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Publications
Distilling semantically aware orders for autoregressive image generation
With the growing pervasiveness of pre-trained protein large language models (pLLMs), pLLM-based methods are increasingly being put forward f… (see more)or the protein-protein interaction (PPI) inference task. Here, we identify and confirm that existing pre-trained pLLMs are a source of data leakage for the downstream PPI task. We characterize the extent of the data leakage problem by training and comparing small and efficient pLLMs on a dataset that controls for data leakage (“strict”) with one that does not (“non-strict”). While data leakage from pre-trained pLLMs cause measurable inflation of testing scores, we find that this does not necessarily extend to other, non-paired biological tasks such as protein keyword annotation. Further, we find no connection between the context-lengths of pLLMs and the performance of pLLM-based PPI inference methods on proteins with sequence lengths that surpass it. Furthermore, we show that pLLM-based and non-pLLM-based models fail to generalize in tasks such as prediction of the human-SARS-CoV-2 PPIs or the effect of point mutations on binding-affinities. This study demonstrates the importance of extending existing protocols for the evaluation of pLLM-based models applied to paired biological datasets and identifies areas of weakness of current pLLM models.
BACKGROUND
The social stigma of families of children living with colostomies due to anorectal malformation (ARM) is significant in low-incom… (see more)e countries (LICs). Improved access to pediatric surgery has resulted in more 1-stage ARM procedures in Southwestern Uganda, avoiding colostomy creation, but the impact on social stigma experienced by families is unknown. We hypothesized that this change would decrease the social stigma experienced by families.
METHODS
A single-center mixed retrospective and prospective cohort study with combined qualitative data of families of children with ARM who underwent corrective surgery compared the stigma experienced by those with colostomies to those without. The Kilifi Stigma Scale of Epilepsy (KSSE) was used to assess social stigma. Multivariable regression analysis assessed differences in the stigma experienced, controlling for age at diagnosis, rurality, distance traveled, sex, and parental education. Subgroup analysis assessed the impact of colostomy duration on stigma, stratified over parental education.
RESULTS
Patient/family dyads with 238 ARM were included; 177 (74%) received a colostomy. Most patients were male (51%), lived in rural areas (71%), and had parents with primary school education (65%). For those without a colostomy, the median KSSE was 0 (Q1-Q3 0-0), compared to 11 (Q1-Q3 3-20) for colostomy. On multivariable analysis, after controlling for age at diagnosis, rurality, distance traveled, sex, and parental education attainment, families of patients with ARM who received a colostomy had a median KSSE score 7.8 points higher than those who did not receive a colostomy (coefficient 7.78, 95% 3.14-12.43, and p = 0.001). When the duration of colostomy (in years) was examined, the median KSSE score increased by 1.58 points for each additional year for a patient who had a colostomy (IRR 1.58, 95% CI: 0.76-2.40, and p 0.001).
CONCLUSION
Adopting a 1-stage ARM repair for the select types, which avoids colostomy creation, significantly reduces the exper
