasoning, math reasoning and summary-dialogue.Latency measurements made on NPU (Samsung Galaxy S25+) as well as GPU (NVIDIA H100) platforms show that the proposed zFLoRA adapters introduce zero to negligible latency overhead.

Message Passing Neural Networks (MPNNs) hold a key position in machine learning on graphs, but they struggle with unintended behaviors, such as over-smoothing and over-squashing, due to irregular data structures. The observation and formulation of these limitations have become foundational in constructing more informative graph representations. In this paper, we delve into the limitations of MPNNs, focusing on aspects that have previously been overlooked. Our observations reveal that even within a single layer, the information specific to an individual node can become significantly diluted. To delve into this phenomenon in depth, we present the concept of Over-dilution and formulate it with two dilution factors: intra-node dilution for attribute-level and inter-node dilution for node-level representations. We also introduce a transformer-based solution that alleviates over-dilution and complements existing node embedding methods like MPNNs. Our findings provide new insights and contribute to the development of informative representations. The implementation and supplementary materials are publicly available at https://github.com/LeeJunHyun/NATR.

Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD) models, which take into account complex three-dimensional interactions and molecular geometries, are particularly promising. Scaffold hopping is an efficient strategy that facilitates the identification of similar active compounds by strategically modifying the core structure of molecules, effectively narrowing the wide chemical space and enhancing the discovery of drug-like products. However, the practical application of 3D-SBDD generative models is hampered by their slow processing speeds. To address this bottleneck, we introduce TurboHopp, an accelerated pocket-conditioned 3D scaffold hopping model that merges the strategic effectiveness of traditional scaffold hopping with rapid generation capabilities of consistency models. This synergy not only enhances efficiency but also significantly boosts generation speeds, achieving up to 30 times faster inference speed as well as superior generation quality compared to existing diffusion-based models, establishing TurboHopp as a powerful tool in drug discovery. Supported by faster inference speed, we further optimize our model, using Reinforcement Learning for Consistency Models (RLCM), to output desirable molecules. We demonstrate the broad applicability of TurboHopp across multiple drug discovery scenarios, underscoring its potential in diverse molecular settings.The code is provided at https://github.com/orgw/TurboHopp

MOTIVATION: Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel pre-training framework that employs masked graph contrastive learning in understanding the underlying decomposable parts in molecules that implicate their core structure and peripheral R-groups. Furthermore, we formulate an additional framework that grants MolPLA the ability to help chemists find replaceable R-groups in lead optimization scenarios. RESULTS: Experimental results on molecular property prediction show that MolPLA exhibits predictability comparable to current state-of-the-art models. Qualitative analysis implicate that MolPLA is capable of distinguishing core and R-group sub-structures, identifying decomposable regions in molecules and contributing to lead optimization scenarios by rationally suggesting R-group replacements given various query core templates. AVAILABILITY AND IMPLEMENTATION: The code implementation for MolPLA and its pre-trained model checkpoint is available at https://github.com/dmis-lab/MolPLA.

Time-to-event analysis, also known as survival analysis, aims to predict the time of occurrence of an event, given a set of features. One of the major challenges in this area is dealing with censored data, which can make learning algorithms more complex. Traditional methods such as Cox’s proportional hazards model and the accelerated failure time (AFT) model have been popular in this field, but they often require assumptions such as proportional hazards and linearity. In particular, the AFT models often require pre-specified parametric distributional assumptions. To improve predictive performance and alleviate strict assumptions, there have been many deep learning approaches for hazard-based models in recent years. However, representation learning for AFT has not been widely explored in the neural network literature, despite its simplicity and interpretability in comparison to hazard-focused methods. In this work, we introduce the Deep AFT Rank-regression model for Time-to-event prediction (DART). This model uses an objective function based on Gehan’s rank statistic, which is efficient and reliable for representation learning. On top of eliminating the requirement to establish a baseline event time distribution, DART retains the advantages of directly predicting event time in standard AFT models. The proposed method is a semiparametric approach to AFT modeling that does not impose any distributional assumptions on the survival time distribution. This also eliminates the need for additional hyperparameters or complex model architectures, unlike existing neural network-based AFT models. Through quantitative analysis on various benchmark datasets, we have shown that DART has significant potential for modeling high-throughput censored time-to-event data.

Human-Object Interaction (HOI) detection is the task of identifying a set of (human, object, interaction) triplets from an image. Recent work proposed transformer encoder-decoder architectures that successfully eliminated the need for many hand-designed components in HOI detection through end-to-end training. However, they are limited to single-scale feature resolution, providing suboptimal performance in scenes containing humans, objects, and their interactions with vastly different scales and distances. To tackle this problem, we propose a Multi-Scale TRansformer (MSTR) for HOI detection powered by two novel HOI-aware deformable attention modules called Dual-Entity attention and Entity-conditioned Context attention. While existing deformable attention comes at a huge cost in HOI detection performance, our proposed attention modules of MSTR learn to effectively attend to sampling points that are essential to identify interactions. In experiments, we achieve the new state-of-the-art performance on two HOI detection benchmarks.

Human-Object Interaction (HOI) detection is a task of identifying "a set of interactions" in an image, which involves the i) localization of the subject (i.e., humans) and target (i.e., objects) of interaction, and ii) the classification of the interaction labels. Most existing methods have indirectly addressed this task by detecting human and object instances and individually inferring every pair of the detected instances. In this paper, we present a novel framework, referred by HOTR, which directly predicts a set of 〈human, object, interaction〉 triplets from an image based on a transformer encoder-decoder architecture. Through the set prediction, our method effectively exploits the inherent semantic relationships in an image and does not require time-consuming post-processing which is the main bottleneck of existing methods. Our proposed algorithm achieves the state-of-the-art performance in two HOI detection benchmarks with an inference time under 1 ms after object detection.

Graph Neural Networks (GNNs) have been widely applied to various fields for learning over graph-structured data. They have shown significant improvements over traditional heuristic methods in various tasks such as node classification and graph classification. However, since GNNs heavily rely on smoothed node features rather than graph structure, they often show poor performance than simple heuristic methods in link prediction where the structural information, e.g., overlapped neighborhoods, degrees, and shortest paths, is crucial. To address this limitation, we propose Neighborhood Overlap-aware Graph Neural Networks (Neo-GNNs) that learn useful structural features from an adjacency matrix and estimate overlapped neighborhoods for link prediction. Our Neo-GNNs generalize neighborhood overlap-based heuristic methods and handle overlapped multi-hop neighborhoods. Our extensive experiments on Open Graph Benchmark datasets (OGB) demonstrate that Neo-GNNs consistently achieve state-of-the-art performance in link prediction.

Advanced methods of applying deep learning to structured data such as graphs have been proposed in recent years. In particular, studies have focused on generalizing convolutional neural networks to graph data, which includes redefining the convolution and the downsampling (pooling) operations for graphs. The method of generalizing the convolution operation to graphs has been proven to improve performance and is widely used. However, the method of applying downsampling to graphs is still difficult to perform and has room for improvement. In this paper, we propose a graph pooling method based on self-attention. Self-attention using graph convolution allows our pooling method to consider both node features and graph topology. To ensure a fair comparison, the same training procedures and model architectures were used for the existing pooling methods and our method. The experimental results demonstrate that our method achieves superior graph classification performance on the benchmark datasets using a reasonable number of parameters.

Chaos communication system has characteristics such as sensitive initial conditions, non-periodic, wide-band, non-predictability and easy implementation. Also, security of chaos system is superior to digital communication systems, but BER (Bit Error Rate) performance is evaluated badly. So, study in order to improve the BER performance is important. At conventional studies, we proposed a novel chaos transceiver. BER performance of proposed chaos transceiver is able to be improved than CDSK(Correlation Delay Shift Keying) system, because self-interference signals are too small. Chaos communication system has many symbols, because it is used the spread spectrum technique. By this reason, study in order to have the good data rate is required. Information bits of CDSK system are modulated as -1 and 1 on the basis of BPSK system. However, instead of BPSK system, if high level modulation systems such as QPSK and 16QAM system are applied to chaos system, many information bits are possible to be transmitted using one symbol. In this paper, we evaluated the SER(Symbol Error Rate) performance of QPSK and 16QAM modulated a novel chaos transceiver. Also, we evaluate the anti-jamming characteristic that is one of advantages of chaos communication system.