Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks
Paper • 1908.10084 • Published • 19
How to use aliRafik/embeddinggemma_300m_finetuned_16bit with sentence-transformers:
from sentence_transformers import SentenceTransformer
model = SentenceTransformer("aliRafik/embeddinggemma_300m_finetuned_16bit")
sentences = [
"What is the significance of maintaining the temperature at 37.8°C during the isolation procedure?\n",
"Cell dispersion was performed from the endocardial layer of the ventricular wall for 30 min in the same solution containing also 660 mg/L collagenase, 2 g/L bovine albumin, and 50 mM CaCl 2 . During the isolation procedure, the solutions were gassed with carbogen and the temperature was maintained at 378C. The cells were stored in JMM solution until use. They were rod shaped and showed clear striation when the external calcium was restored.\n\n The cells were sedimented in a plexiglass chamber allowing continuous superfusion with oxygenized Tyrode solution at 378C. Transmembrane potential (V m ) was recorded using 3 M KCl filled sharp glass microelectrodes having tip resistance between 20 and 40 MV. These electrodes were connected to the input of an Axopatch-200B amplifier (Axon Instruments, Foster City, CA, USA) under current clamp conditions, allowing for injection of inward or outward current pulses. These current pulses, having durations longer than the expected APD, were injected from the upstroke of every 20th action potential. Thus, action potentials with current injections were separated from one another by 19 regular action potential waveforms. The cells were paced through the recording electrode using 1 ms wide rectangular current pulses with twice threshold amplitude. The cycle length (CL) was initially set to 5 s, and following stabilization of action potential configuration the CL was continuously varied to the shorter values. Action potentials were digitized at 100 kHz using Digidata 1200 A/D card (Axon Instruments) and stored for later analysis. Since the cytosol was not dialyzed, time-dependent changes in APD were negligible for at least 60 min under these experimental conditions.\n\n Pharmacological studies were performed in right ventricular papillary muscles and Purkinje fibres. Multicellular preparations were selected to prevent the limitations inherent to single myocyte studies (absence of intercellular clefts, potential damage to channel proteins, etc.) in the generalization to the in vivo condition. I CaL and I Na blockers (nicorandil and lidocaine) were tested in Purkinje fibres, in which the blocked currents are strongly represented during repolarization. Preparations were paced through a pair of platinum electrodes; the pacing CL was initially set to 1 s for at least 60 min allowing the preparations to equilibrate before starting the measurement, then it was gradually reduced from 5 to 3, 2, 1.5, 1, 0.7, 0.5, 0.4, and 0.3 s. In case of Purkinje strands, the longest CL was 3 s. After taking control records, the preparations were superfused for 40 min with the drug tested and the measurement was repeated at each pacing CL. Glass microelectrodes, filled with 3 M KCl and having tip resistances of 5-20 MV, were used to record V m . Efforts were made to maintain the same impalement throughout each experiment. If, however, an impalement became dislodged, adjustment was attempted, and if the action potential characteristics (both APD 90 and maximum rate of depolarization) of the re-established impalement deviated by less than 5% from the previous measurement, the experiment continued.\n\n The experimental results of this study suggested that RRD is the consequence of a general mechanism, i.e. one independent of the specific intervention through which APD modulation is achieved. The purpose of the numerical simulations was to test the working hypothesis that such a general mechanism could be provided by the features of the relation linking net transmembrane current to APD. 'Classical' action potential models were not suitable for this purpose because they include a description of specific channel gating properties potentially contributing to RRD. Exclusion of such a contribution was strictly required for unequivocal testing of the working hypothesis, which is by definition independent of specific channel gating mechanisms. The approach used was a calculation of the point-by-point change in the time-course of repolarization caused by addition of a constant current. The procedure was applied to real action potential waveforms, previously acquired from canine myocytes at two CLs. The expectation was that, because of their different duration, the action potentials recorded at different CLs would be differently prolonged (or shortened) by addition of an identical amount of current. It should be stressed that such an approach, tailored to address the working hypothesis suggested by the experimental results of this study, would be unsuitable to predict action potential modulation by changes in individual conductances.\n\n The simulation is based on the following principles. In a single cell (i.e.",
"DKA in a patient with underlying trisomy 9p.\n\n Initially, a resuscitation volume of 260 mL of 0.9% saline with 10 mmol KCl was administered. In following, the patient was then placed on maintenance fluids. Insulin was administered 1 hour after fluid resuscitation, starting at a rate of 0.65 mL/h (child weight: 13.1 kg [29 lb]). Two-hourly monitoring was scheduled. At 2 hours following administration of resuscitation fluids, the patient's blood glucose remained static at 29.3 mmol/L (527.4 mg/dL). As such, the insulin dose was raised to 1.3 mL/h in accordance with local DKA protocols.\n\n At 4 hours following administration of resuscitation fluids, the patient's blood glucose had reduced to 14.8 mmol/L (266.4 mg/dL). However, his temperature continued to rise, reaching a high point of 38.5°C 12 hours following admission. At this point, the blood glucose had risen back to 23.2 mmol/L (417.6 mg/dL). Blood cultures were then performed, revealing coagulase-negative staphylococci. This was treated with intravenous flucloxacillin and ceftriaxone. Following administration of antibiotics, the patient improved significantly. His blood glucose continued to fall (7.8 mmol/L [140.4 mg/dL] at day 3 [see Figure 1 ]), and the patient was discharged on day 5 of admission with continuous subcutaneous insulin infusion therapy.\n\n During admission, tests for thyroid autoantibodies and coeliac disease were negative. However, the patient's mother has been unresponsive to requests to determine diabetic etiology. \n\n This case raises interesting points for discussion related to both DKA and trisomy 9p.\n\n DKA is a metabolic complication of type 1 diabetes mellitus presenting with a range of symptoms listed in Table 1 .\n\n A lack of insulin results in an inability to transport glucose into cells, inducing utilization of fatty acids for energy: hence the term ketoacidosis. In the United Kingdom, 15.7% of undiagnosed pediatric diabetes cases present as DKA.\n\n 2 This is potentially fatal, with a mortality rate of 2% 3 ; this figure, however, is far greater with comorbid complications such as sepsis. 4 Unfortunately, almost all of these deaths are avoidable, 5 with retrospective identifiable failures in health care and/or patient identification. Regrettably, the failure of the GP in the presented case does not represent an isolated incident. Therefore, an assessment of this case is beneficial, assisting prevention of future errors.\n\n There are 2 major reasons why the GP's primary diagnosis of pneumonia should have been questioned. The first of these is the considerably increased levels of thirst, and the second is a clear chest examination. With reference to the former, although benign in the majority of cases this should have been explored further by the GP on mentioning by the mother. Even with the presence of infective symptoms, the differential diagnosis should include DKA with reported polydipsia: 23.4% of DKA admissions are precipitated by an infective illness. 3 Further to this, a clear chest examination justifies an alternative diagnosis. The reason for these oversights is unclear; nonetheless, increased knowledge on the area would certainly be assistive. Any index of suspicion from the GP could have revealed the diagnosis, as investigations revealing 2 of the 3 diagnostic criteria for DKA are readily available in the community (see Figure 2 ).\n\n As such, local and national educational initiatives on the recognition of DKA may be indicated. In addition to DKA, the reported patient was also a sufferer of trisomy 9p.\n\n To the majority of medical professionals, trisomy 21, 18, and 13 are known as the only duplications compatible with life. However, the next leading chromosomal duplication syndrome is compatible with long-term survival; this is of the short arm of chromosome 9: trisomy 9p. 6 Phenotypic manifestations of trisomy 9p are remarkably similar between individuals 7 ; features include craniofacial malformation, developmental delay, and growth deficiency. Although the latter is due to dysfunction of the growth hormone/insulin-like growth factor-1 axis, 8 no other endocrinological dysfunctions have been reported in the syndrome. Hence, this is the first reported case of insulin-dependent diabetes mellitus in trisomy 9p.",
"There have been some promising results with chemokine inhibition, due to the fact that small peptide chemokine inhibitors display much less side effect.\n\n Another potential therapeutic strategy is directed at stabilizing brain endothelial cell:cell interactions and the junctional complex. For example, S1p or SSeCKS mediators appear to decrease BBB permeability by acting primarily on TJ proteins [89, 90] . Their activity is still the subject of intense investigation and it will be very interesting to see which signal molecules are involved in their actions on TJ proteins.\n\n Another strategy, which is in the recent years has been gaining more attention, is targeting the signals molecules involved in remodeling junctional complexes. For example, targeting Rho, Rho kinase, MLCK, PTKs or PKC isoforms could be a promising strategy. RhoGTPases have significant effects on BBB integrity and the inflammatory response. They act as \"on-and off-switches\" and have a fundamental importance for increased permeability as well as in the timedependent restoration of endothelial barrier function. Selective RhoGTPase inhibitors have produced promising results in some of the vascular as well as cerebrovascular disorders [30, 182] .\n\n In conditions such as brain tumors, neurodegenerative disorders like Alzheimer's disease, Parkinson's disease or different types of metabolic disorders with developing encephalopathy, therapeutic strategies are often limited by the inability of drugs to cross the BBB from blood to brain. There has, therefore, been much interest in devising methods for disrupting the BBB. The ultimate goals of such methods are several: (i) there should be specificity in targeting the brain or preferably the diseased/injured part of the brain; (ii) the action should be brief in duration with the paracellular opening reverting back to control quickly; and (iii) the paracellular leak should be specific for the class of molecules one wishes to deliver.\n\n There are several options for transiently disrupting the BBB. The most widely studied method involves intra-arterial injection of a hyperosmolar osmotic such as mannitol, which leads to endothelial cell shrinkage and opening of TJ. This method has been used extensively to deliver chemotherapeutic agents to gliomas, neuroectodermal tumors, CNS lymphomas, and brain metastases in animal models and patients by Neuwelt and colleagues [63, 84, 152] . Some specificity in targeting is achieved by injecting the hyperosmotic agent unilaterally into the cerebral circulation. Further data is still required before this technique gains widespread use.\n\n Bradikinin and its analog RPM-7 (B2 receptor agonist) have also been investigated as potential inducers of transient BBB disruption [13, 135] . Despite its longer half-life and greater selectivity, the use of RMP-7 in conjunction with chemotherapy showed no benefit in a randomized phase 2 trials for gliomas.\n\n Other potential methods to induce transient \"opening\" of BBB are intra-arterial administration of alkilglycerola, which transiently increases the penetration of drugs or macromolecules across the BBB, and exposure of BBB to radiotherapy (20-30Gy) whilst chemotherapy is administered [47, 84, 138] . These strategies are under intense investigation in order to understand their mechanisms of action at the BBB and possible side effects.\n\n A promising target to induce transient opening of the BBB for drug delivery may also be the signaling molecules involved in regulation of BBB permeability. We would like to point out that effect of Rho and Rho kinase in transient opening of brain endothelial barrier should be take in consideration for the further investigation of drugs deliver into brain.\n\n An alternative strategy for drug delivery across the BBB focuses on transcytosis and transcellular permeability. Enhanced vesicular transport can be used for delivery compounds into the brain. Examples are: liposome-born therapeutic agents that show more transendothelial passage under hypothermic conditions and compounds which bind to lectins and via adsorptive vesicular transport are taken up into brain parenchyma [10, 11, 105, 189] . Modulation of specific endothelial carrier proteins (transporters) is also a therapeutic target for enhancing drug delivery across the BBB. Such transporters may be involved in transport of compounds from blood to brain, in which case drugs which are substrates will have enhanced delivery (e.g. L-DOPA is a substrate for the L-system amino acid transporter). There are, however, also efflux transporters which clear compounds from the brain. P-glycoprotein (P-gp) is the major BBB efflux transporter and mice that lack P-gp have higher brain uptake of a wide range of drugs [96, 180] . There has, therefore, been a major effort by drug companies to develop P-gp inhibitors to enhance the delivery of drugs to the brain. As yet, there have been no clinical trials that have shown a benefit of this approach to enhance drug delivery to brain.\n\n From clinical and neuropathological point of view, controlling BBB permeability has tremendous importance in treatment of the devastating brain disorders. From the neuropharmacological point of view controlling BBB permeability should be effective, and without or with limited side effects. Thus, understanding BBB structure and the molecular mechanisms of regulating BBB permeability opens a new avenue of therapeutic strategies for most brain disorders.\n\n Much exciting progress is being made in understanding the molecular basis of BBB paracellular permeability. Although some details remain obscure, the TJ is likely to be site where multiple cellular signaling pathways converge to regulate paracellular permeability. Due to this fact, further intensive investigation is needed to completely understand the mechanism of regulating permeability, but they promise to make important findings for the treatment of severe CNS diseases such as multiple sclerosis, stroke, infections and brain tumors. Aurrand-Lions, M., Lamagna, C., Dangerfield, J.P., Wang, S., Herrera, P., Nourshargh, S."
]
embeddings = model.encode(sentences)
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [4, 4]This model was finetuned with Unsloth.
based on unsloth/embeddinggemma-300m
This is a sentence-transformers model finetuned from unsloth/embeddinggemma-300m on the generator dataset. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, classification, clustering, and more.
SentenceTransformer(
(0): Transformer({'transformer_task': 'feature-extraction', 'modality_config': {'text': {'method': 'forward', 'method_output_name': 'last_hidden_state'}}, 'module_output_name': 'token_embeddings', 'max_seq_length': 1024, 'do_lower_case': False, 'architecture': 'PeftModelForFeatureExtraction'})
(1): Pooling({'embedding_dimension': 768, 'pooling_mode': 'mean', 'include_prompt': True})
(2): Dense({'in_features': 768, 'out_features': 3072, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity', 'module_input_name': 'sentence_embedding', 'module_output_name': 'sentence_embedding'})
(3): Dense({'in_features': 3072, 'out_features': 768, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity', 'module_input_name': 'sentence_embedding', 'module_output_name': 'sentence_embedding'})
(4): Normalize({})
)
First install the Sentence Transformers library:
pip install -U sentence-transformers
Then you can load this model and run inference.
from sentence_transformers import SentenceTransformer
# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
queries = [
"How do statin drugs potentially reduce the risk of Alzheimer's disease?\n",
]
documents = [
'Reducing cholesterol with drugs in the statin family appears to alleviate this risk dramatically (35, 36) (see "Greasing Aging\'s Downward Slide" ¶ ¶ ). Cholesterol congregates in so-called lipid rafts that float around in the cellular membrane. APP, β-secretase, and γ-secretase are attracted to these rafts, and as Brian Austen of St. George\'s Hospital Medical School in Tooting, U.K., says, they\'re "marooned together" where they can interact and brew up β amyloid. APP appears to exist in two separate pools; those proteins floating on the lipid rafts are clipped by β-secretase and can spawn β amyloid; APP floating free of the rafts is more likely to be cut by α-secretase and yield harmless proteins (37) . At the Stockholm meeting in 2002, Konrad Beyreuther of Heidelberg University in Germany reported preliminary results from a small clinical trial of statins in people with mild AD and normal cholesterol concentrations. Patients taking the drug appeared to decline more slowly than those taking a placebo, he reported.\n\n Other epidemiological studies have uncovered promising hints that estrogen replacement therapy might protect women from Alzheimer\'s. One followed almost 2000 women in Cache County, Utah-the United States\' longest-lived county. Those who had been on hormone replacement therapy (in this study, most women were treated with estrogen only) in the past were less likely to develop AD than were those who had never been on HRT (38) . Current use didn\'t seem to help, leading researchers to conclude that there might be a "critical time" during which estrogen can forestall AD (39) . But the purported benefits of HRT didn\'t hold up in a massive, case-controlled, randomized study. The Women\'s Health Initiative (WHI) showed that estrogen plus progestin increased rather than decreased the risk that postmenopausal women would develop dementia or mild cognitive impairment (see "Weathering the HRT Storm" ## ) (40) . Another arm of the WHI trial examined whether estrogen (without progestin) alleviates the clinical symptoms of women already suffering from mild or moderate AD; it turned up no evidence of such a benefit (41). However, an earlier postmortem neuroanatomical study from the WHI showed that at a cellular level, at least, estrogen did seem to exert a positive effect. Women with early signs of AD who had taken estrogen lost fewer neurons in vulnerable brain regions than did women who had taken placebos (42) .\n\n Other ongoing clinical prevention trials will assess the protective effects, if any, of antioxidants such as vitamin E and ginkgo biloba. One trial of vitamin E in people with established AD showed that the treatment delayed their entry into nursing homes, a major milestone in the progression of the disease (43) . The AD-prevention hypothesis dearest to the hearts of many researchers goes by several different names: the cognitive reserve hypothesis, the cortical reserve hypothesis, and the "use it or lose it" hypothesis. According to the theory, stimulating the brain, say, by regularly reading research or introductory review articles, decreases the risk of developing Alzheimer\'s. Although the mechanism for such a protective factor is a bit murky-scientists talk about building extra neural connections that somehow compensate for early AD neuropathology-a few studies have backed up initial observations that people with more years of education are less likely to develop Alzheimer\'s. For instance, those with AD were less likely to have engaged in intellectual activities in early and middle adulthood than their nondemented peers (44) .\n\n \n\n \n\n Some of the most intriguing evidence for the cognitive reserve hypothesis comes from a longitudinal study of nuns in convents (see "Sister Knows Best" *** ). These women are an epidemiologist\'s dream: They live in similar rooms, eat the same kinds of foods, and have similar chores and hobbies, thus reducing the number of confounding variables that normally plague population studies. Researchers analyzed writing samples gathered when the young women entered their convents. Low grammatical and cognitive complexity correlated with likelihood of AD (45); in contrast, one particularly sharp woman lived to age 101 with all her wits, even though her brain was studded with plaques and tangles at autopsy (46) , providing more anecdotal evidence for the cognitive reserve hypothesis.\n\n Alzheimer\'s disease used to be one of the grimmer areas of research, but these days, AD researchers are remarkably optimistic. New transgenic and knockout mouse lines offer "ways to get into the nervous system of living animals," says Donald Price. The potential for helping millions of people live fuller, longer lives contributes to the new sense of urgency and enthusiasm. But there\'s also the specter of an aging population; a person\'s risk of AD doubles every decade.',
'Furthermore, we showed that heterozygous carriers of the ADAMTS13-related mutations who, thus, have reduced ADAMTS13 bioactivity have a normal phenotype.\n\n The plasma of the patients with congenital TTP did not present the ADAMTS13 band. This may be due to altered synthesis, secretion or antigenicity, or due to increased breakdown of the protease in plasma. The fact that two antibodies directed to two different domains in ADAMTS13 were unable to detect the protease band makes altered antigenicity less likely to be the cause for the lack of the ADAMTS13 band in these patients. Previous studies have shown impaired secretion of the 4143insA (patients 1, 2, 4, and 5) [35, 42, 44] and P353L (patient 3) [42] mutants from cells, thus, indicating that the protease may accumulate intracellularly, at least in some patients with congenital TTP. This may be due to a missing cell sorting signal, as in the case of 4143insA [44] or due to conformational changes in the protein, impairing its secretion. Similar findings regarding two other ADAMTS13 mutations, V88M and G239V, have been recently reported [34] . A total lack of ADAMTS13 activity in the plasma is thought to be incompatible with life [27] , thus, the patients may have very low amounts of ADAMTS13 activity in their plasma, which we were unable to detect with this method. The patients with acquired TTP presented with a normal ADAMTS13 band, which is consistent with the fact that ADAMTS13 protease genotype and expression are normal, but their activity is lower, due auto-antibodies [11, 14, 41, 45, 52] . The finding that the immunoadsorption of immunoglobulins from the plasma of the patients with acquired TTP also led to the removal of the ADAMTS13 antigen from their samples indicates that the protease is complexed with the auto-antibodies in the circulation of these patients, and that this occurs even during clinical remission.\n\n The majority of the ADAMTS13 assays available today detect ADAMTS13 activity levels in plasma (Table 2) . This is performed either by detecting the VWF products resulting from ADAMTS13 cleavage (assays [1] [2] [3] [4] [5] or by measuring the residual VWF activity (assays 6-7). The VWF substrate utilized in these assays may be high molecular weight VWF (plasma-derived or recombinant; assays 1-4) or VWF domains or short synthetic peptides (assay 5). Two multicenter studies evaluating methods 1, 3-5, and 6-7 showed that all assays were able to detect severely ADAMTS13-deficient plasma samples and indicated that methods 1, 6, and 7 were the most consistent and reliable methods [48, 49] . A recent smaller study evaluating the FRETS-VWF73 method (assay 5) showed that this is a reliable assay which provides results in good accordance with other methods [26] .\n\n Few recent studies have shown that ADAMTS13 antigen was detectable in plasma by ELISA (assay 8 in Table 2 ). ELISA assays are a valuable complement to the ADAMTS13 activity assays, and offer a fast analysis of the ADAMTS13 antigen levels in plasma samples using antibodies directed to ADAMTS13. These assays are able to distinguish ADAMTS13-deficient TTP plasma from normal plasma samples. Other methods are capable of detecting anti-ADAMTS13 auto-antibodies ( Table 2 , assays 8-9). Mutational analysis can be carried out by polymerase chain reaction (PCR) in order to detect mutations in the ADAMTS13 gene (assay 11 in Table 2 ).\n\n In the present study, we developed a qualitative, semiquantitative assay capable of detecting ADAMTS13 antigen and anti-ADAMTS13 auto-antibodies in plasma and, IRMA: immunoradiometric assay; FRET: fluorescence resonance energy transfer; FRETS-VWF73: a 73-amino-acid-long synthetic peptide which provides a minimal substrate for ADAMTS13 [24] that has been made fluorogenic; PCR: polymerase chain reaction thus, distinguishing between TTP and normal plasma, as well as distinguishing between congenital and acquired TTP. All patients with congenital TTP, regardless of their ADAMTS13 mutations, presented with undetectable levels of ADAMTS13 antigen, whereas patients with acquired TTP presented a normal phenotype. Heterozygous carriers of ADAMTS13 mutations also revealed a normal ADAMTS13 antigen band. Although not a quantitative method like the above-mentioned ELISA assays, the present assay offers the advantage of not only demonstrating the presence or absence of ADAMTS13 antigen, but also the molecular size of ADAMTS13 present in plasma samples. Furthermore, this assay was able to show the presence of anti-ADAMTS13 antibodies indirectly by performing immunoadsorption of plasma immunoglobulins prior to immunoblotting. In conclusion, this assay is able to distinguish between normal and TTP plasma, and also between congenital and acquired TTP. It is easy to perform and can be used at any hospital laboratory routinely using SDS-PAGE electrophoresis and immunoblotting, and offers a complement to existing ADAMTS13 methods in the diagnosis of TTP.',
'Diabetic-cardiomyopathy-related complications are the major cause of morbidity and mortality in diabetes. Diabetes not only affects the heart causing diabetic-cardiomyopathy independent of coronary artery disease, hypertension, and hyperlipidemia but also exacerbate the cardiac injury after myocardial infarction or IR. Association of cardiac fibrosis, hypertrophy, and cardiomyocyte apoptosis has been discussed in literature. Diabetic mouse models have been used in cardiac research to elucidate the underlying cellular and molecular mechanism of fibrosis and hypertrophy [103] . Hyperglycemia of the left ventricular wall in diabetes stimulates cardiac remodeling and disrupts contractile function, thereby impairing the heart function by declining the systolic and diastolic function of the heart [104] . The mutation in diabetic (db/db) mice results in expression of a non-functional truncated long-form of the leptin receptor leading to hypothalamic resistance to leptin. This results in voracious appetite, marked obesity and overt diabetes at a young age in mice. Obesity and diabetes at young age (4-6 months) results in cardiac interstitial fibrosis in db/db mice and has been documented using both histological and biochemical techniques. Activation and expansion of the resident cardiac fibroblast in diabetes may result in cardiac fibrosis [105] . Further the cardiac fibroblast-dependent matrix accumulation in type II diabetes has been reported using the genetically induced mouse model of type II diabetes (db/db murine model). Increased expression of collagen type I, TIMP2 and TGF-b, and phenotypic changes in diabetic db/db fibroblast isolated from diabetic mouse was associated with collagen accumulation, myocardial stiffness and diastolic dysfunction [106] .\n\n Cardiomyopathies are a heterogeneous group of diseases affecting the heart muscle and frequently lead to progressive heart failure-related disability or cardiovascular death. Since genetics have been shown to play an increasingly important role in the onset of cardiomyopathies [107] , mouse models have emerged as the most commonly used animal model for cardiomyopathy research, based on the availability of genetic information and technologies to manipulate the mouse genome [108, 109] . Hypertrophic cardiomyopathy (HCM) is a disease of the cardiac muscle that occurs due to mutations in genes encoding for the cardiac sarcomere. To date, approximately 1400 mutations have been identified as responsible for HCM pathology. About 70 % of these mutations are in the sarcomere genes encoding cardiac b-myosin heavy chain (MYH7) and cardiac myosin-binding protein C (MYBPC3). Other sarcomeric genes, such as regulatory myosin light chain (MYL2), cardiac troponin T (TNNT2), cardiac troponin I (TNNI3), and actin (ACTC) account for the other cases of HCM [19] . The phenotypic expression of HCM includes massive hypertrophy primarily involving the ventricular septum. The mechanisms of HCM are complex and include dynamic LV outflow tract obstruction due to bulging of the thickened basal anterior septum beneath the aortic valve, mitral regurgitation, diastolic dysfunction, myocardial ischemia, and cardiac arrhythmias that may lead to sudden death [8] . The microscopic hallmarks are myocyte hypertrophy and disarray together with expansion of the interstitial fibrosis. Myocyte disarray is characterized by architectural disorganization of the myocardium, in which adjacent hypertrophied myocytes are aligned perpendicularly or obliquely to each other around central cores of collagen in either a pinwheel configuration or herringbone pattern (Fig. 6) .\n\n A number of myosin heavy chain transgenic animal models of HCM have been created in an attempt to understand the pathogenesis of HCM phenotypes typically seen in humans. A transgenic mouse model with a point mutation of the Arg 403 -Gln in a-myosin heavy chain shows similarities with familial HCM in humans [110] . A similar phenotype has been seen in transgenic mice lacking the light chain-binding domain of b-myosin heavy chain [111] . These models will help in understanding the pathophysiology of HCM. Overexpression of the H-ras gene targeted to the ventricle with MLC2v promoter causes ventricular hypertrophy with myofiber disarray, which causes left ventricular outflow tract obstruction leading to diastolic dysfunction [112] .',
]
query_embeddings = model.encode_query(queries)
document_embeddings = model.encode_document(documents)
print(query_embeddings.shape, document_embeddings.shape)
# [1, 768] [3, 768]
# Get the similarity scores for the embeddings
similarities = model.similarity(query_embeddings, document_embeddings)
print(similarities)
# tensor([[ 0.6547, -0.0359, -0.0823]])
InformationRetrievalEvaluator| Metric | Value |
|---|---|
| cosine_accuracy@1 | 0.8752 |
| cosine_accuracy@3 | 0.9603 |
| cosine_accuracy@5 | 0.9769 |
| cosine_accuracy@10 | 0.9886 |
| cosine_precision@1 | 0.8752 |
| cosine_precision@3 | 0.3201 |
| cosine_precision@5 | 0.1954 |
| cosine_precision@10 | 0.0989 |
| cosine_recall@1 | 0.8752 |
| cosine_recall@3 | 0.9603 |
| cosine_recall@5 | 0.9769 |
| cosine_recall@10 | 0.9886 |
| cosine_ndcg@10 | 0.937 |
| cosine_mrr@10 | 0.9199 |
| cosine_map@100 | 0.9204 |
question and passage_text| question | passage_text | |
|---|---|---|
| type | string | string |
| modality | text | text |
| details |
|
|
| question | passage_text |
|---|---|
What factors may contribute to increased pulmonary conduit durability in patients who undergo the Ross operation compared to those with right ventricular outflow tract obstruction? |
I n 1966, Ross and Somerville 1 reported the first use of an aortic homograft to establish right ventricle-to-pulmonary artery continuity in a patient with tetralogy of Fallot and pulmonary atresia. Since that time, pulmonary position homografts have been used in a variety of right-sided congenital heart lesions. Actuarial 5-year homograft survivals for cryopreserved homografts are reported to range between 55% and 94%, with the shortest durability noted in patients less than 2 years of age. 4 Pulmonary position homografts also are used to replace pulmonary autografts explanted to repair left-sided outflow disease (the Ross operation). Several factors may be likely to favor increased pulmonary conduit durability in Ross patients compared with those with right ventricular outflow tract obstruction, including later age at operation (allowing for larger homografts), more normal pulmonary artery architecture, absence of severe right ventricular hypertrophy, and more natural positioning of ... |
How does MCAM expression in hMSC affect the growth and maintenance of hematopoietic progenitors? |
After culture in a 3-dimensional hydrogel-based matrix, which constitutes hypoxic conditions, MCAM expression is lost. Concordantly, Tormin et al. demonstrated that MCAM is down-regulated under hypoxic conditions. 10 Furthermore, it was shown by others and our group that oxygen tension causes selective modification of hematopoietic cell and mesenchymal stromal cell interactions in co-culture systems as well as influence HSPC metabolism. [44] [45] [46] Thus, the observed differences between Sharma et al. and our data in HSPC supporting capacity of hMSC are likely due to the different culture conditions used. Further studies are required to clarify the influence of hypoxia in our model system. Altogether these findings provide further evidence for the importance of MCAM in supporting HSPC. Furthermore, previous reports have shown that MCAM is down-regulated in MSC after several passages as well as during aging and differentiation. 19, 47 Interestingly, MCAM overexpression in hMSC enhance... |
What is the relationship between Fanconi anemia and breast and ovarian cancer susceptibility genes? |
( 31 ) , of which 5% -10 % may be caused by genetic factors ( 32 ) , up to half a million of these patients may be at risk of secondary hereditary neoplasms. The historic observation of twofold to fi vefold increased risks of cancers of the ovary, thyroid, and connective tissue after breast cancer ( 33 ) presaged the later syndromic association of these tumors with inherited mutations of BRCA1, BRCA2, PTEN, and p53 ( 16 ) . By far the largest cumulative risk of a secondary cancer in BRCA mutation carriers is associated with cancer in the contralateral breast, which may reach a risk of 29.5% at 10 years ( 34 ) . The Breast Cancer Linkage Consortium ( 35 , 36 ) also documented threefold to fi vefold increased risks of subsequent cancers of prostate, pancreas, gallbladder, stomach, skin (melanoma), and uterus in BRCA2 mutation carriers and twofold increased risks of prostate and pancreas cancer in BRCA1 mutation carriers; these results are based largely on self-reported family history inf... |
MultipleNegativesRankingLoss with these parameters:{
"scale": 20.0,
"similarity_fct": "cos_sim",
"gather_across_devices": false,
"directions": [
"query_to_doc"
],
"partition_mode": "joint",
"hardness_mode": null,
"hardness_strength": 0.0
}
question and passage_text| question | passage_text | |
|---|---|---|
| type | string | string |
| modality | text | text |
| details |
|
|
| question | passage_text |
|---|---|
What are some hereditary cancer syndromes that can result in various forms of cancer? |
Hereditary Cancer Syndromes, including Hereditary Breast and Ovarian Cancer (HBOC) and Lynch Syndrome (LS), can result in various forms of cancer due to germline mutations in cancer predisposition genes. While the major contributory genes for these syndromes have been identified and well-studied (BRCA1/ BRCA2 for HBOC and MSH2/MSH6/MLH1/PMS2/ EPCAM for LS), there remains a large percentage of associated cancer cases that are negative for germline mutations in these genes, including 80% of women with a personal or family history of breast cancer who are negative for BRCA1/2 mutations [1] . Similarly, between 30 and 50% of families fulfill stringent criteria for LS and test negative for germline mismatch repair gene mutations [2] . Adding complexity to these disorders is the significant overlap in the spectrum of cancers observed between various hereditary cancer syndromes, including many cancer susceptibility syndromes. Some that contribute to elevated breast cancer risk include Li-Frau... |
How do MAK-4 and MAK-5 exert their antioxidant properties? |
Hybrid F1 mice were injected with urethane (300 mg/kg) at 8 days of age. A group was then put on a MAK-supplemented diet, another group was fed a standard pellet diet. At 36 weeks of age the mice were sacrificed and the livers examined for the presence of tumors mouse (Panel A) and for the number of nodules per mouse (Panel B) (* p < 0.05, ** P < 0.001). Statistical analysis was performed by Two Way ANOVA Test followed by Post Hoc Bonferroni analysis. |
What are the primary indications for a decompressive craniectomy, and what role does neurocritical care play in determining the suitability of a patient for this procedure? |
Decompressive craniectomy is a valid neurosurgical strategy now a day as an alternative to control an elevated intracranial pressure (ICP) and controlling the risk of uncal and/or subfalcine herniation, in refractory cases to the postural, ventilator, and pharmacological measures to control it. The neurocritical care and the ICP monitorization are key determinants to identify and postulate the inclusion criteria to consider a patient as candidate to this procedure, as it is always considered a rescue surgical technique. Head trauma and ischemic or hemorrhagic cerebrovascular disease with progressive deterioration due to mass effect are some of the cases that may require a decompressive craniectomy with its different variants. However, this procedure per se can have complications described in the postcraniectomy syndrome and may occur in short, medium, or even long term. |
MultipleNegativesRankingLoss with these parameters:{
"scale": 20.0,
"similarity_fct": "cos_sim",
"gather_across_devices": false,
"directions": [
"query_to_doc"
],
"partition_mode": "joint",
"hardness_mode": null,
"hardness_strength": 0.0
}
per_device_train_batch_size: 64per_device_eval_batch_size: 64gradient_accumulation_steps: 4learning_rate: 2e-05num_train_epochs: 1warmup_ratio: 0.03bf16: Trueprompts: {'question': 'task: search result | query: ', 'passage_text': 'title: none | text: '}batch_sampler: no_duplicatesoverwrite_output_dir: Falsedo_predict: Falseprediction_loss_only: Trueper_device_train_batch_size: 64per_device_eval_batch_size: 64per_gpu_train_batch_size: Noneper_gpu_eval_batch_size: Nonegradient_accumulation_steps: 4eval_accumulation_steps: Nonetorch_empty_cache_steps: Nonelearning_rate: 2e-05weight_decay: 0.0adam_beta1: 0.9adam_beta2: 0.999adam_epsilon: 1e-08max_grad_norm: 1.0num_train_epochs: 1max_steps: -1lr_scheduler_type: linearlr_scheduler_kwargs: Nonewarmup_ratio: 0.03warmup_steps: 0log_level: passivelog_level_replica: warninglog_on_each_node: Truelogging_nan_inf_filter: Truesave_safetensors: Truesave_on_each_node: Falsesave_only_model: Falserestore_callback_states_from_checkpoint: Falseno_cuda: Falseuse_cpu: Falseuse_mps_device: Falseseed: 42data_seed: Nonejit_mode_eval: Falsebf16: Truefp16: Falsefp16_opt_level: O1half_precision_backend: autobf16_full_eval: Falsefp16_full_eval: Falsetf32: Nonelocal_rank: 0ddp_backend: Nonetpu_num_cores: Nonetpu_metrics_debug: Falsedebug: []dataloader_drop_last: Falsedataloader_num_workers: 0dataloader_prefetch_factor: Nonepast_index: -1disable_tqdm: Falseremove_unused_columns: Truelabel_names: Noneload_best_model_at_end: Falseignore_data_skip: Falsefsdp: []fsdp_min_num_params: 0fsdp_config: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}fsdp_transformer_layer_cls_to_wrap: Noneaccelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}parallelism_config: Nonedeepspeed: Nonelabel_smoothing_factor: 0.0optim: adamw_torch_fusedoptim_args: Noneadafactor: Falsegroup_by_length: Falselength_column_name: lengthproject: huggingfacetrackio_space_id: trackioddp_find_unused_parameters: Noneddp_bucket_cap_mb: Noneddp_broadcast_buffers: Falsedataloader_pin_memory: Truedataloader_persistent_workers: Falseskip_memory_metrics: Trueuse_legacy_prediction_loop: Falsepush_to_hub: Falseresume_from_checkpoint: Nonehub_model_id: Nonehub_strategy: every_savehub_private_repo: Nonehub_always_push: Falsehub_revision: Nonegradient_checkpointing: Falsegradient_checkpointing_kwargs: Noneinclude_inputs_for_metrics: Falseinclude_for_metrics: []eval_do_concat_batches: Truefp16_backend: autopush_to_hub_model_id: Nonepush_to_hub_organization: Nonemp_parameters: auto_find_batch_size: Falsefull_determinism: Falsetorchdynamo: Noneray_scope: lastddp_timeout: 1800torch_compile: Falsetorch_compile_backend: Nonetorch_compile_mode: Noneinclude_tokens_per_second: Falseinclude_num_input_tokens_seen: noneftune_noise_alpha: Noneoptim_target_modules: Nonebatch_eval_metrics: Falseeval_on_start: Falseuse_liger_kernel: Falseliger_kernel_config: Noneeval_use_gather_object: Falseaverage_tokens_across_devices: Trueprompts: {'question': 'task: search result | query: ', 'passage_text': 'title: none | text: '}batch_sampler: no_duplicatesmulti_dataset_batch_sampler: proportionalrouter_mapping: {}learning_rate_mapping: {}| Epoch | Step | Training Loss | Validation Loss | cosine_ndcg@10 |
|---|---|---|---|---|
| -1 | -1 | - | - | 0.8898 |
| 0.0128 | 5 | - | 0.0743 | 0.8908 |
| 0.0256 | 10 | - | 0.0549 | 0.8996 |
| 0.0384 | 15 | 0.0696 | 0.0418 | 0.9052 |
| 0.0512 | 20 | - | 0.0372 | 0.9067 |
| 0.0640 | 25 | - | 0.0346 | 0.9082 |
| 0.0768 | 30 | 0.0344 | 0.0327 | 0.9095 |
| 0.0896 | 35 | - | 0.0309 | 0.9116 |
| 0.1024 | 40 | - | 0.0296 | 0.9136 |
| 0.1152 | 45 | 0.0308 | 0.0285 | 0.9155 |
| 0.1280 | 50 | - | 0.0275 | 0.9171 |
| 0.1408 | 55 | - | 0.0268 | 0.9181 |
| 0.1536 | 60 | 0.0274 | 0.0262 | 0.9194 |
| 0.1663 | 65 | - | 0.0257 | 0.9205 |
| 0.1791 | 70 | - | 0.0250 | 0.9226 |
| 0.1919 | 75 | 0.0231 | 0.0245 | 0.9239 |
| 0.2047 | 80 | - | 0.0242 | 0.9253 |
| 0.2175 | 85 | - | 0.0239 | 0.9262 |
| 0.2303 | 90 | 0.0227 | 0.0238 | 0.9272 |
| 0.2431 | 95 | - | 0.0232 | 0.9283 |
| 0.2559 | 100 | - | 0.0226 | 0.9294 |
| 0.2687 | 105 | 0.024 | 0.0223 | 0.9299 |
| 0.2815 | 110 | - | 0.0220 | 0.9303 |
| 0.2943 | 115 | - | 0.0218 | 0.9305 |
| 0.3071 | 120 | 0.0175 | 0.0216 | 0.9308 |
| 0.3199 | 125 | - | 0.0213 | 0.9312 |
| 0.3327 | 130 | - | 0.0209 | 0.9319 |
| 0.3455 | 135 | 0.0195 | 0.0206 | 0.9324 |
| 0.3583 | 140 | - | 0.0204 | 0.9325 |
| 0.3711 | 145 | - | 0.0201 | 0.9324 |
| 0.3839 | 150 | 0.0199 | 0.0200 | 0.9321 |
| 0.3967 | 155 | - | 0.0198 | 0.9324 |
| 0.4095 | 160 | - | 0.0196 | 0.9330 |
| 0.4223 | 165 | 0.0184 | 0.0195 | 0.9336 |
| 0.4351 | 170 | - | 0.0194 | 0.9343 |
| 0.4479 | 175 | - | 0.0193 | 0.9347 |
| 0.4607 | 180 | 0.0206 | 0.0192 | 0.9348 |
| 0.4734 | 185 | - | 0.0191 | 0.9350 |
| 0.4862 | 190 | - | 0.0191 | 0.9347 |
| 0.4990 | 195 | 0.0176 | 0.0191 | 0.9346 |
| 0.5118 | 200 | - | 0.0188 | 0.9348 |
| 0.5246 | 205 | - | 0.0186 | 0.9354 |
| 0.5374 | 210 | 0.0199 | 0.0185 | 0.9352 |
| 0.5502 | 215 | - | 0.0184 | 0.9350 |
| 0.5630 | 220 | - | 0.0183 | 0.9351 |
| 0.5758 | 225 | 0.0176 | 0.0182 | 0.9355 |
| 0.5886 | 230 | - | 0.0181 | 0.9354 |
| 0.6014 | 235 | - | 0.0181 | 0.9357 |
| 0.6142 | 240 | 0.0167 | 0.0181 | 0.9359 |
| 0.6270 | 245 | - | 0.0180 | 0.9358 |
| 0.6398 | 250 | - | 0.0179 | 0.9356 |
| 0.6526 | 255 | 0.0158 | 0.0178 | 0.9361 |
| 0.6654 | 260 | - | 0.0178 | 0.9359 |
| 0.6782 | 265 | - | 0.0177 | 0.9363 |
| 0.6910 | 270 | 0.016 | 0.0177 | 0.9362 |
| 0.7038 | 275 | - | 0.0177 | 0.9362 |
| 0.7166 | 280 | - | 0.0176 | 0.9363 |
| 0.7294 | 285 | 0.0177 | 0.0176 | 0.9363 |
| 0.7422 | 290 | - | 0.0175 | 0.9366 |
| 0.7550 | 295 | - | 0.0175 | 0.9361 |
| 0.7678 | 300 | 0.0168 | 0.0174 | 0.9361 |
| 0.7806 | 305 | - | 0.0174 | 0.9362 |
| 0.7933 | 310 | - | 0.0173 | 0.9361 |
| 0.8061 | 315 | 0.0198 | 0.0172 | 0.9361 |
| 0.8189 | 320 | - | 0.0172 | 0.9363 |
| 0.8317 | 325 | - | 0.0171 | 0.9369 |
| 0.8445 | 330 | 0.0197 | 0.0171 | 0.9369 |
| 0.8573 | 335 | - | 0.0171 | 0.9367 |
| 0.8701 | 340 | - | 0.0170 | 0.9367 |
| 0.8829 | 345 | 0.0163 | 0.0170 | 0.9369 |
| 0.8957 | 350 | - | 0.0170 | 0.9369 |
| 0.9085 | 355 | - | 0.0170 | 0.9369 |
| 0.9213 | 360 | 0.0156 | 0.0170 | 0.9372 |
| 0.9341 | 365 | - | 0.0169 | 0.9371 |
| 0.9469 | 370 | - | 0.0169 | 0.9368 |
| 0.9597 | 375 | 0.0194 | 0.0169 | 0.9370 |
| 0.9725 | 380 | - | 0.0169 | 0.9369 |
| 0.9853 | 385 | - | 0.0169 | 0.9370 |
| 0.9981 | 390 | 0.018 | 0.0169 | 0.9369 |
| -1 | -1 | - | - | 0.9370 |
@inproceedings{reimers-2019-sentence-bert,
title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
author = "Reimers, Nils and Gurevych, Iryna",
booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
month = "11",
year = "2019",
publisher = "Association for Computational Linguistics",
url = "https://arxiv.org/abs/1908.10084",
}
@misc{oord2019representationlearningcontrastivepredictive,
title={Representation Learning with Contrastive Predictive Coding},
author={Aaron van den Oord and Yazhe Li and Oriol Vinyals},
year={2019},
eprint={1807.03748},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/1807.03748},
}
Base model
unsloth/embeddinggemma-300m