arXiv subjects

Kaiwen Deng

Publications and source records attributed to Kaiwen Deng.

4 recordsLinked to original sources

arXiv2026

Beyond Conditional Computation: Retrieval-Augmented Genomic Foundation Models with Gengram

Current genomic foundation models (GFMs) rely on extensive neural computation to implicitly approximate conserved biological motifs from single-nucleotide inputs. We propose Gengram, a conditional memory module that introduces an explicit and highly efficient lookup primitive for multi-base motifs via a genomic-specific hashing scheme, establishing genomic "syntax". Integrated into the backbone of state-of-the-art GFMs, Gengram achieves substantial gains (up to 14%) across several functional genomics tasks. The module demonstrates robust architectural generalization, while further inspection of Gengram's latent space reveals the emergence of meaningful representations that align closely with fundamental biological knowledge. By establishing structured motif memory as a modeling primitive, Gengram simultaneously boosts empirical performance and mechanistic interpretability, providing a scalable and biology-aligned pathway for the next generation of GFMs. The code is available at https://github.com/zhejianglab/Genos, and the model checkpoint is available at https://huggingface.co/ZhejiangLab/Gengram.

q-bio.GN↗

arXiv2025

The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data

In drug discovery, mapping interactions between genes within cellular systems is a crucial early step. Such maps are not only foundational for understanding the molecular mechanisms underlying disease biology but also pivotal for formulating hypotheses about potential targets for new medicines. Recognizing the need to elevate the construction of these gene-gene interaction networks, especially from large-scale, real-world datasets of perturbed single cells, the CausalBench Challenge was initiated. This challenge aimed to inspire the machine learning community to enhance state-of-the-art methods, emphasizing better utilization of expansive genetic perturbation data. Using the framework provided by the CausalBench benchmark, participants were tasked with refining the current methodologies or proposing new ones. This report provides an analysis and summary of the methods submitted during the challenge to give a partial image of the state of the art at the time of the challenge. Notably, the winning solutions significantly improved performance compared to previous baselines, establishing a new state of the art for this critical task in biology and medicine.

cs.LG↗

arXiv2024

Formation of a streamer blob via the merger of multiple plasma clumps below 2Rs

Context. Propagating streamer blobs could be an important source of disturbances in the solar wind. Direct observations on formation of streamer blobs could be a proxy for understanding the formation of small-scale structures and disturbances in the solar wind. Aims. We aim to investigate how a streamer blob is formed before it is observed in the outer corona. Methods. Usingspecialcoordinated-observationsfromSOHO/LASCO,GOES/SUVIandSDO/AIA, we study the precursors of a streamer blob as seen in the corona below 2.0 solar radii (Rs). Results. We found that the streamer blob was formed due to the gradual merging of three clumps of brightenings initiated from the lower corona at about 1.8Rs, which is likely driven by expansion of the loop system at the base of the streamer. The acceleration of the blob starts from 1.9Rs or lower. It propagates along the south flank of the streamer where an expanding elongated brightening occurs coincidently. Conclusions. Our observations demonstrate that formation of a streamer blob is a complex process. We suggest that the expansion of the loop results in a pinching-off flux-rope-like blob at the loop apex below 2Rs. When the blob moves outward, it can be transferred across the overlying loops through interchange/component magnetic reconnection and then is released into the open field system. When the blob moves toward open field lines, interchange magnetic reconnections might also occur, and that can accelerate the plasma blob intermittently whilst allow it to transfer across the open field lines. Such dynamics in a streamer blob might further trigger small-scale disturbances in the solar wind such as switchbacks in the inner heliosphere.

astro-ph.SR↗

arXiv2022

An EUV jet driven by a series of transition region micro-jets

Jets are one of the most common eruptive events in the solar atmosphere, and they are believed to be important in the context of coronal heating and solar wind acceleration. We present an observational study on a sequence of jets with the data acquired with the Solar Dynamics Observatory (SDO) and the Interface Region Imaging Spectrograph (IRIS). This sequence is peculiar in that an EUV jet, $\sim29\arcsec$ long and with a dome-like base, appears to be a consequence of a series of transition region (TR) micro-jets that are a few arcsecs in length.We find that the occurrence of any TR micro-jets is always associated with the change of geometry of micro-loops at the footpoints of the microjets. A bundle of TR flux ropes is seen to link a TR micro-jet to the dome-like structure at the base of the EUV jet. This bundle rises as a response to the TR micro-jets, with the rising motion eventually triggering the EUV jet. We propose a scenario involving a set of magnetic reconnections, in which the series of TR micro-jets are associated with the processes to remove the constraints to the TR flux ropes and thus allow them to rise and trigger the EUV jet. Our study demonstrates that small-scale dynamics in the lower solar atmosphere are crucial in understanding the energy and mass connection between the corona and the solar lower atmosphere, even though many of them might not pump mass and energy to the corona directly.

astro-ph.SR↗